diff --git a/coverage/class_index.html b/coverage/class_index.html
index 4f5c2b97..a0c76b25 100644
--- a/coverage/class_index.html
+++ b/coverage/class_index.html
@@ -55,7 +55,7 @@ <h2>
         </h2>
         <p class="text">
             <a class="nav" href="https://coverage.readthedocs.io/en/7.5.1">coverage.py v7.5.1</a>,
-            created at 2024-05-07 09:06 +0000
+            created at 2024-05-24 09:29 +0000
         </p>
     </div>
 </header>
@@ -684,7 +684,7 @@ <h2>
     <div class="content">
         <p>
             <a class="nav" href="https://coverage.readthedocs.io/en/7.5.1">coverage.py v7.5.1</a>,
-            created at 2024-05-07 09:06 +0000
+            created at 2024-05-24 09:29 +0000
         </p>
     </div>
     <aside class="hidden">
diff --git a/coverage/coverage.xml b/coverage/coverage.xml
index b86d1be5..41bf9091 100644
--- a/coverage/coverage.xml
+++ b/coverage/coverage.xml
@@ -1,5 +1,5 @@
 <?xml version="1.0" ?>
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 	<!-- Generated by coverage.py: https://coverage.readthedocs.io/en/7.5.1 -->
 	<!-- Based on https://raw.githubusercontent.com/cobertura/web/master/htdocs/xml/coverage-04.dtd -->
 	<sources>
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@@ -801,55 +801,54 @@
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 						<line number="172" hits="1"/>
 						<line number="173" hits="1"/>
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diff --git a/coverage/function_index.html b/coverage/function_index.html
index 170d8591..60d029ea 100644
--- a/coverage/function_index.html
+++ b/coverage/function_index.html
@@ -55,7 +55,7 @@ <h2>
         </h2>
         <p class="text">
             <a class="nav" href="https://coverage.readthedocs.io/en/7.5.1">coverage.py v7.5.1</a>,
-            created at 2024-05-07 09:06 +0000
+            created at 2024-05-24 09:29 +0000
         </p>
     </div>
 </header>
@@ -89,48 +89,48 @@ <h2>
                 <td class="right" data-ratio="2 2">100%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_159731231e5c9c9d_bipopulations_py.html#t62">biobb_dna/backbone/bipopulations.py</a></td>
-                <td class="name left"><a href="z_159731231e5c9c9d_bipopulations_py.html#t62"><data value='init__'>BIPopulations.__init__</data></a></td>
+                <td class="name left"><a href="z_159731231e5c9c9d_bipopulations_py.html#t63">biobb_dna/backbone/bipopulations.py</a></td>
+                <td class="name left"><a href="z_159731231e5c9c9d_bipopulations_py.html#t63"><data value='init__'>BIPopulations.__init__</data></a></td>
                 <td>9</td>
                 <td>0</td>
                 <td>0</td>
                 <td class="right" data-ratio="9 9">100%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_159731231e5c9c9d_bipopulations_py.html#t95">biobb_dna/backbone/bipopulations.py</a></td>
-                <td class="name left"><a href="z_159731231e5c9c9d_bipopulations_py.html#t95"><data value='launch'>BIPopulations.launch</data></a></td>
+                <td class="name left"><a href="z_159731231e5c9c9d_bipopulations_py.html#t96">biobb_dna/backbone/bipopulations.py</a></td>
+                <td class="name left"><a href="z_159731231e5c9c9d_bipopulations_py.html#t96"><data value='launch'>BIPopulations.launch</data></a></td>
                 <td>42</td>
                 <td>6</td>
                 <td>0</td>
                 <td class="right" data-ratio="36 42">86%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_159731231e5c9c9d_bipopulations_py.html#t202">biobb_dna/backbone/bipopulations.py</a></td>
-                <td class="name left"><a href="z_159731231e5c9c9d_bipopulations_py.html#t202"><data value='get_xlabels'>BIPopulations.get_xlabels</data></a></td>
+                <td class="name left"><a href="z_159731231e5c9c9d_bipopulations_py.html#t203">biobb_dna/backbone/bipopulations.py</a></td>
+                <td class="name left"><a href="z_159731231e5c9c9d_bipopulations_py.html#t203"><data value='get_xlabels'>BIPopulations.get_xlabels</data></a></td>
                 <td>13</td>
                 <td>2</td>
                 <td>0</td>
                 <td class="right" data-ratio="11 13">85%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_159731231e5c9c9d_bipopulations_py.html#t221">biobb_dna/backbone/bipopulations.py</a></td>
-                <td class="name left"><a href="z_159731231e5c9c9d_bipopulations_py.html#t221"><data value='get_angles_difference'>BIPopulations.get_angles_difference</data></a></td>
+                <td class="name left"><a href="z_159731231e5c9c9d_bipopulations_py.html#t222">biobb_dna/backbone/bipopulations.py</a></td>
+                <td class="name left"><a href="z_159731231e5c9c9d_bipopulations_py.html#t222"><data value='get_angles_difference'>BIPopulations.get_angles_difference</data></a></td>
                 <td>5</td>
                 <td>0</td>
                 <td>0</td>
                 <td class="right" data-ratio="5 5">100%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_159731231e5c9c9d_bipopulations_py.html#t240">biobb_dna/backbone/bipopulations.py</a></td>
-                <td class="name left"><a href="z_159731231e5c9c9d_bipopulations_py.html#t240"><data value='bipopulations'>bipopulations</data></a></td>
+                <td class="name left"><a href="z_159731231e5c9c9d_bipopulations_py.html#t241">biobb_dna/backbone/bipopulations.py</a></td>
+                <td class="name left"><a href="z_159731231e5c9c9d_bipopulations_py.html#t241"><data value='bipopulations'>bipopulations</data></a></td>
                 <td>1</td>
                 <td>0</td>
                 <td>0</td>
                 <td class="right" data-ratio="1 1">100%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_159731231e5c9c9d_bipopulations_py.html#t258">biobb_dna/backbone/bipopulations.py</a></td>
-                <td class="name left"><a href="z_159731231e5c9c9d_bipopulations_py.html#t258"><data value='main'>main</data></a></td>
+                <td class="name left"><a href="z_159731231e5c9c9d_bipopulations_py.html#t259">biobb_dna/backbone/bipopulations.py</a></td>
+                <td class="name left"><a href="z_159731231e5c9c9d_bipopulations_py.html#t259"><data value='main'>main</data></a></td>
                 <td>13</td>
                 <td>13</td>
                 <td>0</td>
@@ -145,56 +145,56 @@ <h2>
                 <td class="right" data-ratio="21 22">95%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_159731231e5c9c9d_canonicalag_py.html#t64">biobb_dna/backbone/canonicalag.py</a></td>
-                <td class="name left"><a href="z_159731231e5c9c9d_canonicalag_py.html#t64"><data value='init__'>CanonicalAG.__init__</data></a></td>
+                <td class="name left"><a href="z_159731231e5c9c9d_canonicalag_py.html#t65">biobb_dna/backbone/canonicalag.py</a></td>
+                <td class="name left"><a href="z_159731231e5c9c9d_canonicalag_py.html#t65"><data value='init__'>CanonicalAG.__init__</data></a></td>
                 <td>10</td>
                 <td>0</td>
                 <td>0</td>
                 <td class="right" data-ratio="10 10">100%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_159731231e5c9c9d_canonicalag_py.html#t100">biobb_dna/backbone/canonicalag.py</a></td>
-                <td class="name left"><a href="z_159731231e5c9c9d_canonicalag_py.html#t100"><data value='launch'>CanonicalAG.launch</data></a></td>
+                <td class="name left"><a href="z_159731231e5c9c9d_canonicalag_py.html#t101">biobb_dna/backbone/canonicalag.py</a></td>
+                <td class="name left"><a href="z_159731231e5c9c9d_canonicalag_py.html#t101"><data value='launch'>CanonicalAG.launch</data></a></td>
                 <td>44</td>
                 <td>6</td>
                 <td>0</td>
                 <td class="right" data-ratio="38 44">86%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_159731231e5c9c9d_canonicalag_py.html#t203">biobb_dna/backbone/canonicalag.py</a></td>
-                <td class="name left"><a href="z_159731231e5c9c9d_canonicalag_py.html#t203"><data value='get_xlabels'>CanonicalAG.get_xlabels</data></a></td>
+                <td class="name left"><a href="z_159731231e5c9c9d_canonicalag_py.html#t204">biobb_dna/backbone/canonicalag.py</a></td>
+                <td class="name left"><a href="z_159731231e5c9c9d_canonicalag_py.html#t204"><data value='get_xlabels'>CanonicalAG.get_xlabels</data></a></td>
                 <td>13</td>
                 <td>2</td>
                 <td>0</td>
                 <td class="right" data-ratio="11 13">85%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_159731231e5c9c9d_canonicalag_py.html#t222">biobb_dna/backbone/canonicalag.py</a></td>
-                <td class="name left"><a href="z_159731231e5c9c9d_canonicalag_py.html#t222"><data value='check_alpha_gamma'>CanonicalAG.check_alpha_gamma</data></a></td>
+                <td class="name left"><a href="z_159731231e5c9c9d_canonicalag_py.html#t223">biobb_dna/backbone/canonicalag.py</a></td>
+                <td class="name left"><a href="z_159731231e5c9c9d_canonicalag_py.html#t223"><data value='check_alpha_gamma'>CanonicalAG.check_alpha_gamma</data></a></td>
                 <td>7</td>
                 <td>0</td>
                 <td>0</td>
                 <td class="right" data-ratio="7 7">100%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_159731231e5c9c9d_canonicalag_py.html#t242">biobb_dna/backbone/canonicalag.py</a></td>
-                <td class="name left"><a href="z_159731231e5c9c9d_canonicalag_py.html#t242"><data value='fix_angles'>CanonicalAG.fix_angles</data></a></td>
+                <td class="name left"><a href="z_159731231e5c9c9d_canonicalag_py.html#t243">biobb_dna/backbone/canonicalag.py</a></td>
+                <td class="name left"><a href="z_159731231e5c9c9d_canonicalag_py.html#t243"><data value='fix_angles'>CanonicalAG.fix_angles</data></a></td>
                 <td>4</td>
                 <td>0</td>
                 <td>0</td>
                 <td class="right" data-ratio="4 4">100%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_159731231e5c9c9d_canonicalag_py.html#t249">biobb_dna/backbone/canonicalag.py</a></td>
-                <td class="name left"><a href="z_159731231e5c9c9d_canonicalag_py.html#t249"><data value='canonicalag'>canonicalag</data></a></td>
+                <td class="name left"><a href="z_159731231e5c9c9d_canonicalag_py.html#t250">biobb_dna/backbone/canonicalag.py</a></td>
+                <td class="name left"><a href="z_159731231e5c9c9d_canonicalag_py.html#t250"><data value='canonicalag'>canonicalag</data></a></td>
                 <td>1</td>
                 <td>0</td>
                 <td>0</td>
                 <td class="right" data-ratio="1 1">100%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_159731231e5c9c9d_canonicalag_py.html#t267">biobb_dna/backbone/canonicalag.py</a></td>
-                <td class="name left"><a href="z_159731231e5c9c9d_canonicalag_py.html#t267"><data value='main'>main</data></a></td>
+                <td class="name left"><a href="z_159731231e5c9c9d_canonicalag_py.html#t268">biobb_dna/backbone/canonicalag.py</a></td>
+                <td class="name left"><a href="z_159731231e5c9c9d_canonicalag_py.html#t268"><data value='main'>main</data></a></td>
                 <td>13</td>
                 <td>13</td>
                 <td>0</td>
@@ -209,56 +209,56 @@ <h2>
                 <td class="right" data-ratio="22 23">96%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_159731231e5c9c9d_puckering_py.html#t60">biobb_dna/backbone/puckering.py</a></td>
-                <td class="name left"><a href="z_159731231e5c9c9d_puckering_py.html#t60"><data value='init__'>Puckering.__init__</data></a></td>
+                <td class="name left"><a href="z_159731231e5c9c9d_puckering_py.html#t61">biobb_dna/backbone/puckering.py</a></td>
+                <td class="name left"><a href="z_159731231e5c9c9d_puckering_py.html#t61"><data value='init__'>Puckering.__init__</data></a></td>
                 <td>10</td>
                 <td>0</td>
                 <td>0</td>
                 <td class="right" data-ratio="10 10">100%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_159731231e5c9c9d_puckering_py.html#t93">biobb_dna/backbone/puckering.py</a></td>
-                <td class="name left"><a href="z_159731231e5c9c9d_puckering_py.html#t93"><data value='launch'>Puckering.launch</data></a></td>
+                <td class="name left"><a href="z_159731231e5c9c9d_puckering_py.html#t94">biobb_dna/backbone/puckering.py</a></td>
+                <td class="name left"><a href="z_159731231e5c9c9d_puckering_py.html#t94"><data value='launch'>Puckering.launch</data></a></td>
                 <td>40</td>
                 <td>6</td>
                 <td>0</td>
                 <td class="right" data-ratio="34 40">85%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_159731231e5c9c9d_puckering_py.html#t201">biobb_dna/backbone/puckering.py</a></td>
-                <td class="name left"><a href="z_159731231e5c9c9d_puckering_py.html#t201"><data value='get_xlabels'>Puckering.get_xlabels</data></a></td>
+                <td class="name left"><a href="z_159731231e5c9c9d_puckering_py.html#t202">biobb_dna/backbone/puckering.py</a></td>
+                <td class="name left"><a href="z_159731231e5c9c9d_puckering_py.html#t202"><data value='get_xlabels'>Puckering.get_xlabels</data></a></td>
                 <td>13</td>
                 <td>2</td>
                 <td>0</td>
                 <td class="right" data-ratio="11 13">85%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_159731231e5c9c9d_puckering_py.html#t220">biobb_dna/backbone/puckering.py</a></td>
-                <td class="name left"><a href="z_159731231e5c9c9d_puckering_py.html#t220"><data value='check_puckering'>Puckering.check_puckering</data></a></td>
+                <td class="name left"><a href="z_159731231e5c9c9d_puckering_py.html#t221">biobb_dna/backbone/puckering.py</a></td>
+                <td class="name left"><a href="z_159731231e5c9c9d_puckering_py.html#t221"><data value='check_puckering'>Puckering.check_puckering</data></a></td>
                 <td>7</td>
                 <td>0</td>
                 <td>0</td>
                 <td class="right" data-ratio="7 7">100%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_159731231e5c9c9d_puckering_py.html#t235">biobb_dna/backbone/puckering.py</a></td>
-                <td class="name left"><a href="z_159731231e5c9c9d_puckering_py.html#t235"><data value='fix_angles'>Puckering.fix_angles</data></a></td>
+                <td class="name left"><a href="z_159731231e5c9c9d_puckering_py.html#t236">biobb_dna/backbone/puckering.py</a></td>
+                <td class="name left"><a href="z_159731231e5c9c9d_puckering_py.html#t236"><data value='fix_angles'>Puckering.fix_angles</data></a></td>
                 <td>3</td>
                 <td>0</td>
                 <td>0</td>
                 <td class="right" data-ratio="3 3">100%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_159731231e5c9c9d_puckering_py.html#t242">biobb_dna/backbone/puckering.py</a></td>
-                <td class="name left"><a href="z_159731231e5c9c9d_puckering_py.html#t242"><data value='puckering'>puckering</data></a></td>
+                <td class="name left"><a href="z_159731231e5c9c9d_puckering_py.html#t243">biobb_dna/backbone/puckering.py</a></td>
+                <td class="name left"><a href="z_159731231e5c9c9d_puckering_py.html#t243"><data value='puckering'>puckering</data></a></td>
                 <td>1</td>
                 <td>0</td>
                 <td>0</td>
                 <td class="right" data-ratio="1 1">100%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_159731231e5c9c9d_puckering_py.html#t257">biobb_dna/backbone/puckering.py</a></td>
-                <td class="name left"><a href="z_159731231e5c9c9d_puckering_py.html#t257"><data value='main'>main</data></a></td>
+                <td class="name left"><a href="z_159731231e5c9c9d_puckering_py.html#t258">biobb_dna/backbone/puckering.py</a></td>
+                <td class="name left"><a href="z_159731231e5c9c9d_puckering_py.html#t258"><data value='main'>main</data></a></td>
                 <td>11</td>
                 <td>11</td>
                 <td>0</td>
@@ -281,32 +281,32 @@ <h2>
                 <td class="right" data-ratio="2 2">100%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_74fa14c6d0e940a4_biobb_canal_py.html#t64">biobb_dna/curvesplus/biobb_canal.py</a></td>
-                <td class="name left"><a href="z_74fa14c6d0e940a4_biobb_canal_py.html#t64"><data value='init__'>Canal.__init__</data></a></td>
+                <td class="name left"><a href="z_74fa14c6d0e940a4_biobb_canal_py.html#t65">biobb_dna/curvesplus/biobb_canal.py</a></td>
+                <td class="name left"><a href="z_74fa14c6d0e940a4_biobb_canal_py.html#t65"><data value='init__'>Canal.__init__</data></a></td>
                 <td>20</td>
                 <td>0</td>
                 <td>0</td>
                 <td class="right" data-ratio="20 20">100%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_74fa14c6d0e940a4_biobb_canal_py.html#t104">biobb_dna/curvesplus/biobb_canal.py</a></td>
-                <td class="name left"><a href="z_74fa14c6d0e940a4_biobb_canal_py.html#t104"><data value='launch'>Canal.launch</data></a></td>
+                <td class="name left"><a href="z_74fa14c6d0e940a4_biobb_canal_py.html#t105">biobb_dna/curvesplus/biobb_canal.py</a></td>
+                <td class="name left"><a href="z_74fa14c6d0e940a4_biobb_canal_py.html#t105"><data value='launch'>Canal.launch</data></a></td>
                 <td>39</td>
                 <td>13</td>
                 <td>0</td>
                 <td class="right" data-ratio="26 39">67%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_74fa14c6d0e940a4_biobb_canal_py.html#t204">biobb_dna/curvesplus/biobb_canal.py</a></td>
-                <td class="name left"><a href="z_74fa14c6d0e940a4_biobb_canal_py.html#t204"><data value='biobb_canal'>biobb_canal</data></a></td>
+                <td class="name left"><a href="z_74fa14c6d0e940a4_biobb_canal_py.html#t205">biobb_dna/curvesplus/biobb_canal.py</a></td>
+                <td class="name left"><a href="z_74fa14c6d0e940a4_biobb_canal_py.html#t205"><data value='biobb_canal'>biobb_canal</data></a></td>
                 <td>1</td>
                 <td>0</td>
                 <td>0</td>
                 <td class="right" data-ratio="1 1">100%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_74fa14c6d0e940a4_biobb_canal_py.html#t220">biobb_dna/curvesplus/biobb_canal.py</a></td>
-                <td class="name left"><a href="z_74fa14c6d0e940a4_biobb_canal_py.html#t220"><data value='main'>main</data></a></td>
+                <td class="name left"><a href="z_74fa14c6d0e940a4_biobb_canal_py.html#t221">biobb_dna/curvesplus/biobb_canal.py</a></td>
+                <td class="name left"><a href="z_74fa14c6d0e940a4_biobb_canal_py.html#t221"><data value='main'>main</data></a></td>
                 <td>10</td>
                 <td>10</td>
                 <td>0</td>
@@ -321,32 +321,32 @@ <h2>
                 <td class="right" data-ratio="17 18">94%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_74fa14c6d0e940a4_biobb_canion_py.html#t66">biobb_dna/curvesplus/biobb_canion.py</a></td>
-                <td class="name left"><a href="z_74fa14c6d0e940a4_biobb_canion_py.html#t66"><data value='init__'>Canion.__init__</data></a></td>
+                <td class="name left"><a href="z_74fa14c6d0e940a4_biobb_canion_py.html#t67">biobb_dna/curvesplus/biobb_canion.py</a></td>
+                <td class="name left"><a href="z_74fa14c6d0e940a4_biobb_canion_py.html#t67"><data value='init__'>Canion.__init__</data></a></td>
                 <td>21</td>
                 <td>0</td>
                 <td>0</td>
                 <td class="right" data-ratio="21 21">100%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_74fa14c6d0e940a4_biobb_canion_py.html#t109">biobb_dna/curvesplus/biobb_canion.py</a></td>
-                <td class="name left"><a href="z_74fa14c6d0e940a4_biobb_canion_py.html#t109"><data value='launch'>Canion.launch</data></a></td>
+                <td class="name left"><a href="z_74fa14c6d0e940a4_biobb_canion_py.html#t110">biobb_dna/curvesplus/biobb_canion.py</a></td>
+                <td class="name left"><a href="z_74fa14c6d0e940a4_biobb_canion_py.html#t110"><data value='launch'>Canion.launch</data></a></td>
                 <td>34</td>
                 <td>4</td>
                 <td>0</td>
                 <td class="right" data-ratio="30 34">88%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_74fa14c6d0e940a4_biobb_canion_py.html#t207">biobb_dna/curvesplus/biobb_canion.py</a></td>
-                <td class="name left"><a href="z_74fa14c6d0e940a4_biobb_canion_py.html#t207"><data value='biobb_canion'>biobb_canion</data></a></td>
+                <td class="name left"><a href="z_74fa14c6d0e940a4_biobb_canion_py.html#t208">biobb_dna/curvesplus/biobb_canion.py</a></td>
+                <td class="name left"><a href="z_74fa14c6d0e940a4_biobb_canion_py.html#t208"><data value='biobb_canion'>biobb_canion</data></a></td>
                 <td>1</td>
                 <td>0</td>
                 <td>0</td>
                 <td class="right" data-ratio="1 1">100%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_74fa14c6d0e940a4_biobb_canion_py.html#t221">biobb_dna/curvesplus/biobb_canion.py</a></td>
-                <td class="name left"><a href="z_74fa14c6d0e940a4_biobb_canion_py.html#t221"><data value='main'>main</data></a></td>
+                <td class="name left"><a href="z_74fa14c6d0e940a4_biobb_canion_py.html#t222">biobb_dna/curvesplus/biobb_canion.py</a></td>
+                <td class="name left"><a href="z_74fa14c6d0e940a4_biobb_canion_py.html#t222"><data value='main'>main</data></a></td>
                 <td>11</td>
                 <td>11</td>
                 <td>0</td>
@@ -361,32 +361,32 @@ <h2>
                 <td class="right" data-ratio="17 18">94%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_74fa14c6d0e940a4_biobb_curves_py.html#t65">biobb_dna/curvesplus/biobb_curves.py</a></td>
-                <td class="name left"><a href="z_74fa14c6d0e940a4_biobb_curves_py.html#t65"><data value='init__'>Curves.__init__</data></a></td>
+                <td class="name left"><a href="z_74fa14c6d0e940a4_biobb_curves_py.html#t66">biobb_dna/curvesplus/biobb_curves.py</a></td>
+                <td class="name left"><a href="z_74fa14c6d0e940a4_biobb_curves_py.html#t66"><data value='init__'>Curves.__init__</data></a></td>
                 <td>19</td>
                 <td>0</td>
                 <td>0</td>
                 <td class="right" data-ratio="19 19">100%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_74fa14c6d0e940a4_biobb_curves_py.html#t108">biobb_dna/curvesplus/biobb_curves.py</a></td>
-                <td class="name left"><a href="z_74fa14c6d0e940a4_biobb_curves_py.html#t108"><data value='launch'>Curves.launch</data></a></td>
+                <td class="name left"><a href="z_74fa14c6d0e940a4_biobb_curves_py.html#t109">biobb_dna/curvesplus/biobb_curves.py</a></td>
+                <td class="name left"><a href="z_74fa14c6d0e940a4_biobb_curves_py.html#t109"><data value='launch'>Curves.launch</data></a></td>
                 <td>49</td>
                 <td>10</td>
                 <td>0</td>
                 <td class="right" data-ratio="39 49">80%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_74fa14c6d0e940a4_biobb_curves_py.html#t232">biobb_dna/curvesplus/biobb_curves.py</a></td>
-                <td class="name left"><a href="z_74fa14c6d0e940a4_biobb_curves_py.html#t232"><data value='biobb_curves'>biobb_curves</data></a></td>
+                <td class="name left"><a href="z_74fa14c6d0e940a4_biobb_curves_py.html#t233">biobb_dna/curvesplus/biobb_curves.py</a></td>
+                <td class="name left"><a href="z_74fa14c6d0e940a4_biobb_curves_py.html#t233"><data value='biobb_curves'>biobb_curves</data></a></td>
                 <td>1</td>
                 <td>0</td>
                 <td>0</td>
                 <td class="right" data-ratio="1 1">100%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_74fa14c6d0e940a4_biobb_curves_py.html#t248">biobb_dna/curvesplus/biobb_curves.py</a></td>
-                <td class="name left"><a href="z_74fa14c6d0e940a4_biobb_curves_py.html#t248"><data value='main'>main</data></a></td>
+                <td class="name left"><a href="z_74fa14c6d0e940a4_biobb_curves_py.html#t249">biobb_dna/curvesplus/biobb_curves.py</a></td>
+                <td class="name left"><a href="z_74fa14c6d0e940a4_biobb_curves_py.html#t249"><data value='main'>main</data></a></td>
                 <td>12</td>
                 <td>12</td>
                 <td>0</td>
@@ -409,32 +409,32 @@ <h2>
                 <td class="right" data-ratio="2 2">100%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_3afbcd666ed82c91_dna_averages_py.html#t60">biobb_dna/dna/dna_averages.py</a></td>
-                <td class="name left"><a href="z_3afbcd666ed82c91_dna_averages_py.html#t60"><data value='init__'>HelParAverages.__init__</data></a></td>
+                <td class="name left"><a href="z_3afbcd666ed82c91_dna_averages_py.html#t61">biobb_dna/dna/dna_averages.py</a></td>
+                <td class="name left"><a href="z_3afbcd666ed82c91_dna_averages_py.html#t61"><data value='init__'>HelParAverages.__init__</data></a></td>
                 <td>11</td>
                 <td>0</td>
                 <td>0</td>
                 <td class="right" data-ratio="11 11">100%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_3afbcd666ed82c91_dna_averages_py.html#t94">biobb_dna/dna/dna_averages.py</a></td>
-                <td class="name left"><a href="z_3afbcd666ed82c91_dna_averages_py.html#t94"><data value='launch'>HelParAverages.launch</data></a></td>
+                <td class="name left"><a href="z_3afbcd666ed82c91_dna_averages_py.html#t95">biobb_dna/dna/dna_averages.py</a></td>
+                <td class="name left"><a href="z_3afbcd666ed82c91_dna_averages_py.html#t95"><data value='launch'>HelParAverages.launch</data></a></td>
                 <td>55</td>
                 <td>14</td>
                 <td>0</td>
                 <td class="right" data-ratio="41 55">75%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_3afbcd666ed82c91_dna_averages_py.html#t221">biobb_dna/dna/dna_averages.py</a></td>
-                <td class="name left"><a href="z_3afbcd666ed82c91_dna_averages_py.html#t221"><data value='dna_averages'>dna_averages</data></a></td>
+                <td class="name left"><a href="z_3afbcd666ed82c91_dna_averages_py.html#t222">biobb_dna/dna/dna_averages.py</a></td>
+                <td class="name left"><a href="z_3afbcd666ed82c91_dna_averages_py.html#t222"><data value='dna_averages'>dna_averages</data></a></td>
                 <td>1</td>
                 <td>0</td>
                 <td>0</td>
                 <td class="right" data-ratio="1 1">100%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_3afbcd666ed82c91_dna_averages_py.html#t233">biobb_dna/dna/dna_averages.py</a></td>
-                <td class="name left"><a href="z_3afbcd666ed82c91_dna_averages_py.html#t233"><data value='main'>main</data></a></td>
+                <td class="name left"><a href="z_3afbcd666ed82c91_dna_averages_py.html#t234">biobb_dna/dna/dna_averages.py</a></td>
+                <td class="name left"><a href="z_3afbcd666ed82c91_dna_averages_py.html#t234"><data value='main'>main</data></a></td>
                 <td>10</td>
                 <td>10</td>
                 <td>0</td>
@@ -449,56 +449,56 @@ <h2>
                 <td class="right" data-ratio="19 20">95%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_3afbcd666ed82c91_dna_bimodality_py.html#t65">biobb_dna/dna/dna_bimodality.py</a></td>
-                <td class="name left"><a href="z_3afbcd666ed82c91_dna_bimodality_py.html#t65"><data value='init__'>HelParBimodality.__init__</data></a></td>
+                <td class="name left"><a href="z_3afbcd666ed82c91_dna_bimodality_py.html#t66">biobb_dna/dna/dna_bimodality.py</a></td>
+                <td class="name left"><a href="z_3afbcd666ed82c91_dna_bimodality_py.html#t66"><data value='init__'>HelParBimodality.__init__</data></a></td>
                 <td>11</td>
                 <td>0</td>
                 <td>0</td>
                 <td class="right" data-ratio="11 11">100%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_3afbcd666ed82c91_dna_bimodality_py.html#t101">biobb_dna/dna/dna_bimodality.py</a></td>
-                <td class="name left"><a href="z_3afbcd666ed82c91_dna_bimodality_py.html#t101"><data value='launch'>HelParBimodality.launch</data></a></td>
+                <td class="name left"><a href="z_3afbcd666ed82c91_dna_bimodality_py.html#t102">biobb_dna/dna/dna_bimodality.py</a></td>
+                <td class="name left"><a href="z_3afbcd666ed82c91_dna_bimodality_py.html#t102"><data value='launch'>HelParBimodality.launch</data></a></td>
                 <td>77</td>
                 <td>29</td>
                 <td>0</td>
                 <td class="right" data-ratio="48 77">62%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_3afbcd666ed82c91_dna_bimodality_py.html#t250">biobb_dna/dna/dna_bimodality.py</a></td>
-                <td class="name left"><a href="z_3afbcd666ed82c91_dna_bimodality_py.html#t250"><data value='fit_to_model'>HelParBimodality.fit_to_model</data></a></td>
+                <td class="name left"><a href="z_3afbcd666ed82c91_dna_bimodality_py.html#t251">biobb_dna/dna/dna_bimodality.py</a></td>
+                <td class="name left"><a href="z_3afbcd666ed82c91_dna_bimodality_py.html#t251"><data value='fit_to_model'>HelParBimodality.fit_to_model</data></a></td>
                 <td>16</td>
                 <td>0</td>
                 <td>0</td>
                 <td class="right" data-ratio="16 16">100%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_3afbcd666ed82c91_dna_bimodality_py.html#t275">biobb_dna/dna/dna_bimodality.py</a></td>
-                <td class="name left"><a href="z_3afbcd666ed82c91_dna_bimodality_py.html#t275"><data value='bayes_factor_criteria'>HelParBimodality.bayes_factor_criteria</data></a></td>
+                <td class="name left"><a href="z_3afbcd666ed82c91_dna_bimodality_py.html#t276">biobb_dna/dna/dna_bimodality.py</a></td>
+                <td class="name left"><a href="z_3afbcd666ed82c91_dna_bimodality_py.html#t276"><data value='bayes_factor_criteria'>HelParBimodality.bayes_factor_criteria</data></a></td>
                 <td>11</td>
                 <td>4</td>
                 <td>0</td>
                 <td class="right" data-ratio="7 11">64%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_3afbcd666ed82c91_dna_bimodality_py.html#t290">biobb_dna/dna/dna_bimodality.py</a></td>
-                <td class="name left"><a href="z_3afbcd666ed82c91_dna_bimodality_py.html#t290"><data value='helguero_theorem'>HelParBimodality.helguero_theorem</data></a></td>
+                <td class="name left"><a href="z_3afbcd666ed82c91_dna_bimodality_py.html#t291">biobb_dna/dna/dna_bimodality.py</a></td>
+                <td class="name left"><a href="z_3afbcd666ed82c91_dna_bimodality_py.html#t291"><data value='helguero_theorem'>HelParBimodality.helguero_theorem</data></a></td>
                 <td>4</td>
                 <td>4</td>
                 <td>0</td>
                 <td class="right" data-ratio="0 4">0%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_3afbcd666ed82c91_dna_bimodality_py.html#t302">biobb_dna/dna/dna_bimodality.py</a></td>
-                <td class="name left"><a href="z_3afbcd666ed82c91_dna_bimodality_py.html#t302"><data value='dna_bimodality'>dna_bimodality</data></a></td>
+                <td class="name left"><a href="z_3afbcd666ed82c91_dna_bimodality_py.html#t303">biobb_dna/dna/dna_bimodality.py</a></td>
+                <td class="name left"><a href="z_3afbcd666ed82c91_dna_bimodality_py.html#t303"><data value='dna_bimodality'>dna_bimodality</data></a></td>
                 <td>1</td>
                 <td>0</td>
                 <td>0</td>
                 <td class="right" data-ratio="1 1">100%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_3afbcd666ed82c91_dna_bimodality_py.html#t316">biobb_dna/dna/dna_bimodality.py</a></td>
-                <td class="name left"><a href="z_3afbcd666ed82c91_dna_bimodality_py.html#t316"><data value='main'>main</data></a></td>
+                <td class="name left"><a href="z_3afbcd666ed82c91_dna_bimodality_py.html#t317">biobb_dna/dna/dna_bimodality.py</a></td>
+                <td class="name left"><a href="z_3afbcd666ed82c91_dna_bimodality_py.html#t317"><data value='main'>main</data></a></td>
                 <td>11</td>
                 <td>11</td>
                 <td>0</td>
@@ -513,32 +513,32 @@ <h2>
                 <td class="right" data-ratio="26 27">96%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_3afbcd666ed82c91_dna_timeseries_py.html#t60">biobb_dna/dna/dna_timeseries.py</a></td>
-                <td class="name left"><a href="z_3afbcd666ed82c91_dna_timeseries_py.html#t60"><data value='init__'>HelParTimeSeries.__init__</data></a></td>
+                <td class="name left"><a href="z_3afbcd666ed82c91_dna_timeseries_py.html#t61">biobb_dna/dna/dna_timeseries.py</a></td>
+                <td class="name left"><a href="z_3afbcd666ed82c91_dna_timeseries_py.html#t61"><data value='init__'>HelParTimeSeries.__init__</data></a></td>
                 <td>26</td>
                 <td>5</td>
                 <td>0</td>
                 <td class="right" data-ratio="21 26">81%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_3afbcd666ed82c91_dna_timeseries_py.html#t118">biobb_dna/dna/dna_timeseries.py</a></td>
-                <td class="name left"><a href="z_3afbcd666ed82c91_dna_timeseries_py.html#t118"><data value='launch'>HelParTimeSeries.launch</data></a></td>
+                <td class="name left"><a href="z_3afbcd666ed82c91_dna_timeseries_py.html#t119">biobb_dna/dna/dna_timeseries.py</a></td>
+                <td class="name left"><a href="z_3afbcd666ed82c91_dna_timeseries_py.html#t119"><data value='launch'>HelParTimeSeries.launch</data></a></td>
                 <td>53</td>
                 <td>7</td>
                 <td>0</td>
                 <td class="right" data-ratio="46 53">87%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_3afbcd666ed82c91_dna_timeseries_py.html#t237">biobb_dna/dna/dna_timeseries.py</a></td>
-                <td class="name left"><a href="z_3afbcd666ed82c91_dna_timeseries_py.html#t237"><data value='dna_timeseries'>dna_timeseries</data></a></td>
+                <td class="name left"><a href="z_3afbcd666ed82c91_dna_timeseries_py.html#t238">biobb_dna/dna/dna_timeseries.py</a></td>
+                <td class="name left"><a href="z_3afbcd666ed82c91_dna_timeseries_py.html#t238"><data value='dna_timeseries'>dna_timeseries</data></a></td>
                 <td>1</td>
                 <td>0</td>
                 <td>0</td>
                 <td class="right" data-ratio="1 1">100%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_3afbcd666ed82c91_dna_timeseries_py.html#t249">biobb_dna/dna/dna_timeseries.py</a></td>
-                <td class="name left"><a href="z_3afbcd666ed82c91_dna_timeseries_py.html#t249"><data value='main'>main</data></a></td>
+                <td class="name left"><a href="z_3afbcd666ed82c91_dna_timeseries_py.html#t250">biobb_dna/dna/dna_timeseries.py</a></td>
+                <td class="name left"><a href="z_3afbcd666ed82c91_dna_timeseries_py.html#t250"><data value='main'>main</data></a></td>
                 <td>9</td>
                 <td>9</td>
                 <td>0</td>
@@ -561,48 +561,48 @@ <h2>
                 <td class="right" data-ratio="2 2">100%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_8a2a7f872cf1434f_interbpcorr_py.html#t65">biobb_dna/interbp_correlations/interbpcorr.py</a></td>
-                <td class="name left"><a href="z_8a2a7f872cf1434f_interbpcorr_py.html#t65"><data value='init__'>InterBasePairCorrelation.__init__</data></a></td>
+                <td class="name left"><a href="z_8a2a7f872cf1434f_interbpcorr_py.html#t66">biobb_dna/interbp_correlations/interbpcorr.py</a></td>
+                <td class="name left"><a href="z_8a2a7f872cf1434f_interbpcorr_py.html#t66"><data value='init__'>InterBasePairCorrelation.__init__</data></a></td>
                 <td>9</td>
                 <td>0</td>
                 <td>0</td>
                 <td class="right" data-ratio="9 9">100%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_8a2a7f872cf1434f_interbpcorr_py.html#t102">biobb_dna/interbp_correlations/interbpcorr.py</a></td>
-                <td class="name left"><a href="z_8a2a7f872cf1434f_interbpcorr_py.html#t102"><data value='launch'>InterBasePairCorrelation.launch</data></a></td>
+                <td class="name left"><a href="z_8a2a7f872cf1434f_interbpcorr_py.html#t103">biobb_dna/interbp_correlations/interbpcorr.py</a></td>
+                <td class="name left"><a href="z_8a2a7f872cf1434f_interbpcorr_py.html#t103"><data value='launch'>InterBasePairCorrelation.launch</data></a></td>
                 <td>77</td>
                 <td>6</td>
                 <td>0</td>
                 <td class="right" data-ratio="71 77">92%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_8a2a7f872cf1434f_interbpcorr_py.html#t246">biobb_dna/interbp_correlations/interbpcorr.py</a></td>
-                <td class="name left"><a href="z_8a2a7f872cf1434f_interbpcorr_py.html#t246"><data value='circular'>InterBasePairCorrelation.circular</data></a></td>
+                <td class="name left"><a href="z_8a2a7f872cf1434f_interbpcorr_py.html#t247">biobb_dna/interbp_correlations/interbpcorr.py</a></td>
+                <td class="name left"><a href="z_8a2a7f872cf1434f_interbpcorr_py.html#t247"><data value='circular'>InterBasePairCorrelation.circular</data></a></td>
                 <td>7</td>
                 <td>0</td>
                 <td>0</td>
                 <td class="right" data-ratio="7 7">100%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_8a2a7f872cf1434f_interbpcorr_py.html#t256">biobb_dna/interbp_correlations/interbpcorr.py</a></td>
-                <td class="name left"><a href="z_8a2a7f872cf1434f_interbpcorr_py.html#t256"><data value='circlineal'>InterBasePairCorrelation.circlineal</data></a></td>
+                <td class="name left"><a href="z_8a2a7f872cf1434f_interbpcorr_py.html#t257">biobb_dna/interbp_correlations/interbpcorr.py</a></td>
+                <td class="name left"><a href="z_8a2a7f872cf1434f_interbpcorr_py.html#t257"><data value='circlineal'>InterBasePairCorrelation.circlineal</data></a></td>
                 <td>10</td>
                 <td>0</td>
                 <td>0</td>
                 <td class="right" data-ratio="10 10">100%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_8a2a7f872cf1434f_interbpcorr_py.html#t269">biobb_dna/interbp_correlations/interbpcorr.py</a></td>
-                <td class="name left"><a href="z_8a2a7f872cf1434f_interbpcorr_py.html#t269"><data value='interbpcorr'>interbpcorr</data></a></td>
+                <td class="name left"><a href="z_8a2a7f872cf1434f_interbpcorr_py.html#t270">biobb_dna/interbp_correlations/interbpcorr.py</a></td>
+                <td class="name left"><a href="z_8a2a7f872cf1434f_interbpcorr_py.html#t270"><data value='interbpcorr'>interbpcorr</data></a></td>
                 <td>1</td>
                 <td>0</td>
                 <td>0</td>
                 <td class="right" data-ratio="1 1">100%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_8a2a7f872cf1434f_interbpcorr_py.html#t290">biobb_dna/interbp_correlations/interbpcorr.py</a></td>
-                <td class="name left"><a href="z_8a2a7f872cf1434f_interbpcorr_py.html#t290"><data value='main'>main</data></a></td>
+                <td class="name left"><a href="z_8a2a7f872cf1434f_interbpcorr_py.html#t291">biobb_dna/interbp_correlations/interbpcorr.py</a></td>
+                <td class="name left"><a href="z_8a2a7f872cf1434f_interbpcorr_py.html#t291"><data value='main'>main</data></a></td>
                 <td>15</td>
                 <td>15</td>
                 <td>0</td>
@@ -617,56 +617,56 @@ <h2>
                 <td class="right" data-ratio="24 25">96%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_8a2a7f872cf1434f_interhpcorr_py.html#t64">biobb_dna/interbp_correlations/interhpcorr.py</a></td>
-                <td class="name left"><a href="z_8a2a7f872cf1434f_interhpcorr_py.html#t64"><data value='init__'>InterHelParCorrelation.__init__</data></a></td>
+                <td class="name left"><a href="z_8a2a7f872cf1434f_interhpcorr_py.html#t65">biobb_dna/interbp_correlations/interhpcorr.py</a></td>
+                <td class="name left"><a href="z_8a2a7f872cf1434f_interhpcorr_py.html#t65"><data value='init__'>InterHelParCorrelation.__init__</data></a></td>
                 <td>8</td>
                 <td>0</td>
                 <td>0</td>
                 <td class="right" data-ratio="8 8">100%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_8a2a7f872cf1434f_interhpcorr_py.html#t100">biobb_dna/interbp_correlations/interhpcorr.py</a></td>
-                <td class="name left"><a href="z_8a2a7f872cf1434f_interhpcorr_py.html#t100"><data value='launch'>InterHelParCorrelation.launch</data></a></td>
+                <td class="name left"><a href="z_8a2a7f872cf1434f_interhpcorr_py.html#t101">biobb_dna/interbp_correlations/interhpcorr.py</a></td>
+                <td class="name left"><a href="z_8a2a7f872cf1434f_interhpcorr_py.html#t101"><data value='launch'>InterHelParCorrelation.launch</data></a></td>
                 <td>63</td>
                 <td>1</td>
                 <td>0</td>
                 <td class="right" data-ratio="62 63">98%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_8a2a7f872cf1434f_interhpcorr_py.html#t225">biobb_dna/interbp_correlations/interhpcorr.py</a></td>
-                <td class="name left"><a href="z_8a2a7f872cf1434f_interhpcorr_py.html#t225"><data value='get_corr_method'>InterHelParCorrelation.get_corr_method</data></a></td>
+                <td class="name left"><a href="z_8a2a7f872cf1434f_interhpcorr_py.html#t226">biobb_dna/interbp_correlations/interhpcorr.py</a></td>
+                <td class="name left"><a href="z_8a2a7f872cf1434f_interhpcorr_py.html#t226"><data value='get_corr_method'>InterHelParCorrelation.get_corr_method</data></a></td>
                 <td>8</td>
                 <td>8</td>
                 <td>0</td>
                 <td class="right" data-ratio="0 8">0%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_8a2a7f872cf1434f_interhpcorr_py.html#t237">biobb_dna/interbp_correlations/interhpcorr.py</a></td>
-                <td class="name left"><a href="z_8a2a7f872cf1434f_interhpcorr_py.html#t237"><data value='circular'>InterHelParCorrelation.circular</data></a></td>
+                <td class="name left"><a href="z_8a2a7f872cf1434f_interhpcorr_py.html#t238">biobb_dna/interbp_correlations/interhpcorr.py</a></td>
+                <td class="name left"><a href="z_8a2a7f872cf1434f_interhpcorr_py.html#t238"><data value='circular'>InterHelParCorrelation.circular</data></a></td>
                 <td>7</td>
                 <td>0</td>
                 <td>0</td>
                 <td class="right" data-ratio="7 7">100%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_8a2a7f872cf1434f_interhpcorr_py.html#t247">biobb_dna/interbp_correlations/interhpcorr.py</a></td>
-                <td class="name left"><a href="z_8a2a7f872cf1434f_interhpcorr_py.html#t247"><data value='circlineal'>InterHelParCorrelation.circlineal</data></a></td>
+                <td class="name left"><a href="z_8a2a7f872cf1434f_interhpcorr_py.html#t248">biobb_dna/interbp_correlations/interhpcorr.py</a></td>
+                <td class="name left"><a href="z_8a2a7f872cf1434f_interhpcorr_py.html#t248"><data value='circlineal'>InterHelParCorrelation.circlineal</data></a></td>
                 <td>10</td>
                 <td>0</td>
                 <td>0</td>
                 <td class="right" data-ratio="10 10">100%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_8a2a7f872cf1434f_interhpcorr_py.html#t260">biobb_dna/interbp_correlations/interhpcorr.py</a></td>
-                <td class="name left"><a href="z_8a2a7f872cf1434f_interhpcorr_py.html#t260"><data value='interhpcorr'>interhpcorr</data></a></td>
+                <td class="name left"><a href="z_8a2a7f872cf1434f_interhpcorr_py.html#t261">biobb_dna/interbp_correlations/interhpcorr.py</a></td>
+                <td class="name left"><a href="z_8a2a7f872cf1434f_interhpcorr_py.html#t261"><data value='interhpcorr'>interhpcorr</data></a></td>
                 <td>1</td>
                 <td>0</td>
                 <td>0</td>
                 <td class="right" data-ratio="1 1">100%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_8a2a7f872cf1434f_interhpcorr_py.html#t281">biobb_dna/interbp_correlations/interhpcorr.py</a></td>
-                <td class="name left"><a href="z_8a2a7f872cf1434f_interhpcorr_py.html#t281"><data value='main'>main</data></a></td>
+                <td class="name left"><a href="z_8a2a7f872cf1434f_interhpcorr_py.html#t282">biobb_dna/interbp_correlations/interhpcorr.py</a></td>
+                <td class="name left"><a href="z_8a2a7f872cf1434f_interhpcorr_py.html#t282"><data value='main'>main</data></a></td>
                 <td>15</td>
                 <td>15</td>
                 <td>0</td>
@@ -681,40 +681,40 @@ <h2>
                 <td class="right" data-ratio="22 23">96%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_8a2a7f872cf1434f_interseqcorr_py.html#t58">biobb_dna/interbp_correlations/interseqcorr.py</a></td>
-                <td class="name left"><a href="z_8a2a7f872cf1434f_interseqcorr_py.html#t58"><data value='init__'>InterSequenceCorrelation.__init__</data></a></td>
+                <td class="name left"><a href="z_8a2a7f872cf1434f_interseqcorr_py.html#t59">biobb_dna/interbp_correlations/interseqcorr.py</a></td>
+                <td class="name left"><a href="z_8a2a7f872cf1434f_interseqcorr_py.html#t59"><data value='init__'>InterSequenceCorrelation.__init__</data></a></td>
                 <td>10</td>
                 <td>0</td>
                 <td>0</td>
                 <td class="right" data-ratio="10 10">100%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_8a2a7f872cf1434f_interseqcorr_py.html#t88">biobb_dna/interbp_correlations/interseqcorr.py</a></td>
-                <td class="name left"><a href="z_8a2a7f872cf1434f_interseqcorr_py.html#t88"><data value='launch'>InterSequenceCorrelation.launch</data></a></td>
+                <td class="name left"><a href="z_8a2a7f872cf1434f_interseqcorr_py.html#t89">biobb_dna/interbp_correlations/interseqcorr.py</a></td>
+                <td class="name left"><a href="z_8a2a7f872cf1434f_interseqcorr_py.html#t89"><data value='launch'>InterSequenceCorrelation.launch</data></a></td>
                 <td>47</td>
                 <td>9</td>
                 <td>0</td>
                 <td class="right" data-ratio="38 47">81%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_8a2a7f872cf1434f_interseqcorr_py.html#t190">biobb_dna/interbp_correlations/interseqcorr.py</a></td>
-                <td class="name left"><a href="z_8a2a7f872cf1434f_interseqcorr_py.html#t190"><data value='circular'>InterSequenceCorrelation.circular</data></a></td>
+                <td class="name left"><a href="z_8a2a7f872cf1434f_interseqcorr_py.html#t191">biobb_dna/interbp_correlations/interseqcorr.py</a></td>
+                <td class="name left"><a href="z_8a2a7f872cf1434f_interseqcorr_py.html#t191"><data value='circular'>InterSequenceCorrelation.circular</data></a></td>
                 <td>7</td>
                 <td>7</td>
                 <td>0</td>
                 <td class="right" data-ratio="0 7">0%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_8a2a7f872cf1434f_interseqcorr_py.html#t200">biobb_dna/interbp_correlations/interseqcorr.py</a></td>
-                <td class="name left"><a href="z_8a2a7f872cf1434f_interseqcorr_py.html#t200"><data value='interseqcorr'>interseqcorr</data></a></td>
+                <td class="name left"><a href="z_8a2a7f872cf1434f_interseqcorr_py.html#t201">biobb_dna/interbp_correlations/interseqcorr.py</a></td>
+                <td class="name left"><a href="z_8a2a7f872cf1434f_interseqcorr_py.html#t201"><data value='interseqcorr'>interseqcorr</data></a></td>
                 <td>1</td>
                 <td>0</td>
                 <td>0</td>
                 <td class="right" data-ratio="1 1">100%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_8a2a7f872cf1434f_interseqcorr_py.html#t214">biobb_dna/interbp_correlations/interseqcorr.py</a></td>
-                <td class="name left"><a href="z_8a2a7f872cf1434f_interseqcorr_py.html#t214"><data value='main'>main</data></a></td>
+                <td class="name left"><a href="z_8a2a7f872cf1434f_interseqcorr_py.html#t215">biobb_dna/interbp_correlations/interseqcorr.py</a></td>
+                <td class="name left"><a href="z_8a2a7f872cf1434f_interseqcorr_py.html#t215"><data value='main'>main</data></a></td>
                 <td>10</td>
                 <td>10</td>
                 <td>0</td>
@@ -737,48 +737,48 @@ <h2>
                 <td class="right" data-ratio="2 2">100%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_64e03be4370b7ecc_intrabpcorr_py.html#t65">biobb_dna/intrabp_correlations/intrabpcorr.py</a></td>
-                <td class="name left"><a href="z_64e03be4370b7ecc_intrabpcorr_py.html#t65"><data value='init__'>IntraBasePairCorrelation.__init__</data></a></td>
+                <td class="name left"><a href="z_64e03be4370b7ecc_intrabpcorr_py.html#t66">biobb_dna/intrabp_correlations/intrabpcorr.py</a></td>
+                <td class="name left"><a href="z_64e03be4370b7ecc_intrabpcorr_py.html#t66"><data value='init__'>IntraBasePairCorrelation.__init__</data></a></td>
                 <td>9</td>
                 <td>0</td>
                 <td>0</td>
                 <td class="right" data-ratio="9 9">100%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_64e03be4370b7ecc_intrabpcorr_py.html#t102">biobb_dna/intrabp_correlations/intrabpcorr.py</a></td>
-                <td class="name left"><a href="z_64e03be4370b7ecc_intrabpcorr_py.html#t102"><data value='launch'>IntraBasePairCorrelation.launch</data></a></td>
+                <td class="name left"><a href="z_64e03be4370b7ecc_intrabpcorr_py.html#t103">biobb_dna/intrabp_correlations/intrabpcorr.py</a></td>
+                <td class="name left"><a href="z_64e03be4370b7ecc_intrabpcorr_py.html#t103"><data value='launch'>IntraBasePairCorrelation.launch</data></a></td>
                 <td>77</td>
                 <td>6</td>
                 <td>0</td>
                 <td class="right" data-ratio="71 77">92%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_64e03be4370b7ecc_intrabpcorr_py.html#t246">biobb_dna/intrabp_correlations/intrabpcorr.py</a></td>
-                <td class="name left"><a href="z_64e03be4370b7ecc_intrabpcorr_py.html#t246"><data value='circular'>IntraBasePairCorrelation.circular</data></a></td>
+                <td class="name left"><a href="z_64e03be4370b7ecc_intrabpcorr_py.html#t247">biobb_dna/intrabp_correlations/intrabpcorr.py</a></td>
+                <td class="name left"><a href="z_64e03be4370b7ecc_intrabpcorr_py.html#t247"><data value='circular'>IntraBasePairCorrelation.circular</data></a></td>
                 <td>7</td>
                 <td>0</td>
                 <td>0</td>
                 <td class="right" data-ratio="7 7">100%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_64e03be4370b7ecc_intrabpcorr_py.html#t256">biobb_dna/intrabp_correlations/intrabpcorr.py</a></td>
-                <td class="name left"><a href="z_64e03be4370b7ecc_intrabpcorr_py.html#t256"><data value='circlineal'>IntraBasePairCorrelation.circlineal</data></a></td>
+                <td class="name left"><a href="z_64e03be4370b7ecc_intrabpcorr_py.html#t257">biobb_dna/intrabp_correlations/intrabpcorr.py</a></td>
+                <td class="name left"><a href="z_64e03be4370b7ecc_intrabpcorr_py.html#t257"><data value='circlineal'>IntraBasePairCorrelation.circlineal</data></a></td>
                 <td>10</td>
                 <td>0</td>
                 <td>0</td>
                 <td class="right" data-ratio="10 10">100%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_64e03be4370b7ecc_intrabpcorr_py.html#t269">biobb_dna/intrabp_correlations/intrabpcorr.py</a></td>
-                <td class="name left"><a href="z_64e03be4370b7ecc_intrabpcorr_py.html#t269"><data value='intrabpcorr'>intrabpcorr</data></a></td>
+                <td class="name left"><a href="z_64e03be4370b7ecc_intrabpcorr_py.html#t270">biobb_dna/intrabp_correlations/intrabpcorr.py</a></td>
+                <td class="name left"><a href="z_64e03be4370b7ecc_intrabpcorr_py.html#t270"><data value='intrabpcorr'>intrabpcorr</data></a></td>
                 <td>1</td>
                 <td>0</td>
                 <td>0</td>
                 <td class="right" data-ratio="1 1">100%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_64e03be4370b7ecc_intrabpcorr_py.html#t290">biobb_dna/intrabp_correlations/intrabpcorr.py</a></td>
-                <td class="name left"><a href="z_64e03be4370b7ecc_intrabpcorr_py.html#t290"><data value='main'>main</data></a></td>
+                <td class="name left"><a href="z_64e03be4370b7ecc_intrabpcorr_py.html#t291">biobb_dna/intrabp_correlations/intrabpcorr.py</a></td>
+                <td class="name left"><a href="z_64e03be4370b7ecc_intrabpcorr_py.html#t291"><data value='main'>main</data></a></td>
                 <td>15</td>
                 <td>15</td>
                 <td>0</td>
@@ -793,56 +793,56 @@ <h2>
                 <td class="right" data-ratio="24 25">96%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_64e03be4370b7ecc_intrahpcorr_py.html#t64">biobb_dna/intrabp_correlations/intrahpcorr.py</a></td>
-                <td class="name left"><a href="z_64e03be4370b7ecc_intrahpcorr_py.html#t64"><data value='init__'>IntraHelParCorrelation.__init__</data></a></td>
+                <td class="name left"><a href="z_64e03be4370b7ecc_intrahpcorr_py.html#t65">biobb_dna/intrabp_correlations/intrahpcorr.py</a></td>
+                <td class="name left"><a href="z_64e03be4370b7ecc_intrahpcorr_py.html#t65"><data value='init__'>IntraHelParCorrelation.__init__</data></a></td>
                 <td>8</td>
                 <td>0</td>
                 <td>0</td>
                 <td class="right" data-ratio="8 8">100%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_64e03be4370b7ecc_intrahpcorr_py.html#t100">biobb_dna/intrabp_correlations/intrahpcorr.py</a></td>
-                <td class="name left"><a href="z_64e03be4370b7ecc_intrahpcorr_py.html#t100"><data value='launch'>IntraHelParCorrelation.launch</data></a></td>
+                <td class="name left"><a href="z_64e03be4370b7ecc_intrahpcorr_py.html#t101">biobb_dna/intrabp_correlations/intrahpcorr.py</a></td>
+                <td class="name left"><a href="z_64e03be4370b7ecc_intrahpcorr_py.html#t101"><data value='launch'>IntraHelParCorrelation.launch</data></a></td>
                 <td>63</td>
                 <td>1</td>
                 <td>0</td>
                 <td class="right" data-ratio="62 63">98%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_64e03be4370b7ecc_intrahpcorr_py.html#t231">biobb_dna/intrabp_correlations/intrahpcorr.py</a></td>
-                <td class="name left"><a href="z_64e03be4370b7ecc_intrahpcorr_py.html#t231"><data value='get_corr_method'>IntraHelParCorrelation.get_corr_method</data></a></td>
+                <td class="name left"><a href="z_64e03be4370b7ecc_intrahpcorr_py.html#t232">biobb_dna/intrabp_correlations/intrahpcorr.py</a></td>
+                <td class="name left"><a href="z_64e03be4370b7ecc_intrahpcorr_py.html#t232"><data value='get_corr_method'>IntraHelParCorrelation.get_corr_method</data></a></td>
                 <td>8</td>
                 <td>8</td>
                 <td>0</td>
                 <td class="right" data-ratio="0 8">0%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_64e03be4370b7ecc_intrahpcorr_py.html#t243">biobb_dna/intrabp_correlations/intrahpcorr.py</a></td>
-                <td class="name left"><a href="z_64e03be4370b7ecc_intrahpcorr_py.html#t243"><data value='circular'>IntraHelParCorrelation.circular</data></a></td>
+                <td class="name left"><a href="z_64e03be4370b7ecc_intrahpcorr_py.html#t244">biobb_dna/intrabp_correlations/intrahpcorr.py</a></td>
+                <td class="name left"><a href="z_64e03be4370b7ecc_intrahpcorr_py.html#t244"><data value='circular'>IntraHelParCorrelation.circular</data></a></td>
                 <td>7</td>
                 <td>0</td>
                 <td>0</td>
                 <td class="right" data-ratio="7 7">100%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_64e03be4370b7ecc_intrahpcorr_py.html#t253">biobb_dna/intrabp_correlations/intrahpcorr.py</a></td>
-                <td class="name left"><a href="z_64e03be4370b7ecc_intrahpcorr_py.html#t253"><data value='circlineal'>IntraHelParCorrelation.circlineal</data></a></td>
+                <td class="name left"><a href="z_64e03be4370b7ecc_intrahpcorr_py.html#t254">biobb_dna/intrabp_correlations/intrahpcorr.py</a></td>
+                <td class="name left"><a href="z_64e03be4370b7ecc_intrahpcorr_py.html#t254"><data value='circlineal'>IntraHelParCorrelation.circlineal</data></a></td>
                 <td>10</td>
                 <td>0</td>
                 <td>0</td>
                 <td class="right" data-ratio="10 10">100%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_64e03be4370b7ecc_intrahpcorr_py.html#t266">biobb_dna/intrabp_correlations/intrahpcorr.py</a></td>
-                <td class="name left"><a href="z_64e03be4370b7ecc_intrahpcorr_py.html#t266"><data value='intrahpcorr'>intrahpcorr</data></a></td>
+                <td class="name left"><a href="z_64e03be4370b7ecc_intrahpcorr_py.html#t267">biobb_dna/intrabp_correlations/intrahpcorr.py</a></td>
+                <td class="name left"><a href="z_64e03be4370b7ecc_intrahpcorr_py.html#t267"><data value='intrahpcorr'>intrahpcorr</data></a></td>
                 <td>1</td>
                 <td>0</td>
                 <td>0</td>
                 <td class="right" data-ratio="1 1">100%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_64e03be4370b7ecc_intrahpcorr_py.html#t287">biobb_dna/intrabp_correlations/intrahpcorr.py</a></td>
-                <td class="name left"><a href="z_64e03be4370b7ecc_intrahpcorr_py.html#t287"><data value='main'>main</data></a></td>
+                <td class="name left"><a href="z_64e03be4370b7ecc_intrahpcorr_py.html#t288">biobb_dna/intrabp_correlations/intrahpcorr.py</a></td>
+                <td class="name left"><a href="z_64e03be4370b7ecc_intrahpcorr_py.html#t288"><data value='main'>main</data></a></td>
                 <td>15</td>
                 <td>15</td>
                 <td>0</td>
@@ -857,40 +857,40 @@ <h2>
                 <td class="right" data-ratio="22 23">96%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_64e03be4370b7ecc_intraseqcorr_py.html#t54">biobb_dna/intrabp_correlations/intraseqcorr.py</a></td>
-                <td class="name left"><a href="z_64e03be4370b7ecc_intraseqcorr_py.html#t54"><data value='init__'>IntraSequenceCorrelation.__init__</data></a></td>
+                <td class="name left"><a href="z_64e03be4370b7ecc_intraseqcorr_py.html#t55">biobb_dna/intrabp_correlations/intraseqcorr.py</a></td>
+                <td class="name left"><a href="z_64e03be4370b7ecc_intraseqcorr_py.html#t55"><data value='init__'>IntraSequenceCorrelation.__init__</data></a></td>
                 <td>10</td>
                 <td>0</td>
                 <td>0</td>
                 <td class="right" data-ratio="10 10">100%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_64e03be4370b7ecc_intraseqcorr_py.html#t84">biobb_dna/intrabp_correlations/intraseqcorr.py</a></td>
-                <td class="name left"><a href="z_64e03be4370b7ecc_intraseqcorr_py.html#t84"><data value='launch'>IntraSequenceCorrelation.launch</data></a></td>
+                <td class="name left"><a href="z_64e03be4370b7ecc_intraseqcorr_py.html#t85">biobb_dna/intrabp_correlations/intraseqcorr.py</a></td>
+                <td class="name left"><a href="z_64e03be4370b7ecc_intraseqcorr_py.html#t85"><data value='launch'>IntraSequenceCorrelation.launch</data></a></td>
                 <td>47</td>
                 <td>9</td>
                 <td>0</td>
                 <td class="right" data-ratio="38 47">81%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_64e03be4370b7ecc_intraseqcorr_py.html#t186">biobb_dna/intrabp_correlations/intraseqcorr.py</a></td>
-                <td class="name left"><a href="z_64e03be4370b7ecc_intraseqcorr_py.html#t186"><data value='circular'>IntraSequenceCorrelation.circular</data></a></td>
+                <td class="name left"><a href="z_64e03be4370b7ecc_intraseqcorr_py.html#t187">biobb_dna/intrabp_correlations/intraseqcorr.py</a></td>
+                <td class="name left"><a href="z_64e03be4370b7ecc_intraseqcorr_py.html#t187"><data value='circular'>IntraSequenceCorrelation.circular</data></a></td>
                 <td>7</td>
                 <td>7</td>
                 <td>0</td>
                 <td class="right" data-ratio="0 7">0%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_64e03be4370b7ecc_intraseqcorr_py.html#t196">biobb_dna/intrabp_correlations/intraseqcorr.py</a></td>
-                <td class="name left"><a href="z_64e03be4370b7ecc_intraseqcorr_py.html#t196"><data value='intraseqcorr'>intraseqcorr</data></a></td>
+                <td class="name left"><a href="z_64e03be4370b7ecc_intraseqcorr_py.html#t197">biobb_dna/intrabp_correlations/intraseqcorr.py</a></td>
+                <td class="name left"><a href="z_64e03be4370b7ecc_intraseqcorr_py.html#t197"><data value='intraseqcorr'>intraseqcorr</data></a></td>
                 <td>1</td>
                 <td>0</td>
                 <td>0</td>
                 <td class="right" data-ratio="1 1">100%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_64e03be4370b7ecc_intraseqcorr_py.html#t210">biobb_dna/intrabp_correlations/intraseqcorr.py</a></td>
-                <td class="name left"><a href="z_64e03be4370b7ecc_intraseqcorr_py.html#t210"><data value='main'>main</data></a></td>
+                <td class="name left"><a href="z_64e03be4370b7ecc_intraseqcorr_py.html#t211">biobb_dna/intrabp_correlations/intraseqcorr.py</a></td>
+                <td class="name left"><a href="z_64e03be4370b7ecc_intraseqcorr_py.html#t211"><data value='main'>main</data></a></td>
                 <td>10</td>
                 <td>10</td>
                 <td>0</td>
@@ -913,32 +913,32 @@ <h2>
                 <td class="right" data-ratio="2 2">100%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_9de9475b0a6fab52_average_stiffness_py.html#t60">biobb_dna/stiffness/average_stiffness.py</a></td>
-                <td class="name left"><a href="z_9de9475b0a6fab52_average_stiffness_py.html#t60"><data value='init__'>AverageStiffness.__init__</data></a></td>
+                <td class="name left"><a href="z_9de9475b0a6fab52_average_stiffness_py.html#t61">biobb_dna/stiffness/average_stiffness.py</a></td>
+                <td class="name left"><a href="z_9de9475b0a6fab52_average_stiffness_py.html#t61"><data value='init__'>AverageStiffness.__init__</data></a></td>
                 <td>11</td>
                 <td>0</td>
                 <td>0</td>
                 <td class="right" data-ratio="11 11">100%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_9de9475b0a6fab52_average_stiffness_py.html#t91">biobb_dna/stiffness/average_stiffness.py</a></td>
-                <td class="name left"><a href="z_9de9475b0a6fab52_average_stiffness_py.html#t91"><data value='launch'>AverageStiffness.launch</data></a></td>
+                <td class="name left"><a href="z_9de9475b0a6fab52_average_stiffness_py.html#t92">biobb_dna/stiffness/average_stiffness.py</a></td>
+                <td class="name left"><a href="z_9de9475b0a6fab52_average_stiffness_py.html#t92"><data value='launch'>AverageStiffness.launch</data></a></td>
                 <td>51</td>
                 <td>13</td>
                 <td>0</td>
                 <td class="right" data-ratio="38 51">75%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_9de9475b0a6fab52_average_stiffness_py.html#t203">biobb_dna/stiffness/average_stiffness.py</a></td>
-                <td class="name left"><a href="z_9de9475b0a6fab52_average_stiffness_py.html#t203"><data value='average_stiffness'>average_stiffness</data></a></td>
+                <td class="name left"><a href="z_9de9475b0a6fab52_average_stiffness_py.html#t204">biobb_dna/stiffness/average_stiffness.py</a></td>
+                <td class="name left"><a href="z_9de9475b0a6fab52_average_stiffness_py.html#t204"><data value='average_stiffness'>average_stiffness</data></a></td>
                 <td>1</td>
                 <td>0</td>
                 <td>0</td>
                 <td class="right" data-ratio="1 1">100%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_9de9475b0a6fab52_average_stiffness_py.html#t216">biobb_dna/stiffness/average_stiffness.py</a></td>
-                <td class="name left"><a href="z_9de9475b0a6fab52_average_stiffness_py.html#t216"><data value='main'>main</data></a></td>
+                <td class="name left"><a href="z_9de9475b0a6fab52_average_stiffness_py.html#t217">biobb_dna/stiffness/average_stiffness.py</a></td>
+                <td class="name left"><a href="z_9de9475b0a6fab52_average_stiffness_py.html#t217"><data value='main'>main</data></a></td>
                 <td>10</td>
                 <td>10</td>
                 <td>0</td>
@@ -953,32 +953,32 @@ <h2>
                 <td class="right" data-ratio="20 21">95%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_9de9475b0a6fab52_basepair_stiffness_py.html#t67">biobb_dna/stiffness/basepair_stiffness.py</a></td>
-                <td class="name left"><a href="z_9de9475b0a6fab52_basepair_stiffness_py.html#t67"><data value='init__'>BPStiffness.__init__</data></a></td>
+                <td class="name left"><a href="z_9de9475b0a6fab52_basepair_stiffness_py.html#t68">biobb_dna/stiffness/basepair_stiffness.py</a></td>
+                <td class="name left"><a href="z_9de9475b0a6fab52_basepair_stiffness_py.html#t68"><data value='init__'>BPStiffness.__init__</data></a></td>
                 <td>9</td>
                 <td>0</td>
                 <td>0</td>
                 <td class="right" data-ratio="9 9">100%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_9de9475b0a6fab52_basepair_stiffness_py.html#t104">biobb_dna/stiffness/basepair_stiffness.py</a></td>
-                <td class="name left"><a href="z_9de9475b0a6fab52_basepair_stiffness_py.html#t104"><data value='launch'>BPStiffness.launch</data></a></td>
+                <td class="name left"><a href="z_9de9475b0a6fab52_basepair_stiffness_py.html#t105">biobb_dna/stiffness/basepair_stiffness.py</a></td>
+                <td class="name left"><a href="z_9de9475b0a6fab52_basepair_stiffness_py.html#t105"><data value='launch'>BPStiffness.launch</data></a></td>
                 <td>39</td>
                 <td>1</td>
                 <td>0</td>
                 <td class="right" data-ratio="38 39">97%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_9de9475b0a6fab52_basepair_stiffness_py.html#t193">biobb_dna/stiffness/basepair_stiffness.py</a></td>
-                <td class="name left"><a href="z_9de9475b0a6fab52_basepair_stiffness_py.html#t193"><data value='basepair_stiffness'>basepair_stiffness</data></a></td>
+                <td class="name left"><a href="z_9de9475b0a6fab52_basepair_stiffness_py.html#t194">biobb_dna/stiffness/basepair_stiffness.py</a></td>
+                <td class="name left"><a href="z_9de9475b0a6fab52_basepair_stiffness_py.html#t194"><data value='basepair_stiffness'>basepair_stiffness</data></a></td>
                 <td>1</td>
                 <td>0</td>
                 <td>0</td>
                 <td class="right" data-ratio="1 1">100%</td>
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             <tr class="region">
-                <td class="name left"><a href="z_9de9475b0a6fab52_basepair_stiffness_py.html#t213">biobb_dna/stiffness/basepair_stiffness.py</a></td>
-                <td class="name left"><a href="z_9de9475b0a6fab52_basepair_stiffness_py.html#t213"><data value='main'>main</data></a></td>
+                <td class="name left"><a href="z_9de9475b0a6fab52_basepair_stiffness_py.html#t214">biobb_dna/stiffness/basepair_stiffness.py</a></td>
+                <td class="name left"><a href="z_9de9475b0a6fab52_basepair_stiffness_py.html#t214"><data value='main'>main</data></a></td>
                 <td>15</td>
                 <td>15</td>
                 <td>0</td>
@@ -1564,7 +1564,7 @@ <h2>
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diff --git a/coverage/index.html b/coverage/index.html
index 74bd22a1..51e1bf4f 100644
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index 10ba4d48..e617a1a4 100644
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@@ -101,278 +101,279 @@ <h2>
     <p class="pln"><span class="n"><a id="t19" href="#t19">19</a></span><span class="t">    <span class="str">"""</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t20" href="#t20">20</a></span><span class="t"><span class="str">    | biobb_dna BIPopulations</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t21" href="#t21">21</a></span><span class="t"><span class="str">    | Calculate BI/BII populations from epsilon and zeta parameters.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t22" href="#t22">22</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t23" href="#t23">23</a></span><span class="t"><span class="str">    Args:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t24" href="#t24">24</a></span><span class="t"><span class="str">        input_epsilC_path (str): Path to .ser file for helical parameter 'epsilC'. File type: input. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/backbone/canal_output_epsilC.ser>`_. Accepted formats: ser (edam:format_2330).</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t25" href="#t25">25</a></span><span class="t"><span class="str">        input_epsilW_path (str): Path to .ser file for helical parameter 'epsilW'. File type: input. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/backbone/canal_output_epsilW.ser>`_. Accepted formats: ser (edam:format_2330).</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t26" href="#t26">26</a></span><span class="t"><span class="str">        input_zetaC_path (str): Path to .ser file for helical parameter 'zetaC'. File type: input. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/backbone/canal_output_zetaC.ser>`_. Accepted formats: ser (edam:format_2330).</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t27" href="#t27">27</a></span><span class="t"><span class="str">        input_zetaW_path (str): Path to .ser file for helical parameter 'zetaW'. File type: input. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/backbone/canal_output_zetaW.ser>`_. Accepted formats: ser (edam:format_2330).</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t28" href="#t28">28</a></span><span class="t"><span class="str">        output_csv_path (str): Path to .csv file where output is saved. File type: output. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/reference/backbone/bipop_ref.csv>`_. Accepted formats: csv (edam:format_3752).</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t29" href="#t29">29</a></span><span class="t"><span class="str">        output_jpg_path (str): Path to .jpg file where output is saved. File type: output. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/reference/backbone/bipop_ref.jpg>`_. Accepted formats: jpg (edam:format_3579).</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t30" href="#t30">30</a></span><span class="t"><span class="str">        properties (dict):</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t31" href="#t31">31</a></span><span class="t"><span class="str">            * **sequence** (*str*) - (None) Nucleic acid sequence corresponding to the input .ser file. Length of sequence is expected to be the same as the total number of columns in the .ser file, minus the index column (even if later on a subset of columns is selected with the *seqpos* option).</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t32" href="#t32">32</a></span><span class="t"><span class="str">            * **seqpos** (*list*) - (None) list of sequence positions (columns indices starting by 0) to analyze.  If not specified it will analyse the complete sequence.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t33" href="#t33">33</a></span><span class="t"><span class="str">            * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t34" href="#t34">34</a></span><span class="t"><span class="str">            * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t35" href="#t35">35</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t36" href="#t36">36</a></span><span class="t"><span class="str">    Examples:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t37" href="#t37">37</a></span><span class="t"><span class="str">        This is a use example of how to use the building block from Python::</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t38" href="#t38">38</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t39" href="#t39">39</a></span><span class="t"><span class="str">            from biobb_dna.backbone.bipopulations import bipopulations</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t40" href="#t40">40</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t41" href="#t41">41</a></span><span class="t"><span class="str">            prop = {</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t42" href="#t42">42</a></span><span class="t"><span class="str">                'sequence': 'GCAT',</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t43" href="#t43">43</a></span><span class="t"><span class="str">            }</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t44" href="#t44">44</a></span><span class="t"><span class="str">            bipopulations(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t45" href="#t45">45</a></span><span class="t"><span class="str">                input_epsilC_path='/path/to/epsilC.ser',</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t46" href="#t46">46</a></span><span class="t"><span class="str">                input_epsilW_path='/path/to/epsilW.ser',</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t47" href="#t47">47</a></span><span class="t"><span class="str">                input_zetaC_path='/path/to/zetaC.ser',</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t48" href="#t48">48</a></span><span class="t"><span class="str">                input_zetaW_path='/path/to/zetaW.ser',</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t49" href="#t49">49</a></span><span class="t"><span class="str">                output_csv_path='/path/to/table/output.csv',</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t50" href="#t50">50</a></span><span class="t"><span class="str">                output_jpg_path='/path/to/table/output.jpg',</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t51" href="#t51">51</a></span><span class="t"><span class="str">                properties=prop)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t52" href="#t52">52</a></span><span class="t"><span class="str">    Info:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t53" href="#t53">53</a></span><span class="t"><span class="str">        * wrapped_software:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t54" href="#t54">54</a></span><span class="t"><span class="str">            * name: In house</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t55" href="#t55">55</a></span><span class="t"><span class="str">            * license: Apache-2.0</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t56" href="#t56">56</a></span><span class="t"><span class="str">        * ontology:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t57" href="#t57">57</a></span><span class="t"><span class="str">            * name: EDAM</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t58" href="#t58">58</a></span><span class="t"><span class="str">            * schema: http://edamontology.org/EDAM.owl</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t59" href="#t59">59</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t60" href="#t60">60</a></span><span class="t"><span class="str">    """</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t61" href="#t61">61</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t62" href="#t62">62</a></span><span class="t">    <span class="key">def</span> <span class="nam">__init__</span><span class="op">(</span><span class="nam">self</span><span class="op">,</span> <span class="nam">input_epsilC_path</span><span class="op">,</span> <span class="nam">input_epsilW_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t63" href="#t63">63</a></span><span class="t">                 <span class="nam">input_zetaC_path</span><span class="op">,</span> <span class="nam">input_zetaW_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t64" href="#t64">64</a></span><span class="t">                 <span class="nam">output_csv_path</span><span class="op">,</span> <span class="nam">output_jpg_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t65" href="#t65">65</a></span><span class="t">                 <span class="nam">properties</span><span class="op">=</span><span class="key">None</span><span class="op">,</span> <span class="op">**</span><span class="nam">kwargs</span><span class="op">)</span> <span class="op">-></span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t66" href="#t66">66</a></span><span class="t">        <span class="nam">properties</span> <span class="op">=</span> <span class="nam">properties</span> <span class="key">or</span> <span class="op">{</span><span class="op">}</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t67" href="#t67">67</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t68" href="#t68">68</a></span><span class="t">        <span class="com"># Call parent class constructor</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t69" href="#t69">69</a></span><span class="t">        <span class="nam">super</span><span class="op">(</span><span class="op">)</span><span class="op">.</span><span class="nam">__init__</span><span class="op">(</span><span class="nam">properties</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t70" href="#t70">70</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">locals_var_dict</span> <span class="op">=</span> <span class="nam">locals</span><span class="op">(</span><span class="op">)</span><span class="op">.</span><span class="nam">copy</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t71" href="#t71">71</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t72" href="#t72">72</a></span><span class="t">        <span class="com"># Input/Output files</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t73" href="#t73">73</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span> <span class="op">=</span> <span class="op">{</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t74" href="#t74">74</a></span><span class="t">            <span class="str">'in'</span><span class="op">:</span> <span class="op">{</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t75" href="#t75">75</a></span><span class="t">                <span class="str">'input_epsilC_path'</span><span class="op">:</span> <span class="nam">input_epsilC_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t76" href="#t76">76</a></span><span class="t">                <span class="str">'input_epsilW_path'</span><span class="op">:</span> <span class="nam">input_epsilW_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t77" href="#t77">77</a></span><span class="t">                <span class="str">'input_zetaC_path'</span><span class="op">:</span> <span class="nam">input_zetaC_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t78" href="#t78">78</a></span><span class="t">                <span class="str">'input_zetaW_path'</span><span class="op">:</span> <span class="nam">input_zetaW_path</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t79" href="#t79">79</a></span><span class="t">            <span class="op">}</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t80" href="#t80">80</a></span><span class="t">            <span class="str">'out'</span><span class="op">:</span> <span class="op">{</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t81" href="#t81">81</a></span><span class="t">                <span class="str">'output_csv_path'</span><span class="op">:</span> <span class="nam">output_csv_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t82" href="#t82">82</a></span><span class="t">                <span class="str">'output_jpg_path'</span><span class="op">:</span> <span class="nam">output_jpg_path</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t83" href="#t83">83</a></span><span class="t">            <span class="op">}</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t84" href="#t84">84</a></span><span class="t">        <span class="op">}</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t85" href="#t85">85</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t86" href="#t86">86</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">properties</span> <span class="op">=</span> <span class="nam">properties</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t87" href="#t87">87</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"sequence"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t88" href="#t88">88</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"seqpos"</span><span class="op">,</span> <span class="key">None</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t89" href="#t89">89</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t90" href="#t90">90</a></span><span class="t">        <span class="com"># Check the properties</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t91" href="#t91">91</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_properties</span><span class="op">(</span><span class="nam">properties</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t92" href="#t92">92</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_arguments</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t93" href="#t93">93</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t94" href="#t94">94</a></span><span class="t">    <span class="op">@</span><span class="nam">launchlogger</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t95" href="#t95">95</a></span><span class="t">    <span class="key">def</span> <span class="nam">launch</span><span class="op">(</span><span class="nam">self</span><span class="op">)</span> <span class="op">-></span> <span class="nam">int</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t96" href="#t96">96</a></span><span class="t">        <span class="str">"""Execute the :class:`BIPopulations &lt;backbone.bipopulations.BIPopulations>` object."""</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t97" href="#t97">97</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t98" href="#t98">98</a></span><span class="t">        <span class="com"># Setup Biobb</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t99" href="#t99">99</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">check_restart</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t100" href="#t100">100</a></span><span class="t">            <span class="key">return</span> <span class="num">0</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t101" href="#t101">101</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">stage_files</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t102" href="#t102">102</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t103" href="#t103">103</a></span><span class="t">        <span class="com"># check sequence</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t104" href="#t104">104</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span> <span class="key">is</span> <span class="key">None</span> <span class="key">or</span> <span class="nam">len</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span><span class="op">)</span> <span class="op">&lt;</span> <span class="num">2</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t105" href="#t105">105</a></span><span class="t">            <span class="key">raise</span> <span class="nam">ValueError</span><span class="op">(</span><span class="str">"sequence is null or too short!"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t106" href="#t106">106</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t107" href="#t107">107</a></span><span class="t">        <span class="com"># check seqpos</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t108" href="#t108">108</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span> <span class="key">is</span> <span class="key">not</span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t109" href="#t109">109</a></span><span class="t">            <span class="key">if</span> <span class="op">(</span><span class="nam">max</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">)</span> <span class="op">></span> <span class="nam">len</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span><span class="op">)</span> <span class="op">-</span> <span class="num">2</span><span class="op">)</span> <span class="key">or</span> <span class="op">(</span><span class="nam">min</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">)</span> <span class="op">&lt;</span> <span class="num">1</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t110" href="#t110">110</a></span><span class="t">                <span class="key">raise</span> <span class="nam">ValueError</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t111" href="#t111">111</a></span><span class="t">                    <span class="str">f"seqpos values must be between 1 and {len(self.sequence) - 2}"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t112" href="#t112">112</a></span><span class="t">            <span class="key">if</span> <span class="key">not</span> <span class="op">(</span><span class="nam">isinstance</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">,</span> <span class="nam">list</span><span class="op">)</span> <span class="key">and</span> <span class="nam">len</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">)</span> <span class="op">></span> <span class="num">1</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t113" href="#t113">113</a></span><span class="t">                <span class="key">raise</span> <span class="nam">ValueError</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t114" href="#t114">114</a></span><span class="t">                    <span class="str">"seqpos must be a list of at least two integers"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t115" href="#t115">115</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t116" href="#t116">116</a></span><span class="t">        <span class="com"># Creating temporary folder</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t117" href="#t117">117</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span> <span class="op">=</span> <span class="nam">fu</span><span class="op">.</span><span class="nam">create_unique_dir</span><span class="op">(</span><span class="nam">prefix</span><span class="op">=</span><span class="str">"backbone_"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t118" href="#t118">118</a></span><span class="t">        <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="str">'Creating %s temporary folder'</span> <span class="op">%</span> <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t119" href="#t119">119</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t120" href="#t120">120</a></span><span class="t">        <span class="com"># Copy input_file_path1 to temporary folder</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t121" href="#t121">121</a></span><span class="t">        <span class="nam">shutil</span><span class="op">.</span><span class="nam">copy</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'input_epsilC_path'</span><span class="op">]</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t122" href="#t122">122</a></span><span class="t">        <span class="nam">shutil</span><span class="op">.</span><span class="nam">copy</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'input_epsilW_path'</span><span class="op">]</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t123" href="#t123">123</a></span><span class="t">        <span class="nam">shutil</span><span class="op">.</span><span class="nam">copy</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'input_zetaC_path'</span><span class="op">]</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t124" href="#t124">124</a></span><span class="t">        <span class="nam">shutil</span><span class="op">.</span><span class="nam">copy</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'input_zetaW_path'</span><span class="op">]</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t125" href="#t125">125</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t126" href="#t126">126</a></span><span class="t">        <span class="com"># read input files</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t127" href="#t127">127</a></span><span class="t">        <span class="nam">epsilC</span> <span class="op">=</span> <span class="nam">read_series</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t128" href="#t128">128</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'input_epsilC_path'</span><span class="op">]</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t129" href="#t129">129</a></span><span class="t">            <span class="nam">usecols</span><span class="op">=</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t130" href="#t130">130</a></span><span class="t">        <span class="nam">epsilW</span> <span class="op">=</span> <span class="nam">read_series</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t131" href="#t131">131</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'input_epsilW_path'</span><span class="op">]</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t132" href="#t132">132</a></span><span class="t">            <span class="nam">usecols</span><span class="op">=</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t133" href="#t133">133</a></span><span class="t">        <span class="nam">zetaC</span> <span class="op">=</span> <span class="nam">read_series</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t134" href="#t134">134</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'input_zetaC_path'</span><span class="op">]</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t135" href="#t135">135</a></span><span class="t">            <span class="nam">usecols</span><span class="op">=</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t136" href="#t136">136</a></span><span class="t">        <span class="nam">zetaW</span> <span class="op">=</span> <span class="nam">read_series</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t137" href="#t137">137</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'input_zetaW_path'</span><span class="op">]</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t138" href="#t138">138</a></span><span class="t">            <span class="nam">usecols</span><span class="op">=</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t139" href="#t139">139</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t140" href="#t140">140</a></span><span class="t">        <span class="com"># calculate difference between epsil and zeta parameters</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t141" href="#t141">141</a></span><span class="t">        <span class="nam">xlabels</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">get_xlabels</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t142" href="#t142">142</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t143" href="#t143">143</a></span><span class="t">            <span class="nam">inverse_complement</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t144" href="#t144">144</a></span><span class="t">        <span class="nam">diff_epsil_zeta</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">get_angles_difference</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t145" href="#t145">145</a></span><span class="t">            <span class="nam">epsilC</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t146" href="#t146">146</a></span><span class="t">            <span class="nam">zetaC</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t147" href="#t147">147</a></span><span class="t">            <span class="nam">epsilW</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t148" href="#t148">148</a></span><span class="t">            <span class="nam">zetaW</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t149" href="#t149">149</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t150" href="#t150">150</a></span><span class="t">        <span class="com"># calculate BI population</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t151" href="#t151">151</a></span><span class="t">        <span class="nam">BI</span> <span class="op">=</span> <span class="op">(</span><span class="nam">diff_epsil_zeta</span> <span class="op">&lt;</span> <span class="num">0</span><span class="op">)</span><span class="op">.</span><span class="nam">sum</span><span class="op">(</span><span class="nam">axis</span><span class="op">=</span><span class="num">0</span><span class="op">)</span> <span class="op">*</span> <span class="num">100</span> <span class="op">/</span> <span class="nam">len</span><span class="op">(</span><span class="nam">diff_epsil_zeta</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t152" href="#t152">152</a></span><span class="t">        <span class="nam">BII</span> <span class="op">=</span> <span class="num">100</span> <span class="op">-</span> <span class="nam">BI</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t153" href="#t153">153</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t154" href="#t154">154</a></span><span class="t">        <span class="com"># save table</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t155" href="#t155">155</a></span><span class="t">        <span class="nam">Bpopulations_df</span> <span class="op">=</span> <span class="nam">pd</span><span class="op">.</span><span class="nam">DataFrame</span><span class="op">(</span><span class="op">{</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t156" href="#t156">156</a></span><span class="t">            <span class="str">"Nucleotide"</span><span class="op">:</span> <span class="nam">xlabels</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t157" href="#t157">157</a></span><span class="t">            <span class="str">"BI population"</span><span class="op">:</span> <span class="nam">BI</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t158" href="#t158">158</a></span><span class="t">            <span class="str">"BII population"</span><span class="op">:</span> <span class="nam">BII</span><span class="op">}</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t159" href="#t159">159</a></span><span class="t">        <span class="nam">Bpopulations_df</span><span class="op">.</span><span class="nam">to_csv</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t160" href="#t160">160</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'out'</span><span class="op">]</span><span class="op">[</span><span class="str">'output_csv_path'</span><span class="op">]</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t161" href="#t161">161</a></span><span class="t">            <span class="nam">index</span><span class="op">=</span><span class="key">False</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t162" href="#t162">162</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t163" href="#t163">163</a></span><span class="t">        <span class="com"># save plot</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t164" href="#t164">164</a></span><span class="t">        <span class="nam">fig</span><span class="op">,</span> <span class="nam">axs</span> <span class="op">=</span> <span class="nam">plt</span><span class="op">.</span><span class="nam">subplots</span><span class="op">(</span><span class="num">1</span><span class="op">,</span> <span class="num">1</span><span class="op">,</span> <span class="nam">dpi</span><span class="op">=</span><span class="num">300</span><span class="op">,</span> <span class="nam">tight_layout</span><span class="op">=</span><span class="key">True</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t165" href="#t165">165</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">bar</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t166" href="#t166">166</a></span><span class="t">            <span class="nam">range</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">xlabels</span><span class="op">)</span><span class="op">)</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t167" href="#t167">167</a></span><span class="t">            <span class="nam">BI</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t168" href="#t168">168</a></span><span class="t">            <span class="nam">label</span><span class="op">=</span><span class="str">"BI"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t169" href="#t169">169</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">bar</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t170" href="#t170">170</a></span><span class="t">            <span class="nam">range</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">xlabels</span><span class="op">)</span><span class="op">)</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t171" href="#t171">171</a></span><span class="t">            <span class="nam">BII</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t172" href="#t172">172</a></span><span class="t">            <span class="nam">bottom</span><span class="op">=</span><span class="nam">BI</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t173" href="#t173">173</a></span><span class="t">            <span class="nam">label</span><span class="op">=</span><span class="str">"BII"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t174" href="#t174">174</a></span><span class="t">        <span class="com"># empty bar to divide both sequences</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t175" href="#t175">175</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">bar</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t176" href="#t176">176</a></span><span class="t">            <span class="op">[</span><span class="nam">len</span><span class="op">(</span><span class="nam">BI</span><span class="op">)</span><span class="op">//</span><span class="num">2</span><span class="op">]</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t177" href="#t177">177</a></span><span class="t">            <span class="op">[</span><span class="num">100</span><span class="op">]</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t178" href="#t178">178</a></span><span class="t">            <span class="nam">color</span><span class="op">=</span><span class="str">'white'</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t179" href="#t179">179</a></span><span class="t">            <span class="nam">label</span><span class="op">=</span><span class="key">None</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t180" href="#t180">180</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">legend</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t181" href="#t181">181</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_xticks</span><span class="op">(</span><span class="nam">range</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">xlabels</span><span class="op">)</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t182" href="#t182">182</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_xticklabels</span><span class="op">(</span><span class="nam">xlabels</span><span class="op">,</span> <span class="nam">rotation</span><span class="op">=</span><span class="num">90</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t183" href="#t183">183</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_xlabel</span><span class="op">(</span><span class="str">"Nucleotide Sequence"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t184" href="#t184">184</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_ylabel</span><span class="op">(</span><span class="str">"BI/BII Population (%)"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t185" href="#t185">185</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_title</span><span class="op">(</span><span class="str">"Nucleotide parameter: BI/BII Population"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t186" href="#t186">186</a></span><span class="t">        <span class="nam">fig</span><span class="op">.</span><span class="nam">savefig</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t187" href="#t187">187</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'out'</span><span class="op">]</span><span class="op">[</span><span class="str">'output_jpg_path'</span><span class="op">]</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t188" href="#t188">188</a></span><span class="t">            <span class="nam">format</span><span class="op">=</span><span class="str">"jpg"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t189" href="#t189">189</a></span><span class="t">        <span class="nam">plt</span><span class="op">.</span><span class="nam">close</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t190" href="#t190">190</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t191" href="#t191">191</a></span><span class="t">        <span class="com"># Remove temporary file(s)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t192" href="#t192">192</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_files</span><span class="op">.</span><span class="nam">extend</span><span class="op">(</span><span class="op">[</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t193" href="#t193">193</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"unique_dir"</span><span class="op">)</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t194" href="#t194">194</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t195" href="#t195">195</a></span><span class="t">        <span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t196" href="#t196">196</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">remove_tmp_files</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t197" href="#t197">197</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t198" href="#t198">198</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_arguments</span><span class="op">(</span><span class="nam">output_files_created</span><span class="op">=</span><span class="key">True</span><span class="op">,</span> <span class="nam">raise_exception</span><span class="op">=</span><span class="key">False</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t199" href="#t199">199</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t200" href="#t200">200</a></span><span class="t">        <span class="key">return</span> <span class="num">0</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t201" href="#t201">201</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t202" href="#t202">202</a></span><span class="t">    <span class="key">def</span> <span class="nam">get_xlabels</span><span class="op">(</span><span class="nam">self</span><span class="op">,</span> <span class="nam">strand1</span><span class="op">,</span> <span class="nam">strand2</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t203" href="#t203">203</a></span><span class="t">        <span class="com"># get list of tetramers, except first and last two bases</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t204" href="#t204">204</a></span><span class="t">        <span class="nam">labelsW</span> <span class="op">=</span> <span class="nam">list</span><span class="op">(</span><span class="nam">strand1</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t205" href="#t205">205</a></span><span class="t">        <span class="nam">labelsW</span><span class="op">[</span><span class="num">0</span><span class="op">]</span> <span class="op">=</span> <span class="str">f"{labelsW[0]}5\'"</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t206" href="#t206">206</a></span><span class="t">        <span class="nam">labelsW</span><span class="op">[</span><span class="op">-</span><span class="num">1</span><span class="op">]</span> <span class="op">=</span> <span class="str">f"{labelsW[-1]}3\'"</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t207" href="#t207">207</a></span><span class="t">        <span class="nam">labelsW</span> <span class="op">=</span> <span class="op">[</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t208" href="#t208">208</a></span><span class="t">            <span class="str">f"{i}-{j}"</span> <span class="key">for</span> <span class="nam">i</span><span class="op">,</span> <span class="nam">j</span> <span class="key">in</span> <span class="nam">zip</span><span class="op">(</span><span class="nam">labelsW</span><span class="op">,</span> <span class="nam">range</span><span class="op">(</span><span class="num">1</span><span class="op">,</span> <span class="nam">len</span><span class="op">(</span><span class="nam">labelsW</span><span class="op">)</span><span class="op">+</span><span class="num">1</span><span class="op">)</span><span class="op">)</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t209" href="#t209">209</a></span><span class="t">        <span class="nam">labelsC</span> <span class="op">=</span> <span class="nam">list</span><span class="op">(</span><span class="nam">strand2</span><span class="op">)</span><span class="op">[</span><span class="op">:</span><span class="op">:</span><span class="op">-</span><span class="num">1</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t210" href="#t210">210</a></span><span class="t">        <span class="nam">labelsC</span><span class="op">[</span><span class="num">0</span><span class="op">]</span> <span class="op">=</span> <span class="str">f"{labelsC[0]}5\'"</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t211" href="#t211">211</a></span><span class="t">        <span class="nam">labelsC</span><span class="op">[</span><span class="op">-</span><span class="num">1</span><span class="op">]</span> <span class="op">=</span> <span class="str">f"{labelsC[-1]}3\'"</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t212" href="#t212">212</a></span><span class="t">        <span class="nam">labelsC</span> <span class="op">=</span> <span class="op">[</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t213" href="#t213">213</a></span><span class="t">            <span class="str">f"{i}-{j}"</span> <span class="key">for</span> <span class="nam">i</span><span class="op">,</span> <span class="nam">j</span> <span class="key">in</span> <span class="nam">zip</span><span class="op">(</span><span class="nam">labelsC</span><span class="op">,</span> <span class="nam">range</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">labelsC</span><span class="op">)</span><span class="op">,</span> <span class="num">0</span><span class="op">,</span> <span class="op">-</span><span class="num">1</span><span class="op">)</span><span class="op">)</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t214" href="#t214">214</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t215" href="#t215">215</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span> <span class="key">is</span> <span class="key">not</span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t216" href="#t216">216</a></span><span class="t">            <span class="nam">labelsC</span> <span class="op">=</span> <span class="op">[</span><span class="nam">labelsC</span><span class="op">[</span><span class="nam">i</span><span class="op">]</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t217" href="#t217">217</a></span><span class="t">            <span class="nam">labelsW</span> <span class="op">=</span> <span class="op">[</span><span class="nam">labelsW</span><span class="op">[</span><span class="nam">i</span><span class="op">]</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t218" href="#t218">218</a></span><span class="t">        <span class="nam">xlabels</span> <span class="op">=</span> <span class="nam">labelsW</span> <span class="op">+</span> <span class="op">[</span><span class="str">'-'</span><span class="op">]</span> <span class="op">+</span> <span class="nam">labelsC</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t219" href="#t219">219</a></span><span class="t">        <span class="key">return</span> <span class="nam">xlabels</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t220" href="#t220">220</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t221" href="#t221">221</a></span><span class="t">    <span class="key">def</span> <span class="nam">get_angles_difference</span><span class="op">(</span><span class="nam">self</span><span class="op">,</span> <span class="nam">epsilC</span><span class="op">,</span> <span class="nam">zetaC</span><span class="op">,</span> <span class="nam">epsilW</span><span class="op">,</span> <span class="nam">zetaW</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t222" href="#t222">222</a></span><span class="t">        <span class="com"># concatenate zeta and epsil arrays</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t223" href="#t223">223</a></span><span class="t">        <span class="nam">separator_df</span> <span class="op">=</span> <span class="nam">pd</span><span class="op">.</span><span class="nam">DataFrame</span><span class="op">(</span><span class="op">{</span><span class="str">"-"</span><span class="op">:</span> <span class="nam">nan</span><span class="op">}</span><span class="op">,</span> <span class="nam">index</span><span class="op">=</span><span class="nam">range</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">zetaW</span><span class="op">)</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t224" href="#t224">224</a></span><span class="t">        <span class="nam">zeta</span> <span class="op">=</span> <span class="nam">pd</span><span class="op">.</span><span class="nam">concat</span><span class="op">(</span><span class="op">[</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t225" href="#t225">225</a></span><span class="t">            <span class="nam">zetaW</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t226" href="#t226">226</a></span><span class="t">            <span class="nam">separator_df</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t227" href="#t227">227</a></span><span class="t">            <span class="nam">zetaC</span><span class="op">[</span><span class="nam">zetaC</span><span class="op">.</span><span class="nam">columns</span><span class="op">[</span><span class="op">:</span><span class="op">:</span><span class="op">-</span><span class="num">1</span><span class="op">]</span><span class="op">]</span><span class="op">]</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t228" href="#t228">228</a></span><span class="t">            <span class="nam">axis</span><span class="op">=</span><span class="num">1</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t229" href="#t229">229</a></span><span class="t">        <span class="nam">epsil</span> <span class="op">=</span> <span class="nam">pd</span><span class="op">.</span><span class="nam">concat</span><span class="op">(</span><span class="op">[</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t230" href="#t230">230</a></span><span class="t">            <span class="nam">epsilW</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t231" href="#t231">231</a></span><span class="t">            <span class="nam">separator_df</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t232" href="#t232">232</a></span><span class="t">            <span class="nam">epsilC</span><span class="op">[</span><span class="nam">epsilC</span><span class="op">.</span><span class="nam">columns</span><span class="op">[</span><span class="op">:</span><span class="op">:</span><span class="op">-</span><span class="num">1</span><span class="op">]</span><span class="op">]</span><span class="op">]</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t233" href="#t233">233</a></span><span class="t">            <span class="nam">axis</span><span class="op">=</span><span class="num">1</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t234" href="#t234">234</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t235" href="#t235">235</a></span><span class="t">        <span class="com"># difference between epsilon and zeta coordinates</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t236" href="#t236">236</a></span><span class="t">        <span class="nam">diff_epsil_zeta</span> <span class="op">=</span> <span class="nam">epsil</span> <span class="op">-</span> <span class="nam">zeta</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t237" href="#t237">237</a></span><span class="t">        <span class="key">return</span> <span class="nam">diff_epsil_zeta</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t238" href="#t238">238</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t22" href="#t22">22</a></span><span class="t"><span class="str">    | Calculate BI/BII populations from epsilon and zeta parameters.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t23" href="#t23">23</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t24" href="#t24">24</a></span><span class="t"><span class="str">    Args:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t25" href="#t25">25</a></span><span class="t"><span class="str">        input_epsilC_path (str): Path to .ser file for helical parameter 'epsilC'. File type: input. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/backbone/canal_output_epsilC.ser>`_. Accepted formats: ser (edam:format_2330).</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t26" href="#t26">26</a></span><span class="t"><span class="str">        input_epsilW_path (str): Path to .ser file for helical parameter 'epsilW'. File type: input. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/backbone/canal_output_epsilW.ser>`_. Accepted formats: ser (edam:format_2330).</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t27" href="#t27">27</a></span><span class="t"><span class="str">        input_zetaC_path (str): Path to .ser file for helical parameter 'zetaC'. File type: input. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/backbone/canal_output_zetaC.ser>`_. Accepted formats: ser (edam:format_2330).</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t28" href="#t28">28</a></span><span class="t"><span class="str">        input_zetaW_path (str): Path to .ser file for helical parameter 'zetaW'. File type: input. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/backbone/canal_output_zetaW.ser>`_. Accepted formats: ser (edam:format_2330).</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t29" href="#t29">29</a></span><span class="t"><span class="str">        output_csv_path (str): Path to .csv file where output is saved. File type: output. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/reference/backbone/bipop_ref.csv>`_. Accepted formats: csv (edam:format_3752).</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t30" href="#t30">30</a></span><span class="t"><span class="str">        output_jpg_path (str): Path to .jpg file where output is saved. File type: output. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/reference/backbone/bipop_ref.jpg>`_. Accepted formats: jpg (edam:format_3579).</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t31" href="#t31">31</a></span><span class="t"><span class="str">        properties (dict):</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t32" href="#t32">32</a></span><span class="t"><span class="str">            * **sequence** (*str*) - (None) Nucleic acid sequence corresponding to the input .ser file. Length of sequence is expected to be the same as the total number of columns in the .ser file, minus the index column (even if later on a subset of columns is selected with the *seqpos* option).</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t33" href="#t33">33</a></span><span class="t"><span class="str">            * **seqpos** (*list*) - (None) list of sequence positions (columns indices starting by 0) to analyze.  If not specified it will analyse the complete sequence.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t34" href="#t34">34</a></span><span class="t"><span class="str">            * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t35" href="#t35">35</a></span><span class="t"><span class="str">            * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t36" href="#t36">36</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t37" href="#t37">37</a></span><span class="t"><span class="str">    Examples:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t38" href="#t38">38</a></span><span class="t"><span class="str">        This is a use example of how to use the building block from Python::</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t39" href="#t39">39</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t40" href="#t40">40</a></span><span class="t"><span class="str">            from biobb_dna.backbone.bipopulations import bipopulations</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t41" href="#t41">41</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t42" href="#t42">42</a></span><span class="t"><span class="str">            prop = {</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t43" href="#t43">43</a></span><span class="t"><span class="str">                'sequence': 'GCAT',</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t44" href="#t44">44</a></span><span class="t"><span class="str">            }</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t45" href="#t45">45</a></span><span class="t"><span class="str">            bipopulations(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t46" href="#t46">46</a></span><span class="t"><span class="str">                input_epsilC_path='/path/to/epsilC.ser',</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t47" href="#t47">47</a></span><span class="t"><span class="str">                input_epsilW_path='/path/to/epsilW.ser',</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t48" href="#t48">48</a></span><span class="t"><span class="str">                input_zetaC_path='/path/to/zetaC.ser',</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t49" href="#t49">49</a></span><span class="t"><span class="str">                input_zetaW_path='/path/to/zetaW.ser',</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t50" href="#t50">50</a></span><span class="t"><span class="str">                output_csv_path='/path/to/table/output.csv',</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t51" href="#t51">51</a></span><span class="t"><span class="str">                output_jpg_path='/path/to/table/output.jpg',</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t52" href="#t52">52</a></span><span class="t"><span class="str">                properties=prop)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t53" href="#t53">53</a></span><span class="t"><span class="str">    Info:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t54" href="#t54">54</a></span><span class="t"><span class="str">        * wrapped_software:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t55" href="#t55">55</a></span><span class="t"><span class="str">            * name: In house</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t56" href="#t56">56</a></span><span class="t"><span class="str">            * license: Apache-2.0</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t57" href="#t57">57</a></span><span class="t"><span class="str">        * ontology:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t58" href="#t58">58</a></span><span class="t"><span class="str">            * name: EDAM</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t59" href="#t59">59</a></span><span class="t"><span class="str">            * schema: http://edamontology.org/EDAM.owl</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t60" href="#t60">60</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t61" href="#t61">61</a></span><span class="t"><span class="str">    """</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t62" href="#t62">62</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t63" href="#t63">63</a></span><span class="t">    <span class="key">def</span> <span class="nam">__init__</span><span class="op">(</span><span class="nam">self</span><span class="op">,</span> <span class="nam">input_epsilC_path</span><span class="op">,</span> <span class="nam">input_epsilW_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t64" href="#t64">64</a></span><span class="t">                 <span class="nam">input_zetaC_path</span><span class="op">,</span> <span class="nam">input_zetaW_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t65" href="#t65">65</a></span><span class="t">                 <span class="nam">output_csv_path</span><span class="op">,</span> <span class="nam">output_jpg_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t66" href="#t66">66</a></span><span class="t">                 <span class="nam">properties</span><span class="op">=</span><span class="key">None</span><span class="op">,</span> <span class="op">**</span><span class="nam">kwargs</span><span class="op">)</span> <span class="op">-></span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t67" href="#t67">67</a></span><span class="t">        <span class="nam">properties</span> <span class="op">=</span> <span class="nam">properties</span> <span class="key">or</span> <span class="op">{</span><span class="op">}</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t68" href="#t68">68</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t69" href="#t69">69</a></span><span class="t">        <span class="com"># Call parent class constructor</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t70" href="#t70">70</a></span><span class="t">        <span class="nam">super</span><span class="op">(</span><span class="op">)</span><span class="op">.</span><span class="nam">__init__</span><span class="op">(</span><span class="nam">properties</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t71" href="#t71">71</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">locals_var_dict</span> <span class="op">=</span> <span class="nam">locals</span><span class="op">(</span><span class="op">)</span><span class="op">.</span><span class="nam">copy</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t72" href="#t72">72</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t73" href="#t73">73</a></span><span class="t">        <span class="com"># Input/Output files</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t74" href="#t74">74</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span> <span class="op">=</span> <span class="op">{</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t75" href="#t75">75</a></span><span class="t">            <span class="str">'in'</span><span class="op">:</span> <span class="op">{</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t76" href="#t76">76</a></span><span class="t">                <span class="str">'input_epsilC_path'</span><span class="op">:</span> <span class="nam">input_epsilC_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t77" href="#t77">77</a></span><span class="t">                <span class="str">'input_epsilW_path'</span><span class="op">:</span> <span class="nam">input_epsilW_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t78" href="#t78">78</a></span><span class="t">                <span class="str">'input_zetaC_path'</span><span class="op">:</span> <span class="nam">input_zetaC_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t79" href="#t79">79</a></span><span class="t">                <span class="str">'input_zetaW_path'</span><span class="op">:</span> <span class="nam">input_zetaW_path</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t80" href="#t80">80</a></span><span class="t">            <span class="op">}</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t81" href="#t81">81</a></span><span class="t">            <span class="str">'out'</span><span class="op">:</span> <span class="op">{</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t82" href="#t82">82</a></span><span class="t">                <span class="str">'output_csv_path'</span><span class="op">:</span> <span class="nam">output_csv_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t83" href="#t83">83</a></span><span class="t">                <span class="str">'output_jpg_path'</span><span class="op">:</span> <span class="nam">output_jpg_path</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t84" href="#t84">84</a></span><span class="t">            <span class="op">}</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t85" href="#t85">85</a></span><span class="t">        <span class="op">}</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t86" href="#t86">86</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t87" href="#t87">87</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">properties</span> <span class="op">=</span> <span class="nam">properties</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t88" href="#t88">88</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"sequence"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t89" href="#t89">89</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"seqpos"</span><span class="op">,</span> <span class="key">None</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t90" href="#t90">90</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t91" href="#t91">91</a></span><span class="t">        <span class="com"># Check the properties</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t92" href="#t92">92</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_properties</span><span class="op">(</span><span class="nam">properties</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t93" href="#t93">93</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_arguments</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t94" href="#t94">94</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t95" href="#t95">95</a></span><span class="t">    <span class="op">@</span><span class="nam">launchlogger</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t96" href="#t96">96</a></span><span class="t">    <span class="key">def</span> <span class="nam">launch</span><span class="op">(</span><span class="nam">self</span><span class="op">)</span> <span class="op">-></span> <span class="nam">int</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t97" href="#t97">97</a></span><span class="t">        <span class="str">"""Execute the :class:`BIPopulations &lt;backbone.bipopulations.BIPopulations>` object."""</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t98" href="#t98">98</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t99" href="#t99">99</a></span><span class="t">        <span class="com"># Setup Biobb</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t100" href="#t100">100</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">check_restart</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t101" href="#t101">101</a></span><span class="t">            <span class="key">return</span> <span class="num">0</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t102" href="#t102">102</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">stage_files</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t103" href="#t103">103</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t104" href="#t104">104</a></span><span class="t">        <span class="com"># check sequence</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t105" href="#t105">105</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span> <span class="key">is</span> <span class="key">None</span> <span class="key">or</span> <span class="nam">len</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span><span class="op">)</span> <span class="op">&lt;</span> <span class="num">2</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t106" href="#t106">106</a></span><span class="t">            <span class="key">raise</span> <span class="nam">ValueError</span><span class="op">(</span><span class="str">"sequence is null or too short!"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t107" href="#t107">107</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t108" href="#t108">108</a></span><span class="t">        <span class="com"># check seqpos</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t109" href="#t109">109</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span> <span class="key">is</span> <span class="key">not</span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t110" href="#t110">110</a></span><span class="t">            <span class="key">if</span> <span class="op">(</span><span class="nam">max</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">)</span> <span class="op">></span> <span class="nam">len</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span><span class="op">)</span> <span class="op">-</span> <span class="num">2</span><span class="op">)</span> <span class="key">or</span> <span class="op">(</span><span class="nam">min</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">)</span> <span class="op">&lt;</span> <span class="num">1</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t111" href="#t111">111</a></span><span class="t">                <span class="key">raise</span> <span class="nam">ValueError</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t112" href="#t112">112</a></span><span class="t">                    <span class="str">f"seqpos values must be between 1 and {len(self.sequence) - 2}"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t113" href="#t113">113</a></span><span class="t">            <span class="key">if</span> <span class="key">not</span> <span class="op">(</span><span class="nam">isinstance</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">,</span> <span class="nam">list</span><span class="op">)</span> <span class="key">and</span> <span class="nam">len</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">)</span> <span class="op">></span> <span class="num">1</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t114" href="#t114">114</a></span><span class="t">                <span class="key">raise</span> <span class="nam">ValueError</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t115" href="#t115">115</a></span><span class="t">                    <span class="str">"seqpos must be a list of at least two integers"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t116" href="#t116">116</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t117" href="#t117">117</a></span><span class="t">        <span class="com"># Creating temporary folder</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t118" href="#t118">118</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span> <span class="op">=</span> <span class="nam">fu</span><span class="op">.</span><span class="nam">create_unique_dir</span><span class="op">(</span><span class="nam">prefix</span><span class="op">=</span><span class="str">"backbone_"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t119" href="#t119">119</a></span><span class="t">        <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="str">'Creating %s temporary folder'</span> <span class="op">%</span> <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t120" href="#t120">120</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t121" href="#t121">121</a></span><span class="t">        <span class="com"># Copy input_file_path1 to temporary folder</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t122" href="#t122">122</a></span><span class="t">        <span class="nam">shutil</span><span class="op">.</span><span class="nam">copy</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'input_epsilC_path'</span><span class="op">]</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t123" href="#t123">123</a></span><span class="t">        <span class="nam">shutil</span><span class="op">.</span><span class="nam">copy</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'input_epsilW_path'</span><span class="op">]</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t124" href="#t124">124</a></span><span class="t">        <span class="nam">shutil</span><span class="op">.</span><span class="nam">copy</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'input_zetaC_path'</span><span class="op">]</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t125" href="#t125">125</a></span><span class="t">        <span class="nam">shutil</span><span class="op">.</span><span class="nam">copy</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'input_zetaW_path'</span><span class="op">]</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t126" href="#t126">126</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t127" href="#t127">127</a></span><span class="t">        <span class="com"># read input files</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t128" href="#t128">128</a></span><span class="t">        <span class="nam">epsilC</span> <span class="op">=</span> <span class="nam">read_series</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t129" href="#t129">129</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'input_epsilC_path'</span><span class="op">]</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t130" href="#t130">130</a></span><span class="t">            <span class="nam">usecols</span><span class="op">=</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t131" href="#t131">131</a></span><span class="t">        <span class="nam">epsilW</span> <span class="op">=</span> <span class="nam">read_series</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t132" href="#t132">132</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'input_epsilW_path'</span><span class="op">]</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t133" href="#t133">133</a></span><span class="t">            <span class="nam">usecols</span><span class="op">=</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t134" href="#t134">134</a></span><span class="t">        <span class="nam">zetaC</span> <span class="op">=</span> <span class="nam">read_series</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t135" href="#t135">135</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'input_zetaC_path'</span><span class="op">]</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t136" href="#t136">136</a></span><span class="t">            <span class="nam">usecols</span><span class="op">=</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t137" href="#t137">137</a></span><span class="t">        <span class="nam">zetaW</span> <span class="op">=</span> <span class="nam">read_series</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t138" href="#t138">138</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'input_zetaW_path'</span><span class="op">]</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t139" href="#t139">139</a></span><span class="t">            <span class="nam">usecols</span><span class="op">=</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t140" href="#t140">140</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t141" href="#t141">141</a></span><span class="t">        <span class="com"># calculate difference between epsil and zeta parameters</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t142" href="#t142">142</a></span><span class="t">        <span class="nam">xlabels</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">get_xlabels</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t143" href="#t143">143</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t144" href="#t144">144</a></span><span class="t">            <span class="nam">inverse_complement</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t145" href="#t145">145</a></span><span class="t">        <span class="nam">diff_epsil_zeta</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">get_angles_difference</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t146" href="#t146">146</a></span><span class="t">            <span class="nam">epsilC</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t147" href="#t147">147</a></span><span class="t">            <span class="nam">zetaC</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t148" href="#t148">148</a></span><span class="t">            <span class="nam">epsilW</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t149" href="#t149">149</a></span><span class="t">            <span class="nam">zetaW</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t150" href="#t150">150</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t151" href="#t151">151</a></span><span class="t">        <span class="com"># calculate BI population</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t152" href="#t152">152</a></span><span class="t">        <span class="nam">BI</span> <span class="op">=</span> <span class="op">(</span><span class="nam">diff_epsil_zeta</span> <span class="op">&lt;</span> <span class="num">0</span><span class="op">)</span><span class="op">.</span><span class="nam">sum</span><span class="op">(</span><span class="nam">axis</span><span class="op">=</span><span class="num">0</span><span class="op">)</span> <span class="op">*</span> <span class="num">100</span> <span class="op">/</span> <span class="nam">len</span><span class="op">(</span><span class="nam">diff_epsil_zeta</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t153" href="#t153">153</a></span><span class="t">        <span class="nam">BII</span> <span class="op">=</span> <span class="num">100</span> <span class="op">-</span> <span class="nam">BI</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t154" href="#t154">154</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t155" href="#t155">155</a></span><span class="t">        <span class="com"># save table</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t156" href="#t156">156</a></span><span class="t">        <span class="nam">Bpopulations_df</span> <span class="op">=</span> <span class="nam">pd</span><span class="op">.</span><span class="nam">DataFrame</span><span class="op">(</span><span class="op">{</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t157" href="#t157">157</a></span><span class="t">            <span class="str">"Nucleotide"</span><span class="op">:</span> <span class="nam">xlabels</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t158" href="#t158">158</a></span><span class="t">            <span class="str">"BI population"</span><span class="op">:</span> <span class="nam">BI</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t159" href="#t159">159</a></span><span class="t">            <span class="str">"BII population"</span><span class="op">:</span> <span class="nam">BII</span><span class="op">}</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t160" href="#t160">160</a></span><span class="t">        <span class="nam">Bpopulations_df</span><span class="op">.</span><span class="nam">to_csv</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t161" href="#t161">161</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'out'</span><span class="op">]</span><span class="op">[</span><span class="str">'output_csv_path'</span><span class="op">]</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t162" href="#t162">162</a></span><span class="t">            <span class="nam">index</span><span class="op">=</span><span class="key">False</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t163" href="#t163">163</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t164" href="#t164">164</a></span><span class="t">        <span class="com"># save plot</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t165" href="#t165">165</a></span><span class="t">        <span class="nam">fig</span><span class="op">,</span> <span class="nam">axs</span> <span class="op">=</span> <span class="nam">plt</span><span class="op">.</span><span class="nam">subplots</span><span class="op">(</span><span class="num">1</span><span class="op">,</span> <span class="num">1</span><span class="op">,</span> <span class="nam">dpi</span><span class="op">=</span><span class="num">300</span><span class="op">,</span> <span class="nam">tight_layout</span><span class="op">=</span><span class="key">True</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t166" href="#t166">166</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">bar</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t167" href="#t167">167</a></span><span class="t">            <span class="nam">range</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">xlabels</span><span class="op">)</span><span class="op">)</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t168" href="#t168">168</a></span><span class="t">            <span class="nam">BI</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t169" href="#t169">169</a></span><span class="t">            <span class="nam">label</span><span class="op">=</span><span class="str">"BI"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t170" href="#t170">170</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">bar</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t171" href="#t171">171</a></span><span class="t">            <span class="nam">range</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">xlabels</span><span class="op">)</span><span class="op">)</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t172" href="#t172">172</a></span><span class="t">            <span class="nam">BII</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t173" href="#t173">173</a></span><span class="t">            <span class="nam">bottom</span><span class="op">=</span><span class="nam">BI</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t174" href="#t174">174</a></span><span class="t">            <span class="nam">label</span><span class="op">=</span><span class="str">"BII"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t175" href="#t175">175</a></span><span class="t">        <span class="com"># empty bar to divide both sequences</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t176" href="#t176">176</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">bar</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t177" href="#t177">177</a></span><span class="t">            <span class="op">[</span><span class="nam">len</span><span class="op">(</span><span class="nam">BI</span><span class="op">)</span><span class="op">//</span><span class="num">2</span><span class="op">]</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t178" href="#t178">178</a></span><span class="t">            <span class="op">[</span><span class="num">100</span><span class="op">]</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t179" href="#t179">179</a></span><span class="t">            <span class="nam">color</span><span class="op">=</span><span class="str">'white'</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t180" href="#t180">180</a></span><span class="t">            <span class="nam">label</span><span class="op">=</span><span class="key">None</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t181" href="#t181">181</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">legend</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t182" href="#t182">182</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_xticks</span><span class="op">(</span><span class="nam">range</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">xlabels</span><span class="op">)</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t183" href="#t183">183</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_xticklabels</span><span class="op">(</span><span class="nam">xlabels</span><span class="op">,</span> <span class="nam">rotation</span><span class="op">=</span><span class="num">90</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t184" href="#t184">184</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_xlabel</span><span class="op">(</span><span class="str">"Nucleotide Sequence"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t185" href="#t185">185</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_ylabel</span><span class="op">(</span><span class="str">"BI/BII Population (%)"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t186" href="#t186">186</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_title</span><span class="op">(</span><span class="str">"Nucleotide parameter: BI/BII Population"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t187" href="#t187">187</a></span><span class="t">        <span class="nam">fig</span><span class="op">.</span><span class="nam">savefig</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t188" href="#t188">188</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'out'</span><span class="op">]</span><span class="op">[</span><span class="str">'output_jpg_path'</span><span class="op">]</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t189" href="#t189">189</a></span><span class="t">            <span class="nam">format</span><span class="op">=</span><span class="str">"jpg"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t190" href="#t190">190</a></span><span class="t">        <span class="nam">plt</span><span class="op">.</span><span class="nam">close</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t191" href="#t191">191</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t192" href="#t192">192</a></span><span class="t">        <span class="com"># Remove temporary file(s)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t193" href="#t193">193</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_files</span><span class="op">.</span><span class="nam">extend</span><span class="op">(</span><span class="op">[</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t194" href="#t194">194</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"unique_dir"</span><span class="op">)</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t195" href="#t195">195</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t196" href="#t196">196</a></span><span class="t">        <span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t197" href="#t197">197</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">remove_tmp_files</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t198" href="#t198">198</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t199" href="#t199">199</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_arguments</span><span class="op">(</span><span class="nam">output_files_created</span><span class="op">=</span><span class="key">True</span><span class="op">,</span> <span class="nam">raise_exception</span><span class="op">=</span><span class="key">False</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t200" href="#t200">200</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t201" href="#t201">201</a></span><span class="t">        <span class="key">return</span> <span class="num">0</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t202" href="#t202">202</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t203" href="#t203">203</a></span><span class="t">    <span class="key">def</span> <span class="nam">get_xlabels</span><span class="op">(</span><span class="nam">self</span><span class="op">,</span> <span class="nam">strand1</span><span class="op">,</span> <span class="nam">strand2</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t204" href="#t204">204</a></span><span class="t">        <span class="com"># get list of tetramers, except first and last two bases</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t205" href="#t205">205</a></span><span class="t">        <span class="nam">labelsW</span> <span class="op">=</span> <span class="nam">list</span><span class="op">(</span><span class="nam">strand1</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t206" href="#t206">206</a></span><span class="t">        <span class="nam">labelsW</span><span class="op">[</span><span class="num">0</span><span class="op">]</span> <span class="op">=</span> <span class="str">f"{labelsW[0]}5\'"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t207" href="#t207">207</a></span><span class="t">        <span class="nam">labelsW</span><span class="op">[</span><span class="op">-</span><span class="num">1</span><span class="op">]</span> <span class="op">=</span> <span class="str">f"{labelsW[-1]}3\'"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t208" href="#t208">208</a></span><span class="t">        <span class="nam">labelsW</span> <span class="op">=</span> <span class="op">[</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t209" href="#t209">209</a></span><span class="t">            <span class="str">f"{i}-{j}"</span> <span class="key">for</span> <span class="nam">i</span><span class="op">,</span> <span class="nam">j</span> <span class="key">in</span> <span class="nam">zip</span><span class="op">(</span><span class="nam">labelsW</span><span class="op">,</span> <span class="nam">range</span><span class="op">(</span><span class="num">1</span><span class="op">,</span> <span class="nam">len</span><span class="op">(</span><span class="nam">labelsW</span><span class="op">)</span><span class="op">+</span><span class="num">1</span><span class="op">)</span><span class="op">)</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t210" href="#t210">210</a></span><span class="t">        <span class="nam">labelsC</span> <span class="op">=</span> <span class="nam">list</span><span class="op">(</span><span class="nam">strand2</span><span class="op">)</span><span class="op">[</span><span class="op">:</span><span class="op">:</span><span class="op">-</span><span class="num">1</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t211" href="#t211">211</a></span><span class="t">        <span class="nam">labelsC</span><span class="op">[</span><span class="num">0</span><span class="op">]</span> <span class="op">=</span> <span class="str">f"{labelsC[0]}5\'"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t212" href="#t212">212</a></span><span class="t">        <span class="nam">labelsC</span><span class="op">[</span><span class="op">-</span><span class="num">1</span><span class="op">]</span> <span class="op">=</span> <span class="str">f"{labelsC[-1]}3\'"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t213" href="#t213">213</a></span><span class="t">        <span class="nam">labelsC</span> <span class="op">=</span> <span class="op">[</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t214" href="#t214">214</a></span><span class="t">            <span class="str">f"{i}-{j}"</span> <span class="key">for</span> <span class="nam">i</span><span class="op">,</span> <span class="nam">j</span> <span class="key">in</span> <span class="nam">zip</span><span class="op">(</span><span class="nam">labelsC</span><span class="op">,</span> <span class="nam">range</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">labelsC</span><span class="op">)</span><span class="op">,</span> <span class="num">0</span><span class="op">,</span> <span class="op">-</span><span class="num">1</span><span class="op">)</span><span class="op">)</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t215" href="#t215">215</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t216" href="#t216">216</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span> <span class="key">is</span> <span class="key">not</span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t217" href="#t217">217</a></span><span class="t">            <span class="nam">labelsC</span> <span class="op">=</span> <span class="op">[</span><span class="nam">labelsC</span><span class="op">[</span><span class="nam">i</span><span class="op">]</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t218" href="#t218">218</a></span><span class="t">            <span class="nam">labelsW</span> <span class="op">=</span> <span class="op">[</span><span class="nam">labelsW</span><span class="op">[</span><span class="nam">i</span><span class="op">]</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t219" href="#t219">219</a></span><span class="t">        <span class="nam">xlabels</span> <span class="op">=</span> <span class="nam">labelsW</span> <span class="op">+</span> <span class="op">[</span><span class="str">'-'</span><span class="op">]</span> <span class="op">+</span> <span class="nam">labelsC</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t220" href="#t220">220</a></span><span class="t">        <span class="key">return</span> <span class="nam">xlabels</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t221" href="#t221">221</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t222" href="#t222">222</a></span><span class="t">    <span class="key">def</span> <span class="nam">get_angles_difference</span><span class="op">(</span><span class="nam">self</span><span class="op">,</span> <span class="nam">epsilC</span><span class="op">,</span> <span class="nam">zetaC</span><span class="op">,</span> <span class="nam">epsilW</span><span class="op">,</span> <span class="nam">zetaW</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t223" href="#t223">223</a></span><span class="t">        <span class="com"># concatenate zeta and epsil arrays</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t224" href="#t224">224</a></span><span class="t">        <span class="nam">separator_df</span> <span class="op">=</span> <span class="nam">pd</span><span class="op">.</span><span class="nam">DataFrame</span><span class="op">(</span><span class="op">{</span><span class="str">"-"</span><span class="op">:</span> <span class="nam">nan</span><span class="op">}</span><span class="op">,</span> <span class="nam">index</span><span class="op">=</span><span class="nam">range</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">zetaW</span><span class="op">)</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t225" href="#t225">225</a></span><span class="t">        <span class="nam">zeta</span> <span class="op">=</span> <span class="nam">pd</span><span class="op">.</span><span class="nam">concat</span><span class="op">(</span><span class="op">[</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t226" href="#t226">226</a></span><span class="t">            <span class="nam">zetaW</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t227" href="#t227">227</a></span><span class="t">            <span class="nam">separator_df</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t228" href="#t228">228</a></span><span class="t">            <span class="nam">zetaC</span><span class="op">[</span><span class="nam">zetaC</span><span class="op">.</span><span class="nam">columns</span><span class="op">[</span><span class="op">:</span><span class="op">:</span><span class="op">-</span><span class="num">1</span><span class="op">]</span><span class="op">]</span><span class="op">]</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t229" href="#t229">229</a></span><span class="t">            <span class="nam">axis</span><span class="op">=</span><span class="num">1</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t230" href="#t230">230</a></span><span class="t">        <span class="nam">epsil</span> <span class="op">=</span> <span class="nam">pd</span><span class="op">.</span><span class="nam">concat</span><span class="op">(</span><span class="op">[</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t231" href="#t231">231</a></span><span class="t">            <span class="nam">epsilW</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t232" href="#t232">232</a></span><span class="t">            <span class="nam">separator_df</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t233" href="#t233">233</a></span><span class="t">            <span class="nam">epsilC</span><span class="op">[</span><span class="nam">epsilC</span><span class="op">.</span><span class="nam">columns</span><span class="op">[</span><span class="op">:</span><span class="op">:</span><span class="op">-</span><span class="num">1</span><span class="op">]</span><span class="op">]</span><span class="op">]</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t234" href="#t234">234</a></span><span class="t">            <span class="nam">axis</span><span class="op">=</span><span class="num">1</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t235" href="#t235">235</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t236" href="#t236">236</a></span><span class="t">        <span class="com"># difference between epsilon and zeta coordinates</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t237" href="#t237">237</a></span><span class="t">        <span class="nam">diff_epsil_zeta</span> <span class="op">=</span> <span class="nam">epsil</span> <span class="op">-</span> <span class="nam">zeta</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t238" href="#t238">238</a></span><span class="t">        <span class="key">return</span> <span class="nam">diff_epsil_zeta</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t239" href="#t239">239</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t240" href="#t240">240</a></span><span class="t"><span class="key">def</span> <span class="nam">bipopulations</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t241" href="#t241">241</a></span><span class="t">        <span class="nam">input_epsilC_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span> <span class="nam">input_epsilW_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t242" href="#t242">242</a></span><span class="t">        <span class="nam">input_zetaC_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span> <span class="nam">input_zetaW_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t243" href="#t243">243</a></span><span class="t">        <span class="nam">output_csv_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span> <span class="nam">output_jpg_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t244" href="#t244">244</a></span><span class="t">        <span class="nam">properties</span><span class="op">:</span> <span class="nam">dict</span> <span class="op">=</span> <span class="key">None</span><span class="op">,</span> <span class="op">**</span><span class="nam">kwargs</span><span class="op">)</span> <span class="op">-></span> <span class="nam">int</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t245" href="#t245">245</a></span><span class="t">    <span class="str">"""Create :class:`BIPopulations &lt;dna.backbone.bipopulations.BIPopulations>` class and</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t246" href="#t246">246</a></span><span class="t"><span class="str">    execute the: meth: `launch() &lt;dna.backbone.bipopulations.BIPopulations.launch>` method. """</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t247" href="#t247">247</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t248" href="#t248">248</a></span><span class="t">    <span class="key">return</span> <span class="nam">BIPopulations</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t249" href="#t249">249</a></span><span class="t">        <span class="nam">input_epsilC_path</span><span class="op">=</span><span class="nam">input_epsilC_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t250" href="#t250">250</a></span><span class="t">        <span class="nam">input_epsilW_path</span><span class="op">=</span><span class="nam">input_epsilW_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t251" href="#t251">251</a></span><span class="t">        <span class="nam">input_zetaC_path</span><span class="op">=</span><span class="nam">input_zetaC_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t252" href="#t252">252</a></span><span class="t">        <span class="nam">input_zetaW_path</span><span class="op">=</span><span class="nam">input_zetaW_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t253" href="#t253">253</a></span><span class="t">        <span class="nam">output_csv_path</span><span class="op">=</span><span class="nam">output_csv_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t254" href="#t254">254</a></span><span class="t">        <span class="nam">output_jpg_path</span><span class="op">=</span><span class="nam">output_jpg_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t255" href="#t255">255</a></span><span class="t">        <span class="nam">properties</span><span class="op">=</span><span class="nam">properties</span><span class="op">,</span> <span class="op">**</span><span class="nam">kwargs</span><span class="op">)</span><span class="op">.</span><span class="nam">launch</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t256" href="#t256">256</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t240" href="#t240">240</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t241" href="#t241">241</a></span><span class="t"><span class="key">def</span> <span class="nam">bipopulations</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t242" href="#t242">242</a></span><span class="t">        <span class="nam">input_epsilC_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span> <span class="nam">input_epsilW_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t243" href="#t243">243</a></span><span class="t">        <span class="nam">input_zetaC_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span> <span class="nam">input_zetaW_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t244" href="#t244">244</a></span><span class="t">        <span class="nam">output_csv_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span> <span class="nam">output_jpg_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t245" href="#t245">245</a></span><span class="t">        <span class="nam">properties</span><span class="op">:</span> <span class="nam">dict</span> <span class="op">=</span> <span class="key">None</span><span class="op">,</span> <span class="op">**</span><span class="nam">kwargs</span><span class="op">)</span> <span class="op">-></span> <span class="nam">int</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t246" href="#t246">246</a></span><span class="t">    <span class="str">"""Create :class:`BIPopulations &lt;dna.backbone.bipopulations.BIPopulations>` class and</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t247" href="#t247">247</a></span><span class="t"><span class="str">    execute the: meth: `launch() &lt;dna.backbone.bipopulations.BIPopulations.launch>` method. """</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t248" href="#t248">248</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t249" href="#t249">249</a></span><span class="t">    <span class="key">return</span> <span class="nam">BIPopulations</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t250" href="#t250">250</a></span><span class="t">        <span class="nam">input_epsilC_path</span><span class="op">=</span><span class="nam">input_epsilC_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t251" href="#t251">251</a></span><span class="t">        <span class="nam">input_epsilW_path</span><span class="op">=</span><span class="nam">input_epsilW_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t252" href="#t252">252</a></span><span class="t">        <span class="nam">input_zetaC_path</span><span class="op">=</span><span class="nam">input_zetaC_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t253" href="#t253">253</a></span><span class="t">        <span class="nam">input_zetaW_path</span><span class="op">=</span><span class="nam">input_zetaW_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t254" href="#t254">254</a></span><span class="t">        <span class="nam">output_csv_path</span><span class="op">=</span><span class="nam">output_csv_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t255" href="#t255">255</a></span><span class="t">        <span class="nam">output_jpg_path</span><span class="op">=</span><span class="nam">output_jpg_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t256" href="#t256">256</a></span><span class="t">        <span class="nam">properties</span><span class="op">=</span><span class="nam">properties</span><span class="op">,</span> <span class="op">**</span><span class="nam">kwargs</span><span class="op">)</span><span class="op">.</span><span class="nam">launch</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t257" href="#t257">257</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t258" href="#t258">258</a></span><span class="t"><span class="key">def</span> <span class="nam">main</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t259" href="#t259">259</a></span><span class="t">    <span class="str">"""Command line execution of this building block. Please check the command line documentation."""</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t260" href="#t260">260</a></span><span class="t">    <span class="nam">parser</span> <span class="op">=</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">ArgumentParser</span><span class="op">(</span><span class="nam">description</span><span class="op">=</span><span class="str">'Calculate BI/BII populations.'</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t261" href="#t261">261</a></span><span class="t">                                     <span class="nam">formatter_class</span><span class="op">=</span><span class="key">lambda</span> <span class="nam">prog</span><span class="op">:</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">RawTextHelpFormatter</span><span class="op">(</span><span class="nam">prog</span><span class="op">,</span> <span class="nam">width</span><span class="op">=</span><span class="num">99999</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t262" href="#t262">262</a></span><span class="t">    <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--config'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">False</span><span class="op">,</span> <span class="nam">help</span><span class="op">=</span><span class="str">'Configuration file'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t263" href="#t263">263</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t264" href="#t264">264</a></span><span class="t">    <span class="nam">required_args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument_group</span><span class="op">(</span><span class="str">'required arguments'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t265" href="#t265">265</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--input_epsilC_path'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t266" href="#t266">266</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Helical parameter &lt;epsilC> input ser file path. Accepted formats: ser.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t267" href="#t267">267</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--input_epsilW_path'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t268" href="#t268">268</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Helical parameter &lt;epsilW> input ser file path. Accepted formats: ser.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t269" href="#t269">269</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--input_zetaC_path'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t270" href="#t270">270</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Helical parameter &lt;zetaC> input ser file path. Accepted formats: ser.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t271" href="#t271">271</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--input_zetaW_path'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t272" href="#t272">272</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Helical parameter &lt;zetaW> input ser file path. Accepted formats: ser.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t273" href="#t273">273</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--output_csv_path'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t274" href="#t274">274</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Path to output csv file. Accepted formats: csv.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t275" href="#t275">275</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--output_jpg_path'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t276" href="#t276">276</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Path to output jpg file. Accepted formats: jpg.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t277" href="#t277">277</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t278" href="#t278">278</a></span><span class="t">    <span class="nam">args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">parse_args</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t279" href="#t279">279</a></span><span class="t">    <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="op">=</span> <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="key">or</span> <span class="str">"{}"</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t280" href="#t280">280</a></span><span class="t">    <span class="nam">properties</span> <span class="op">=</span> <span class="nam">settings</span><span class="op">.</span><span class="nam">ConfReader</span><span class="op">(</span><span class="nam">config</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">config</span><span class="op">)</span><span class="op">.</span><span class="nam">get_prop_dic</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t281" href="#t281">281</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t282" href="#t282">282</a></span><span class="t">    <span class="nam">bipopulations</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t283" href="#t283">283</a></span><span class="t">        <span class="nam">input_epsilC_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_epsilC_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t284" href="#t284">284</a></span><span class="t">        <span class="nam">input_epsilW_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_epsilW_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t285" href="#t285">285</a></span><span class="t">        <span class="nam">input_zetaC_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_zetaC_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t286" href="#t286">286</a></span><span class="t">        <span class="nam">input_zetaW_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_zetaW_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t287" href="#t287">287</a></span><span class="t">        <span class="nam">output_csv_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">output_csv_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t288" href="#t288">288</a></span><span class="t">        <span class="nam">output_jpg_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">output_jpg_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t289" href="#t289">289</a></span><span class="t">        <span class="nam">properties</span><span class="op">=</span><span class="nam">properties</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t290" href="#t290">290</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t258" href="#t258">258</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t259" href="#t259">259</a></span><span class="t"><span class="key">def</span> <span class="nam">main</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t260" href="#t260">260</a></span><span class="t">    <span class="str">"""Command line execution of this building block. Please check the command line documentation."""</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t261" href="#t261">261</a></span><span class="t">    <span class="nam">parser</span> <span class="op">=</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">ArgumentParser</span><span class="op">(</span><span class="nam">description</span><span class="op">=</span><span class="str">'Calculate BI/BII populations.'</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t262" href="#t262">262</a></span><span class="t">                                     <span class="nam">formatter_class</span><span class="op">=</span><span class="key">lambda</span> <span class="nam">prog</span><span class="op">:</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">RawTextHelpFormatter</span><span class="op">(</span><span class="nam">prog</span><span class="op">,</span> <span class="nam">width</span><span class="op">=</span><span class="num">99999</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t263" href="#t263">263</a></span><span class="t">    <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--config'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">False</span><span class="op">,</span> <span class="nam">help</span><span class="op">=</span><span class="str">'Configuration file'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t264" href="#t264">264</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t265" href="#t265">265</a></span><span class="t">    <span class="nam">required_args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument_group</span><span class="op">(</span><span class="str">'required arguments'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t266" href="#t266">266</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--input_epsilC_path'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t267" href="#t267">267</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Helical parameter &lt;epsilC> input ser file path. Accepted formats: ser.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t268" href="#t268">268</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--input_epsilW_path'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t269" href="#t269">269</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Helical parameter &lt;epsilW> input ser file path. Accepted formats: ser.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t270" href="#t270">270</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--input_zetaC_path'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t271" href="#t271">271</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Helical parameter &lt;zetaC> input ser file path. Accepted formats: ser.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t272" href="#t272">272</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--input_zetaW_path'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t273" href="#t273">273</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Helical parameter &lt;zetaW> input ser file path. Accepted formats: ser.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t274" href="#t274">274</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--output_csv_path'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t275" href="#t275">275</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Path to output csv file. Accepted formats: csv.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t276" href="#t276">276</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--output_jpg_path'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t277" href="#t277">277</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Path to output jpg file. Accepted formats: jpg.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t278" href="#t278">278</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t279" href="#t279">279</a></span><span class="t">    <span class="nam">args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">parse_args</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t280" href="#t280">280</a></span><span class="t">    <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="op">=</span> <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="key">or</span> <span class="str">"{}"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t281" href="#t281">281</a></span><span class="t">    <span class="nam">properties</span> <span class="op">=</span> <span class="nam">settings</span><span class="op">.</span><span class="nam">ConfReader</span><span class="op">(</span><span class="nam">config</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">config</span><span class="op">)</span><span class="op">.</span><span class="nam">get_prop_dic</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t282" href="#t282">282</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t283" href="#t283">283</a></span><span class="t">    <span class="nam">bipopulations</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t284" href="#t284">284</a></span><span class="t">        <span class="nam">input_epsilC_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_epsilC_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t285" href="#t285">285</a></span><span class="t">        <span class="nam">input_epsilW_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_epsilW_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t286" href="#t286">286</a></span><span class="t">        <span class="nam">input_zetaC_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_zetaC_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t287" href="#t287">287</a></span><span class="t">        <span class="nam">input_zetaW_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_zetaW_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t288" href="#t288">288</a></span><span class="t">        <span class="nam">output_csv_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">output_csv_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t289" href="#t289">289</a></span><span class="t">        <span class="nam">output_jpg_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">output_jpg_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t290" href="#t290">290</a></span><span class="t">        <span class="nam">properties</span><span class="op">=</span><span class="nam">properties</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t291" href="#t291">291</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t292" href="#t292">292</a></span><span class="t"><span class="key">if</span> <span class="nam">__name__</span> <span class="op">==</span> <span class="str">'__main__'</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t293" href="#t293">293</a></span><span class="t">    <span class="nam">main</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t292" href="#t292">292</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t293" href="#t293">293</a></span><span class="t"><span class="key">if</span> <span class="nam">__name__</span> <span class="op">==</span> <span class="str">'__main__'</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t294" href="#t294">294</a></span><span class="t">    <span class="nam">main</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
 </main>
 <footer>
     <div class="content">
@@ -382,7 +383,7 @@ <h2>
             <a class="nav" href="z_159731231e5c9c9d_canonicalag_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.5.1">coverage.py v7.5.1</a>,
-            created at 2024-05-07 09:06 +0000
+            created at 2024-05-24 09:29 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_159731231e5c9c9d_canonicalag_py.html b/coverage/z_159731231e5c9c9d_canonicalag_py.html
index 429b923d..45c3dc38 100644
--- a/coverage/z_159731231e5c9c9d_canonicalag_py.html
+++ b/coverage/z_159731231e5c9c9d_canonicalag_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_159731231e5c9c9d_puckering_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.5.1">coverage.py v7.5.1</a>,
-            created at 2024-05-07 09:06 +0000
+            created at 2024-05-24 09:29 +0000
         </p>
         <aside class="hidden">
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@@ -101,287 +101,288 @@ <h2>
     <p class="pln"><span class="n"><a id="t19" href="#t19">19</a></span><span class="t">    <span class="str">"""</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t20" href="#t20">20</a></span><span class="t"><span class="str">    | biobb_dna CanonicalAG</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t21" href="#t21">21</a></span><span class="t"><span class="str">    | Calculate Canonical Alpha/Gamma populations from alpha and gamma parameters.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t22" href="#t22">22</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t23" href="#t23">23</a></span><span class="t"><span class="str">    Args:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t24" href="#t24">24</a></span><span class="t"><span class="str">        input_alphaC_path (str): Path to .ser file for helical parameter 'alphaC'. File type: input. File type: input. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/backbone/canal_output_alphaC.ser>`_. Accepted formats: ser (edam:format_2330).</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t25" href="#t25">25</a></span><span class="t"><span class="str">        input_alphaW_path (str): Path to .ser file for helical parameter 'alphaW'. File type: input. File type: input. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/backbone/canal_output_alphaW.ser>`_. Accepted formats: ser (edam:format_2330).</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t26" href="#t26">26</a></span><span class="t"><span class="str">        input_gammaC_path (str): Path to .ser file for helical parameter 'gammaC'. File type: input. File type: input. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/backbone/canal_output_gammaC.ser>`_. Accepted formats: ser (edam:format_2330).</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t27" href="#t27">27</a></span><span class="t"><span class="str">        input_gammaW_path (str): Path to .ser file for helical parameter 'gammaW'. File type: input. File type: input. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/backbone/canal_output_gammaW.ser>`_. Accepted formats: ser (edam:format_2330).</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t28" href="#t28">28</a></span><span class="t"><span class="str">        output_csv_path (str): Path to .csv file where output is saved. File type: output. File type: output. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/reference/backbone/canonag_ref.csv>`_. Accepted formats: csv (edam:format_3752).</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t29" href="#t29">29</a></span><span class="t"><span class="str">        output_jpg_path (str): Path to .jpg file where output is saved. File type: output. File type: output. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/reference/backbone/canonag_ref.jpg>`_. Accepted formats: jpg (edam:format_3579).</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t30" href="#t30">30</a></span><span class="t"><span class="str">        properties (dict):</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t31" href="#t31">31</a></span><span class="t"><span class="str">            * **sequence** (*str*) - (None) Nucleic acid sequence corresponding to the input .ser file. Length of sequence is expected to be the same as the total number of columns in the .ser file, minus the index column (even if later on a subset of columns is selected with the *seqpos* option).</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t32" href="#t32">32</a></span><span class="t"><span class="str">            * **seqpos** (*list*) - (None) list of sequence positions (columns indices starting by 0) to analyze.  If not specified it will analyse the complete sequence.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t33" href="#t33">33</a></span><span class="t"><span class="str">            * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t34" href="#t34">34</a></span><span class="t"><span class="str">            * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t35" href="#t35">35</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t36" href="#t36">36</a></span><span class="t"><span class="str">    Examples:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t37" href="#t37">37</a></span><span class="t"><span class="str">        This is a use example of how to use the building block from Python::</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t38" href="#t38">38</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t39" href="#t39">39</a></span><span class="t"><span class="str">            from biobb_dna.backbone.canonicalag import canonicalag</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t40" href="#t40">40</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t41" href="#t41">41</a></span><span class="t"><span class="str">            prop = {</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t42" href="#t42">42</a></span><span class="t"><span class="str">                'helpar_name': 'twist',</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t43" href="#t43">43</a></span><span class="t"><span class="str">                'seqpos': [1,2],</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t44" href="#t44">44</a></span><span class="t"><span class="str">                'sequence': 'GCAT',</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t45" href="#t45">45</a></span><span class="t"><span class="str">            }</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t46" href="#t46">46</a></span><span class="t"><span class="str">            canonicalag(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t47" href="#t47">47</a></span><span class="t"><span class="str">                input_alphaC_path='/path/to/alphaC.ser',</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t48" href="#t48">48</a></span><span class="t"><span class="str">                input_alphaW_path='/path/to/alphaW.ser',</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t49" href="#t49">49</a></span><span class="t"><span class="str">                input_gammaC_path='/path/to/gammaC.ser',</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t50" href="#t50">50</a></span><span class="t"><span class="str">                input_gammaW_path='/path/to/gammaW.ser',</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t51" href="#t51">51</a></span><span class="t"><span class="str">                output_csv_path='/path/to/table/output.csv',</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t52" href="#t52">52</a></span><span class="t"><span class="str">                output_jpg_path='/path/to/table/output.jpg',</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t53" href="#t53">53</a></span><span class="t"><span class="str">                properties=prop)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t54" href="#t54">54</a></span><span class="t"><span class="str">    Info:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t55" href="#t55">55</a></span><span class="t"><span class="str">        * wrapped_software:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t56" href="#t56">56</a></span><span class="t"><span class="str">            * name: In house</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t57" href="#t57">57</a></span><span class="t"><span class="str">            * license: Apache-2.0</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t58" href="#t58">58</a></span><span class="t"><span class="str">        * ontology:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t59" href="#t59">59</a></span><span class="t"><span class="str">            * name: EDAM</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t60" href="#t60">60</a></span><span class="t"><span class="str">            * schema: http://edamontology.org/EDAM.owl</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t61" href="#t61">61</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t62" href="#t62">62</a></span><span class="t"><span class="str">    """</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t63" href="#t63">63</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t64" href="#t64">64</a></span><span class="t">    <span class="key">def</span> <span class="nam">__init__</span><span class="op">(</span><span class="nam">self</span><span class="op">,</span> <span class="nam">input_alphaC_path</span><span class="op">,</span> <span class="nam">input_alphaW_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t65" href="#t65">65</a></span><span class="t">                 <span class="nam">input_gammaC_path</span><span class="op">,</span> <span class="nam">input_gammaW_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t66" href="#t66">66</a></span><span class="t">                 <span class="nam">output_csv_path</span><span class="op">,</span> <span class="nam">output_jpg_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t67" href="#t67">67</a></span><span class="t">                 <span class="nam">properties</span><span class="op">=</span><span class="key">None</span><span class="op">,</span> <span class="op">**</span><span class="nam">kwargs</span><span class="op">)</span> <span class="op">-></span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t68" href="#t68">68</a></span><span class="t">        <span class="nam">properties</span> <span class="op">=</span> <span class="nam">properties</span> <span class="key">or</span> <span class="op">{</span><span class="op">}</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t69" href="#t69">69</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t70" href="#t70">70</a></span><span class="t">        <span class="com"># Call parent class constructor</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t71" href="#t71">71</a></span><span class="t">        <span class="nam">super</span><span class="op">(</span><span class="op">)</span><span class="op">.</span><span class="nam">__init__</span><span class="op">(</span><span class="nam">properties</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t72" href="#t72">72</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">locals_var_dict</span> <span class="op">=</span> <span class="nam">locals</span><span class="op">(</span><span class="op">)</span><span class="op">.</span><span class="nam">copy</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t73" href="#t73">73</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t74" href="#t74">74</a></span><span class="t">        <span class="com"># Input/Output files</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t75" href="#t75">75</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span> <span class="op">=</span> <span class="op">{</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t76" href="#t76">76</a></span><span class="t">            <span class="str">'in'</span><span class="op">:</span> <span class="op">{</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t77" href="#t77">77</a></span><span class="t">                <span class="str">'input_alphaC_path'</span><span class="op">:</span> <span class="nam">input_alphaC_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t78" href="#t78">78</a></span><span class="t">                <span class="str">'input_alphaW_path'</span><span class="op">:</span> <span class="nam">input_alphaW_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t79" href="#t79">79</a></span><span class="t">                <span class="str">'input_gammaC_path'</span><span class="op">:</span> <span class="nam">input_gammaC_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t80" href="#t80">80</a></span><span class="t">                <span class="str">'input_gammaW_path'</span><span class="op">:</span> <span class="nam">input_gammaW_path</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t81" href="#t81">81</a></span><span class="t">            <span class="op">}</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t82" href="#t82">82</a></span><span class="t">            <span class="str">'out'</span><span class="op">:</span> <span class="op">{</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t83" href="#t83">83</a></span><span class="t">                <span class="str">'output_csv_path'</span><span class="op">:</span> <span class="nam">output_csv_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t84" href="#t84">84</a></span><span class="t">                <span class="str">'output_jpg_path'</span><span class="op">:</span> <span class="nam">output_jpg_path</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t85" href="#t85">85</a></span><span class="t">            <span class="op">}</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t86" href="#t86">86</a></span><span class="t">        <span class="op">}</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t87" href="#t87">87</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t88" href="#t88">88</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">properties</span> <span class="op">=</span> <span class="nam">properties</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t89" href="#t89">89</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"sequence"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t90" href="#t90">90</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">stride</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t91" href="#t91">91</a></span><span class="t">            <span class="str">"stride"</span><span class="op">,</span> <span class="num">1000</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t92" href="#t92">92</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t93" href="#t93">93</a></span><span class="t">            <span class="str">"seqpos"</span><span class="op">,</span> <span class="key">None</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t94" href="#t94">94</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t95" href="#t95">95</a></span><span class="t">        <span class="com"># Check the properties</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t96" href="#t96">96</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_properties</span><span class="op">(</span><span class="nam">properties</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t97" href="#t97">97</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_arguments</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t98" href="#t98">98</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t99" href="#t99">99</a></span><span class="t">    <span class="op">@</span><span class="nam">launchlogger</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t100" href="#t100">100</a></span><span class="t">    <span class="key">def</span> <span class="nam">launch</span><span class="op">(</span><span class="nam">self</span><span class="op">)</span> <span class="op">-></span> <span class="nam">int</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t101" href="#t101">101</a></span><span class="t">        <span class="str">"""Execute the :class:`CanonicalAG &lt;backbone.canonicalag.CanonicalAG>` object."""</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t102" href="#t102">102</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t103" href="#t103">103</a></span><span class="t">        <span class="com"># Setup Biobb</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t104" href="#t104">104</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">check_restart</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t105" href="#t105">105</a></span><span class="t">            <span class="key">return</span> <span class="num">0</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t106" href="#t106">106</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">stage_files</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t107" href="#t107">107</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t108" href="#t108">108</a></span><span class="t">        <span class="com"># check sequence</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t109" href="#t109">109</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span> <span class="key">is</span> <span class="key">None</span> <span class="key">or</span> <span class="nam">len</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span><span class="op">)</span> <span class="op">&lt;</span> <span class="num">2</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t110" href="#t110">110</a></span><span class="t">            <span class="key">raise</span> <span class="nam">ValueError</span><span class="op">(</span><span class="str">"sequence is null or too short!"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t111" href="#t111">111</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t112" href="#t112">112</a></span><span class="t">        <span class="com"># check seqpos</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t113" href="#t113">113</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span> <span class="key">is</span> <span class="key">not</span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t114" href="#t114">114</a></span><span class="t">            <span class="key">if</span> <span class="op">(</span><span class="nam">max</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">)</span> <span class="op">></span> <span class="nam">len</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span><span class="op">)</span> <span class="op">-</span> <span class="num">2</span><span class="op">)</span> <span class="key">or</span> <span class="op">(</span><span class="nam">min</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">)</span> <span class="op">&lt;</span> <span class="num">1</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t115" href="#t115">115</a></span><span class="t">                <span class="key">raise</span> <span class="nam">ValueError</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t116" href="#t116">116</a></span><span class="t">                    <span class="str">f"seqpos values must be between 1 and {len(self.sequence) - 2}"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t117" href="#t117">117</a></span><span class="t">            <span class="key">if</span> <span class="key">not</span> <span class="op">(</span><span class="nam">isinstance</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">,</span> <span class="nam">list</span><span class="op">)</span> <span class="key">and</span> <span class="nam">len</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">)</span> <span class="op">></span> <span class="num">1</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t118" href="#t118">118</a></span><span class="t">                <span class="key">raise</span> <span class="nam">ValueError</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t119" href="#t119">119</a></span><span class="t">                    <span class="str">"seqpos must be a list of at least two integers"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t120" href="#t120">120</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t121" href="#t121">121</a></span><span class="t">        <span class="com"># Creating temporary folder</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t122" href="#t122">122</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span> <span class="op">=</span> <span class="nam">fu</span><span class="op">.</span><span class="nam">create_unique_dir</span><span class="op">(</span><span class="nam">prefix</span><span class="op">=</span><span class="str">"backbone_"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t123" href="#t123">123</a></span><span class="t">        <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="str">'Creating %s temporary folder'</span> <span class="op">%</span> <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t124" href="#t124">124</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t125" href="#t125">125</a></span><span class="t">        <span class="com"># Copy input_file_path1 to temporary folder</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t126" href="#t126">126</a></span><span class="t">        <span class="nam">shutil</span><span class="op">.</span><span class="nam">copy</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'input_alphaC_path'</span><span class="op">]</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t127" href="#t127">127</a></span><span class="t">        <span class="nam">shutil</span><span class="op">.</span><span class="nam">copy</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'input_alphaW_path'</span><span class="op">]</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t128" href="#t128">128</a></span><span class="t">        <span class="nam">shutil</span><span class="op">.</span><span class="nam">copy</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'input_gammaC_path'</span><span class="op">]</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t129" href="#t129">129</a></span><span class="t">        <span class="nam">shutil</span><span class="op">.</span><span class="nam">copy</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'input_gammaW_path'</span><span class="op">]</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t130" href="#t130">130</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t131" href="#t131">131</a></span><span class="t">        <span class="com"># read input files</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t132" href="#t132">132</a></span><span class="t">        <span class="nam">alphaC</span> <span class="op">=</span> <span class="nam">read_series</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t133" href="#t133">133</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'input_alphaC_path'</span><span class="op">]</span><span class="op">,</span> <span class="nam">usecols</span><span class="op">=</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t134" href="#t134">134</a></span><span class="t">        <span class="nam">alphaW</span> <span class="op">=</span> <span class="nam">read_series</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t135" href="#t135">135</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'input_alphaW_path'</span><span class="op">]</span><span class="op">,</span> <span class="nam">usecols</span><span class="op">=</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t136" href="#t136">136</a></span><span class="t">        <span class="nam">gammaC</span> <span class="op">=</span> <span class="nam">read_series</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t137" href="#t137">137</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'input_gammaC_path'</span><span class="op">]</span><span class="op">,</span> <span class="nam">usecols</span><span class="op">=</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t138" href="#t138">138</a></span><span class="t">        <span class="nam">gammaW</span> <span class="op">=</span> <span class="nam">read_series</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t139" href="#t139">139</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'input_gammaW_path'</span><span class="op">]</span><span class="op">,</span> <span class="nam">usecols</span><span class="op">=</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t140" href="#t140">140</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t141" href="#t141">141</a></span><span class="t">        <span class="com"># fix angle range so its not negative</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t142" href="#t142">142</a></span><span class="t">        <span class="nam">alphaC</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">fix_angles</span><span class="op">(</span><span class="nam">alphaC</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t143" href="#t143">143</a></span><span class="t">        <span class="nam">alphaW</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">fix_angles</span><span class="op">(</span><span class="nam">alphaW</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t144" href="#t144">144</a></span><span class="t">        <span class="nam">gammaC</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">fix_angles</span><span class="op">(</span><span class="nam">gammaC</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t145" href="#t145">145</a></span><span class="t">        <span class="nam">gammaW</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">fix_angles</span><span class="op">(</span><span class="nam">gammaW</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t146" href="#t146">146</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t147" href="#t147">147</a></span><span class="t">        <span class="com"># calculate difference between epsil and zeta parameters</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t148" href="#t148">148</a></span><span class="t">        <span class="nam">xlabels</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">get_xlabels</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t149" href="#t149">149</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t150" href="#t150">150</a></span><span class="t">            <span class="nam">inverse_complement</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t151" href="#t151">151</a></span><span class="t">        <span class="nam">canonical_populations</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">check_alpha_gamma</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t152" href="#t152">152</a></span><span class="t">            <span class="nam">alphaC</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t153" href="#t153">153</a></span><span class="t">            <span class="nam">gammaC</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t154" href="#t154">154</a></span><span class="t">            <span class="nam">alphaW</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t155" href="#t155">155</a></span><span class="t">            <span class="nam">gammaW</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t156" href="#t156">156</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t157" href="#t157">157</a></span><span class="t">        <span class="com"># save table</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t158" href="#t158">158</a></span><span class="t">        <span class="nam">canonical_populations</span><span class="op">.</span><span class="nam">name</span> <span class="op">=</span> <span class="str">"Canonical alpha/gamma"</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t159" href="#t159">159</a></span><span class="t">        <span class="nam">ag_populations_df</span> <span class="op">=</span> <span class="nam">pd</span><span class="op">.</span><span class="nam">DataFrame</span><span class="op">(</span><span class="op">{</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t160" href="#t160">160</a></span><span class="t">            <span class="str">"Nucleotide"</span><span class="op">:</span> <span class="nam">xlabels</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t161" href="#t161">161</a></span><span class="t">            <span class="str">"Canonical alpha/gamma"</span><span class="op">:</span> <span class="nam">canonical_populations</span><span class="op">}</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t162" href="#t162">162</a></span><span class="t">        <span class="nam">ag_populations_df</span><span class="op">.</span><span class="nam">to_csv</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t163" href="#t163">163</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'out'</span><span class="op">]</span><span class="op">[</span><span class="str">'output_csv_path'</span><span class="op">]</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t164" href="#t164">164</a></span><span class="t">            <span class="nam">index</span><span class="op">=</span><span class="key">False</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t165" href="#t165">165</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t166" href="#t166">166</a></span><span class="t">        <span class="com"># save plot</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t167" href="#t167">167</a></span><span class="t">        <span class="nam">fig</span><span class="op">,</span> <span class="nam">axs</span> <span class="op">=</span> <span class="nam">plt</span><span class="op">.</span><span class="nam">subplots</span><span class="op">(</span><span class="num">1</span><span class="op">,</span> <span class="num">1</span><span class="op">,</span> <span class="nam">dpi</span><span class="op">=</span><span class="num">300</span><span class="op">,</span> <span class="nam">tight_layout</span><span class="op">=</span><span class="key">True</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t168" href="#t168">168</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">bar</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t169" href="#t169">169</a></span><span class="t">            <span class="nam">range</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">xlabels</span><span class="op">)</span><span class="op">)</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t170" href="#t170">170</a></span><span class="t">            <span class="nam">canonical_populations</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t171" href="#t171">171</a></span><span class="t">            <span class="nam">label</span><span class="op">=</span><span class="str">"canonical alpha/gamma"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t172" href="#t172">172</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">bar</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t173" href="#t173">173</a></span><span class="t">            <span class="nam">range</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">xlabels</span><span class="op">)</span><span class="op">)</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t174" href="#t174">174</a></span><span class="t">            <span class="num">100</span> <span class="op">-</span> <span class="nam">canonical_populations</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t175" href="#t175">175</a></span><span class="t">            <span class="nam">bottom</span><span class="op">=</span><span class="nam">canonical_populations</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t176" href="#t176">176</a></span><span class="t">            <span class="nam">label</span><span class="op">=</span><span class="key">None</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t177" href="#t177">177</a></span><span class="t">        <span class="com"># empty bar to divide both sequences</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t178" href="#t178">178</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">bar</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t179" href="#t179">179</a></span><span class="t">            <span class="op">[</span><span class="nam">len</span><span class="op">(</span><span class="nam">alphaC</span><span class="op">.</span><span class="nam">columns</span><span class="op">)</span><span class="op">]</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t180" href="#t180">180</a></span><span class="t">            <span class="op">[</span><span class="num">100</span><span class="op">]</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t181" href="#t181">181</a></span><span class="t">            <span class="nam">color</span><span class="op">=</span><span class="str">'white'</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t182" href="#t182">182</a></span><span class="t">            <span class="nam">label</span><span class="op">=</span><span class="key">None</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t183" href="#t183">183</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">legend</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t184" href="#t184">184</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_xticks</span><span class="op">(</span><span class="nam">range</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">xlabels</span><span class="op">)</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t185" href="#t185">185</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_xticklabels</span><span class="op">(</span><span class="nam">xlabels</span><span class="op">,</span> <span class="nam">rotation</span><span class="op">=</span><span class="num">90</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t186" href="#t186">186</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_xlabel</span><span class="op">(</span><span class="str">"Nucleotide Sequence"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t187" href="#t187">187</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_ylabel</span><span class="op">(</span><span class="str">"Canonical Alpha-Gamma (%)"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t188" href="#t188">188</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_title</span><span class="op">(</span><span class="str">"Nucleotide parameter: Canonical Alpha-Gamma"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t189" href="#t189">189</a></span><span class="t">        <span class="nam">fig</span><span class="op">.</span><span class="nam">savefig</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t190" href="#t190">190</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'out'</span><span class="op">]</span><span class="op">[</span><span class="str">'output_jpg_path'</span><span class="op">]</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t191" href="#t191">191</a></span><span class="t">            <span class="nam">format</span><span class="op">=</span><span class="str">"jpg"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t192" href="#t192">192</a></span><span class="t">        <span class="nam">plt</span><span class="op">.</span><span class="nam">close</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t193" href="#t193">193</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t194" href="#t194">194</a></span><span class="t">        <span class="com"># Remove temporary file(s)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t195" href="#t195">195</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_files</span><span class="op">.</span><span class="nam">extend</span><span class="op">(</span><span class="op">[</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t196" href="#t196">196</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"unique_dir"</span><span class="op">)</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t197" href="#t197">197</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t198" href="#t198">198</a></span><span class="t">        <span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t199" href="#t199">199</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">remove_tmp_files</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t200" href="#t200">200</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t201" href="#t201">201</a></span><span class="t">        <span class="key">return</span> <span class="num">0</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t202" href="#t202">202</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t203" href="#t203">203</a></span><span class="t">    <span class="key">def</span> <span class="nam">get_xlabels</span><span class="op">(</span><span class="nam">self</span><span class="op">,</span> <span class="nam">strand1</span><span class="op">,</span> <span class="nam">strand2</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t204" href="#t204">204</a></span><span class="t">        <span class="com"># get list of tetramers, except first and last two bases</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t205" href="#t205">205</a></span><span class="t">        <span class="nam">labelsW</span> <span class="op">=</span> <span class="nam">list</span><span class="op">(</span><span class="nam">strand1</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t206" href="#t206">206</a></span><span class="t">        <span class="nam">labelsW</span><span class="op">[</span><span class="num">0</span><span class="op">]</span> <span class="op">=</span> <span class="str">f"{labelsW[0]}5\'"</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t207" href="#t207">207</a></span><span class="t">        <span class="nam">labelsW</span><span class="op">[</span><span class="op">-</span><span class="num">1</span><span class="op">]</span> <span class="op">=</span> <span class="str">f"{labelsW[-1]}3\'"</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t208" href="#t208">208</a></span><span class="t">        <span class="nam">labelsW</span> <span class="op">=</span> <span class="op">[</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t209" href="#t209">209</a></span><span class="t">            <span class="str">f"{i}-{j}"</span> <span class="key">for</span> <span class="nam">i</span><span class="op">,</span> <span class="nam">j</span> <span class="key">in</span> <span class="nam">zip</span><span class="op">(</span><span class="nam">labelsW</span><span class="op">,</span> <span class="nam">range</span><span class="op">(</span><span class="num">1</span><span class="op">,</span> <span class="nam">len</span><span class="op">(</span><span class="nam">labelsW</span><span class="op">)</span><span class="op">+</span><span class="num">1</span><span class="op">)</span><span class="op">)</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t210" href="#t210">210</a></span><span class="t">        <span class="nam">labelsC</span> <span class="op">=</span> <span class="nam">list</span><span class="op">(</span><span class="nam">strand2</span><span class="op">)</span><span class="op">[</span><span class="op">:</span><span class="op">:</span><span class="op">-</span><span class="num">1</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t211" href="#t211">211</a></span><span class="t">        <span class="nam">labelsC</span><span class="op">[</span><span class="num">0</span><span class="op">]</span> <span class="op">=</span> <span class="str">f"{labelsC[0]}5\'"</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t212" href="#t212">212</a></span><span class="t">        <span class="nam">labelsC</span><span class="op">[</span><span class="op">-</span><span class="num">1</span><span class="op">]</span> <span class="op">=</span> <span class="str">f"{labelsC[-1]}3\'"</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t213" href="#t213">213</a></span><span class="t">        <span class="nam">labelsC</span> <span class="op">=</span> <span class="op">[</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t214" href="#t214">214</a></span><span class="t">            <span class="str">f"{i}-{j}"</span> <span class="key">for</span> <span class="nam">i</span><span class="op">,</span> <span class="nam">j</span> <span class="key">in</span> <span class="nam">zip</span><span class="op">(</span><span class="nam">labelsC</span><span class="op">,</span> <span class="nam">range</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">labelsC</span><span class="op">)</span><span class="op">,</span> <span class="num">0</span><span class="op">,</span> <span class="op">-</span><span class="num">1</span><span class="op">)</span><span class="op">)</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t215" href="#t215">215</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t216" href="#t216">216</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span> <span class="key">is</span> <span class="key">not</span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t217" href="#t217">217</a></span><span class="t">            <span class="nam">labelsC</span> <span class="op">=</span> <span class="op">[</span><span class="nam">labelsC</span><span class="op">[</span><span class="nam">i</span><span class="op">]</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t218" href="#t218">218</a></span><span class="t">            <span class="nam">labelsW</span> <span class="op">=</span> <span class="op">[</span><span class="nam">labelsW</span><span class="op">[</span><span class="nam">i</span><span class="op">]</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t219" href="#t219">219</a></span><span class="t">        <span class="nam">xlabels</span> <span class="op">=</span> <span class="nam">labelsW</span> <span class="op">+</span> <span class="op">[</span><span class="str">'-'</span><span class="op">]</span> <span class="op">+</span> <span class="nam">labelsC</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t220" href="#t220">220</a></span><span class="t">        <span class="key">return</span> <span class="nam">xlabels</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t221" href="#t221">221</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t222" href="#t222">222</a></span><span class="t">    <span class="key">def</span> <span class="nam">check_alpha_gamma</span><span class="op">(</span><span class="nam">self</span><span class="op">,</span> <span class="nam">alphaC</span><span class="op">,</span> <span class="nam">gammaC</span><span class="op">,</span> <span class="nam">alphaW</span><span class="op">,</span> <span class="nam">gammaW</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t223" href="#t223">223</a></span><span class="t">        <span class="nam">separator_df</span> <span class="op">=</span> <span class="nam">pd</span><span class="op">.</span><span class="nam">DataFrame</span><span class="op">(</span><span class="op">{</span><span class="str">"-"</span><span class="op">:</span> <span class="nam">np</span><span class="op">.</span><span class="nam">nan</span><span class="op">}</span><span class="op">,</span> <span class="nam">index</span><span class="op">=</span><span class="nam">range</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">gammaW</span><span class="op">)</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t224" href="#t224">224</a></span><span class="t">        <span class="nam">gamma</span> <span class="op">=</span> <span class="nam">pd</span><span class="op">.</span><span class="nam">concat</span><span class="op">(</span><span class="op">[</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t225" href="#t225">225</a></span><span class="t">            <span class="nam">gammaW</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t226" href="#t226">226</a></span><span class="t">            <span class="nam">separator_df</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t227" href="#t227">227</a></span><span class="t">            <span class="nam">gammaC</span><span class="op">[</span><span class="nam">gammaC</span><span class="op">.</span><span class="nam">columns</span><span class="op">[</span><span class="op">:</span><span class="op">:</span><span class="op">-</span><span class="num">1</span><span class="op">]</span><span class="op">]</span><span class="op">]</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t228" href="#t228">228</a></span><span class="t">            <span class="nam">axis</span><span class="op">=</span><span class="num">1</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t229" href="#t229">229</a></span><span class="t">        <span class="nam">alpha</span> <span class="op">=</span> <span class="nam">pd</span><span class="op">.</span><span class="nam">concat</span><span class="op">(</span><span class="op">[</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t230" href="#t230">230</a></span><span class="t">            <span class="nam">alphaW</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t231" href="#t231">231</a></span><span class="t">            <span class="nam">separator_df</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t232" href="#t232">232</a></span><span class="t">            <span class="nam">alphaC</span><span class="op">[</span><span class="nam">alphaC</span><span class="op">.</span><span class="nam">columns</span><span class="op">[</span><span class="op">:</span><span class="op">:</span><span class="op">-</span><span class="num">1</span><span class="op">]</span><span class="op">]</span><span class="op">]</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t233" href="#t233">233</a></span><span class="t">            <span class="nam">axis</span><span class="op">=</span><span class="num">1</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t234" href="#t234">234</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t235" href="#t235">235</a></span><span class="t">        <span class="nam">alpha_filter</span> <span class="op">=</span> <span class="nam">np</span><span class="op">.</span><span class="nam">logical_and</span><span class="op">(</span><span class="nam">alpha</span> <span class="op">></span> <span class="num">240</span><span class="op">,</span> <span class="nam">alpha</span> <span class="op">&lt;</span> <span class="num">360</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t236" href="#t236">236</a></span><span class="t">        <span class="nam">gamma_filter</span> <span class="op">=</span> <span class="nam">np</span><span class="op">.</span><span class="nam">logical_and</span><span class="op">(</span><span class="nam">gamma</span> <span class="op">></span> <span class="num">0</span><span class="op">,</span> <span class="nam">gamma</span> <span class="op">&lt;</span> <span class="num">120</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t237" href="#t237">237</a></span><span class="t">        <span class="nam">canonical_alpha_gamma</span> <span class="op">=</span> <span class="nam">np</span><span class="op">.</span><span class="nam">logical_and</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t238" href="#t238">238</a></span><span class="t">            <span class="nam">alpha_filter</span><span class="op">,</span> <span class="nam">gamma_filter</span><span class="op">)</span><span class="op">.</span><span class="nam">mean</span><span class="op">(</span><span class="op">)</span> <span class="op">*</span> <span class="num">100</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t239" href="#t239">239</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t240" href="#t240">240</a></span><span class="t">        <span class="key">return</span> <span class="nam">canonical_alpha_gamma</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t241" href="#t241">241</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t242" href="#t242">242</a></span><span class="t">    <span class="key">def</span> <span class="nam">fix_angles</span><span class="op">(</span><span class="nam">self</span><span class="op">,</span> <span class="nam">dataset</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t243" href="#t243">243</a></span><span class="t">        <span class="nam">values</span> <span class="op">=</span> <span class="nam">np</span><span class="op">.</span><span class="nam">where</span><span class="op">(</span><span class="nam">dataset</span> <span class="op">&lt;</span> <span class="num">0</span><span class="op">,</span> <span class="nam">dataset</span> <span class="op">+</span> <span class="num">360</span><span class="op">,</span> <span class="nam">dataset</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t244" href="#t244">244</a></span><span class="t">        <span class="nam">values</span> <span class="op">=</span> <span class="nam">np</span><span class="op">.</span><span class="nam">where</span><span class="op">(</span><span class="nam">values</span> <span class="op">></span> <span class="num">360</span><span class="op">,</span> <span class="nam">values</span> <span class="op">-</span> <span class="num">360</span><span class="op">,</span> <span class="nam">values</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t245" href="#t245">245</a></span><span class="t">        <span class="nam">dataset</span> <span class="op">=</span> <span class="nam">pd</span><span class="op">.</span><span class="nam">DataFrame</span><span class="op">(</span><span class="nam">values</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t246" href="#t246">246</a></span><span class="t">        <span class="key">return</span> <span class="nam">dataset</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t247" href="#t247">247</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t22" href="#t22">22</a></span><span class="t"><span class="str">    | Calculate Canonical Alpha/Gamma populations from alpha and gamma parameters.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t23" href="#t23">23</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t24" href="#t24">24</a></span><span class="t"><span class="str">    Args:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t25" href="#t25">25</a></span><span class="t"><span class="str">        input_alphaC_path (str): Path to .ser file for helical parameter 'alphaC'. File type: input. File type: input. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/backbone/canal_output_alphaC.ser>`_. Accepted formats: ser (edam:format_2330).</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t26" href="#t26">26</a></span><span class="t"><span class="str">        input_alphaW_path (str): Path to .ser file for helical parameter 'alphaW'. File type: input. File type: input. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/backbone/canal_output_alphaW.ser>`_. Accepted formats: ser (edam:format_2330).</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t27" href="#t27">27</a></span><span class="t"><span class="str">        input_gammaC_path (str): Path to .ser file for helical parameter 'gammaC'. File type: input. File type: input. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/backbone/canal_output_gammaC.ser>`_. Accepted formats: ser (edam:format_2330).</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t28" href="#t28">28</a></span><span class="t"><span class="str">        input_gammaW_path (str): Path to .ser file for helical parameter 'gammaW'. File type: input. File type: input. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/backbone/canal_output_gammaW.ser>`_. Accepted formats: ser (edam:format_2330).</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t29" href="#t29">29</a></span><span class="t"><span class="str">        output_csv_path (str): Path to .csv file where output is saved. File type: output. File type: output. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/reference/backbone/canonag_ref.csv>`_. Accepted formats: csv (edam:format_3752).</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t30" href="#t30">30</a></span><span class="t"><span class="str">        output_jpg_path (str): Path to .jpg file where output is saved. File type: output. File type: output. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/reference/backbone/canonag_ref.jpg>`_. Accepted formats: jpg (edam:format_3579).</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t31" href="#t31">31</a></span><span class="t"><span class="str">        properties (dict):</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t32" href="#t32">32</a></span><span class="t"><span class="str">            * **sequence** (*str*) - (None) Nucleic acid sequence corresponding to the input .ser file. Length of sequence is expected to be the same as the total number of columns in the .ser file, minus the index column (even if later on a subset of columns is selected with the *seqpos* option).</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t33" href="#t33">33</a></span><span class="t"><span class="str">            * **seqpos** (*list*) - (None) list of sequence positions (columns indices starting by 0) to analyze.  If not specified it will analyse the complete sequence.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t34" href="#t34">34</a></span><span class="t"><span class="str">            * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t35" href="#t35">35</a></span><span class="t"><span class="str">            * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t36" href="#t36">36</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t37" href="#t37">37</a></span><span class="t"><span class="str">    Examples:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t38" href="#t38">38</a></span><span class="t"><span class="str">        This is a use example of how to use the building block from Python::</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t39" href="#t39">39</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t40" href="#t40">40</a></span><span class="t"><span class="str">            from biobb_dna.backbone.canonicalag import canonicalag</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t41" href="#t41">41</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t42" href="#t42">42</a></span><span class="t"><span class="str">            prop = {</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t43" href="#t43">43</a></span><span class="t"><span class="str">                'helpar_name': 'twist',</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t44" href="#t44">44</a></span><span class="t"><span class="str">                'seqpos': [1,2],</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t45" href="#t45">45</a></span><span class="t"><span class="str">                'sequence': 'GCAT',</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t46" href="#t46">46</a></span><span class="t"><span class="str">            }</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t47" href="#t47">47</a></span><span class="t"><span class="str">            canonicalag(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t48" href="#t48">48</a></span><span class="t"><span class="str">                input_alphaC_path='/path/to/alphaC.ser',</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t49" href="#t49">49</a></span><span class="t"><span class="str">                input_alphaW_path='/path/to/alphaW.ser',</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t50" href="#t50">50</a></span><span class="t"><span class="str">                input_gammaC_path='/path/to/gammaC.ser',</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t51" href="#t51">51</a></span><span class="t"><span class="str">                input_gammaW_path='/path/to/gammaW.ser',</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t52" href="#t52">52</a></span><span class="t"><span class="str">                output_csv_path='/path/to/table/output.csv',</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t53" href="#t53">53</a></span><span class="t"><span class="str">                output_jpg_path='/path/to/table/output.jpg',</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t54" href="#t54">54</a></span><span class="t"><span class="str">                properties=prop)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t55" href="#t55">55</a></span><span class="t"><span class="str">    Info:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t56" href="#t56">56</a></span><span class="t"><span class="str">        * wrapped_software:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t57" href="#t57">57</a></span><span class="t"><span class="str">            * name: In house</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t58" href="#t58">58</a></span><span class="t"><span class="str">            * license: Apache-2.0</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t59" href="#t59">59</a></span><span class="t"><span class="str">        * ontology:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t60" href="#t60">60</a></span><span class="t"><span class="str">            * name: EDAM</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t61" href="#t61">61</a></span><span class="t"><span class="str">            * schema: http://edamontology.org/EDAM.owl</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t62" href="#t62">62</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t63" href="#t63">63</a></span><span class="t"><span class="str">    """</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t64" href="#t64">64</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t65" href="#t65">65</a></span><span class="t">    <span class="key">def</span> <span class="nam">__init__</span><span class="op">(</span><span class="nam">self</span><span class="op">,</span> <span class="nam">input_alphaC_path</span><span class="op">,</span> <span class="nam">input_alphaW_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t66" href="#t66">66</a></span><span class="t">                 <span class="nam">input_gammaC_path</span><span class="op">,</span> <span class="nam">input_gammaW_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t67" href="#t67">67</a></span><span class="t">                 <span class="nam">output_csv_path</span><span class="op">,</span> <span class="nam">output_jpg_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t68" href="#t68">68</a></span><span class="t">                 <span class="nam">properties</span><span class="op">=</span><span class="key">None</span><span class="op">,</span> <span class="op">**</span><span class="nam">kwargs</span><span class="op">)</span> <span class="op">-></span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t69" href="#t69">69</a></span><span class="t">        <span class="nam">properties</span> <span class="op">=</span> <span class="nam">properties</span> <span class="key">or</span> <span class="op">{</span><span class="op">}</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t70" href="#t70">70</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t71" href="#t71">71</a></span><span class="t">        <span class="com"># Call parent class constructor</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t72" href="#t72">72</a></span><span class="t">        <span class="nam">super</span><span class="op">(</span><span class="op">)</span><span class="op">.</span><span class="nam">__init__</span><span class="op">(</span><span class="nam">properties</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t73" href="#t73">73</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">locals_var_dict</span> <span class="op">=</span> <span class="nam">locals</span><span class="op">(</span><span class="op">)</span><span class="op">.</span><span class="nam">copy</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t74" href="#t74">74</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t75" href="#t75">75</a></span><span class="t">        <span class="com"># Input/Output files</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t76" href="#t76">76</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span> <span class="op">=</span> <span class="op">{</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t77" href="#t77">77</a></span><span class="t">            <span class="str">'in'</span><span class="op">:</span> <span class="op">{</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t78" href="#t78">78</a></span><span class="t">                <span class="str">'input_alphaC_path'</span><span class="op">:</span> <span class="nam">input_alphaC_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t79" href="#t79">79</a></span><span class="t">                <span class="str">'input_alphaW_path'</span><span class="op">:</span> <span class="nam">input_alphaW_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t80" href="#t80">80</a></span><span class="t">                <span class="str">'input_gammaC_path'</span><span class="op">:</span> <span class="nam">input_gammaC_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t81" href="#t81">81</a></span><span class="t">                <span class="str">'input_gammaW_path'</span><span class="op">:</span> <span class="nam">input_gammaW_path</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t82" href="#t82">82</a></span><span class="t">            <span class="op">}</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t83" href="#t83">83</a></span><span class="t">            <span class="str">'out'</span><span class="op">:</span> <span class="op">{</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t84" href="#t84">84</a></span><span class="t">                <span class="str">'output_csv_path'</span><span class="op">:</span> <span class="nam">output_csv_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t85" href="#t85">85</a></span><span class="t">                <span class="str">'output_jpg_path'</span><span class="op">:</span> <span class="nam">output_jpg_path</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t86" href="#t86">86</a></span><span class="t">            <span class="op">}</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t87" href="#t87">87</a></span><span class="t">        <span class="op">}</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t88" href="#t88">88</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t89" href="#t89">89</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">properties</span> <span class="op">=</span> <span class="nam">properties</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t90" href="#t90">90</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"sequence"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t91" href="#t91">91</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">stride</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t92" href="#t92">92</a></span><span class="t">            <span class="str">"stride"</span><span class="op">,</span> <span class="num">1000</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t93" href="#t93">93</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t94" href="#t94">94</a></span><span class="t">            <span class="str">"seqpos"</span><span class="op">,</span> <span class="key">None</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t95" href="#t95">95</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t96" href="#t96">96</a></span><span class="t">        <span class="com"># Check the properties</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t97" href="#t97">97</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_properties</span><span class="op">(</span><span class="nam">properties</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t98" href="#t98">98</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_arguments</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t99" href="#t99">99</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t100" href="#t100">100</a></span><span class="t">    <span class="op">@</span><span class="nam">launchlogger</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t101" href="#t101">101</a></span><span class="t">    <span class="key">def</span> <span class="nam">launch</span><span class="op">(</span><span class="nam">self</span><span class="op">)</span> <span class="op">-></span> <span class="nam">int</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t102" href="#t102">102</a></span><span class="t">        <span class="str">"""Execute the :class:`CanonicalAG &lt;backbone.canonicalag.CanonicalAG>` object."""</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t103" href="#t103">103</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t104" href="#t104">104</a></span><span class="t">        <span class="com"># Setup Biobb</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t105" href="#t105">105</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">check_restart</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t106" href="#t106">106</a></span><span class="t">            <span class="key">return</span> <span class="num">0</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t107" href="#t107">107</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">stage_files</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t108" href="#t108">108</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t109" href="#t109">109</a></span><span class="t">        <span class="com"># check sequence</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t110" href="#t110">110</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span> <span class="key">is</span> <span class="key">None</span> <span class="key">or</span> <span class="nam">len</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span><span class="op">)</span> <span class="op">&lt;</span> <span class="num">2</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t111" href="#t111">111</a></span><span class="t">            <span class="key">raise</span> <span class="nam">ValueError</span><span class="op">(</span><span class="str">"sequence is null or too short!"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t112" href="#t112">112</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t113" href="#t113">113</a></span><span class="t">        <span class="com"># check seqpos</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t114" href="#t114">114</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span> <span class="key">is</span> <span class="key">not</span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t115" href="#t115">115</a></span><span class="t">            <span class="key">if</span> <span class="op">(</span><span class="nam">max</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">)</span> <span class="op">></span> <span class="nam">len</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span><span class="op">)</span> <span class="op">-</span> <span class="num">2</span><span class="op">)</span> <span class="key">or</span> <span class="op">(</span><span class="nam">min</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">)</span> <span class="op">&lt;</span> <span class="num">1</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t116" href="#t116">116</a></span><span class="t">                <span class="key">raise</span> <span class="nam">ValueError</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t117" href="#t117">117</a></span><span class="t">                    <span class="str">f"seqpos values must be between 1 and {len(self.sequence) - 2}"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t118" href="#t118">118</a></span><span class="t">            <span class="key">if</span> <span class="key">not</span> <span class="op">(</span><span class="nam">isinstance</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">,</span> <span class="nam">list</span><span class="op">)</span> <span class="key">and</span> <span class="nam">len</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">)</span> <span class="op">></span> <span class="num">1</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t119" href="#t119">119</a></span><span class="t">                <span class="key">raise</span> <span class="nam">ValueError</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t120" href="#t120">120</a></span><span class="t">                    <span class="str">"seqpos must be a list of at least two integers"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t121" href="#t121">121</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t122" href="#t122">122</a></span><span class="t">        <span class="com"># Creating temporary folder</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t123" href="#t123">123</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span> <span class="op">=</span> <span class="nam">fu</span><span class="op">.</span><span class="nam">create_unique_dir</span><span class="op">(</span><span class="nam">prefix</span><span class="op">=</span><span class="str">"backbone_"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t124" href="#t124">124</a></span><span class="t">        <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="str">'Creating %s temporary folder'</span> <span class="op">%</span> <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t125" href="#t125">125</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t126" href="#t126">126</a></span><span class="t">        <span class="com"># Copy input_file_path1 to temporary folder</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t127" href="#t127">127</a></span><span class="t">        <span class="nam">shutil</span><span class="op">.</span><span class="nam">copy</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'input_alphaC_path'</span><span class="op">]</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t128" href="#t128">128</a></span><span class="t">        <span class="nam">shutil</span><span class="op">.</span><span class="nam">copy</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'input_alphaW_path'</span><span class="op">]</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t129" href="#t129">129</a></span><span class="t">        <span class="nam">shutil</span><span class="op">.</span><span class="nam">copy</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'input_gammaC_path'</span><span class="op">]</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t130" href="#t130">130</a></span><span class="t">        <span class="nam">shutil</span><span class="op">.</span><span class="nam">copy</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'input_gammaW_path'</span><span class="op">]</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t131" href="#t131">131</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t132" href="#t132">132</a></span><span class="t">        <span class="com"># read input files</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t133" href="#t133">133</a></span><span class="t">        <span class="nam">alphaC</span> <span class="op">=</span> <span class="nam">read_series</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t134" href="#t134">134</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'input_alphaC_path'</span><span class="op">]</span><span class="op">,</span> <span class="nam">usecols</span><span class="op">=</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t135" href="#t135">135</a></span><span class="t">        <span class="nam">alphaW</span> <span class="op">=</span> <span class="nam">read_series</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t136" href="#t136">136</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'input_alphaW_path'</span><span class="op">]</span><span class="op">,</span> <span class="nam">usecols</span><span class="op">=</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t137" href="#t137">137</a></span><span class="t">        <span class="nam">gammaC</span> <span class="op">=</span> <span class="nam">read_series</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t138" href="#t138">138</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'input_gammaC_path'</span><span class="op">]</span><span class="op">,</span> <span class="nam">usecols</span><span class="op">=</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t139" href="#t139">139</a></span><span class="t">        <span class="nam">gammaW</span> <span class="op">=</span> <span class="nam">read_series</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t140" href="#t140">140</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'input_gammaW_path'</span><span class="op">]</span><span class="op">,</span> <span class="nam">usecols</span><span class="op">=</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t141" href="#t141">141</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t142" href="#t142">142</a></span><span class="t">        <span class="com"># fix angle range so its not negative</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t143" href="#t143">143</a></span><span class="t">        <span class="nam">alphaC</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">fix_angles</span><span class="op">(</span><span class="nam">alphaC</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t144" href="#t144">144</a></span><span class="t">        <span class="nam">alphaW</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">fix_angles</span><span class="op">(</span><span class="nam">alphaW</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t145" href="#t145">145</a></span><span class="t">        <span class="nam">gammaC</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">fix_angles</span><span class="op">(</span><span class="nam">gammaC</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t146" href="#t146">146</a></span><span class="t">        <span class="nam">gammaW</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">fix_angles</span><span class="op">(</span><span class="nam">gammaW</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t147" href="#t147">147</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t148" href="#t148">148</a></span><span class="t">        <span class="com"># calculate difference between epsil and zeta parameters</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t149" href="#t149">149</a></span><span class="t">        <span class="nam">xlabels</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">get_xlabels</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t150" href="#t150">150</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t151" href="#t151">151</a></span><span class="t">            <span class="nam">inverse_complement</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t152" href="#t152">152</a></span><span class="t">        <span class="nam">canonical_populations</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">check_alpha_gamma</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t153" href="#t153">153</a></span><span class="t">            <span class="nam">alphaC</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t154" href="#t154">154</a></span><span class="t">            <span class="nam">gammaC</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t155" href="#t155">155</a></span><span class="t">            <span class="nam">alphaW</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t156" href="#t156">156</a></span><span class="t">            <span class="nam">gammaW</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t157" href="#t157">157</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t158" href="#t158">158</a></span><span class="t">        <span class="com"># save table</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t159" href="#t159">159</a></span><span class="t">        <span class="nam">canonical_populations</span><span class="op">.</span><span class="nam">name</span> <span class="op">=</span> <span class="str">"Canonical alpha/gamma"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t160" href="#t160">160</a></span><span class="t">        <span class="nam">ag_populations_df</span> <span class="op">=</span> <span class="nam">pd</span><span class="op">.</span><span class="nam">DataFrame</span><span class="op">(</span><span class="op">{</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t161" href="#t161">161</a></span><span class="t">            <span class="str">"Nucleotide"</span><span class="op">:</span> <span class="nam">xlabels</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t162" href="#t162">162</a></span><span class="t">            <span class="str">"Canonical alpha/gamma"</span><span class="op">:</span> <span class="nam">canonical_populations</span><span class="op">}</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t163" href="#t163">163</a></span><span class="t">        <span class="nam">ag_populations_df</span><span class="op">.</span><span class="nam">to_csv</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t164" href="#t164">164</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'out'</span><span class="op">]</span><span class="op">[</span><span class="str">'output_csv_path'</span><span class="op">]</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t165" href="#t165">165</a></span><span class="t">            <span class="nam">index</span><span class="op">=</span><span class="key">False</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t166" href="#t166">166</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t167" href="#t167">167</a></span><span class="t">        <span class="com"># save plot</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t168" href="#t168">168</a></span><span class="t">        <span class="nam">fig</span><span class="op">,</span> <span class="nam">axs</span> <span class="op">=</span> <span class="nam">plt</span><span class="op">.</span><span class="nam">subplots</span><span class="op">(</span><span class="num">1</span><span class="op">,</span> <span class="num">1</span><span class="op">,</span> <span class="nam">dpi</span><span class="op">=</span><span class="num">300</span><span class="op">,</span> <span class="nam">tight_layout</span><span class="op">=</span><span class="key">True</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t169" href="#t169">169</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">bar</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t170" href="#t170">170</a></span><span class="t">            <span class="nam">range</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">xlabels</span><span class="op">)</span><span class="op">)</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t171" href="#t171">171</a></span><span class="t">            <span class="nam">canonical_populations</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t172" href="#t172">172</a></span><span class="t">            <span class="nam">label</span><span class="op">=</span><span class="str">"canonical alpha/gamma"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t173" href="#t173">173</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">bar</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t174" href="#t174">174</a></span><span class="t">            <span class="nam">range</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">xlabels</span><span class="op">)</span><span class="op">)</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t175" href="#t175">175</a></span><span class="t">            <span class="num">100</span> <span class="op">-</span> <span class="nam">canonical_populations</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t176" href="#t176">176</a></span><span class="t">            <span class="nam">bottom</span><span class="op">=</span><span class="nam">canonical_populations</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t177" href="#t177">177</a></span><span class="t">            <span class="nam">label</span><span class="op">=</span><span class="key">None</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t178" href="#t178">178</a></span><span class="t">        <span class="com"># empty bar to divide both sequences</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t179" href="#t179">179</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">bar</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t180" href="#t180">180</a></span><span class="t">            <span class="op">[</span><span class="nam">len</span><span class="op">(</span><span class="nam">alphaC</span><span class="op">.</span><span class="nam">columns</span><span class="op">)</span><span class="op">]</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t181" href="#t181">181</a></span><span class="t">            <span class="op">[</span><span class="num">100</span><span class="op">]</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t182" href="#t182">182</a></span><span class="t">            <span class="nam">color</span><span class="op">=</span><span class="str">'white'</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t183" href="#t183">183</a></span><span class="t">            <span class="nam">label</span><span class="op">=</span><span class="key">None</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t184" href="#t184">184</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">legend</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t185" href="#t185">185</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_xticks</span><span class="op">(</span><span class="nam">range</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">xlabels</span><span class="op">)</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t186" href="#t186">186</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_xticklabels</span><span class="op">(</span><span class="nam">xlabels</span><span class="op">,</span> <span class="nam">rotation</span><span class="op">=</span><span class="num">90</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t187" href="#t187">187</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_xlabel</span><span class="op">(</span><span class="str">"Nucleotide Sequence"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t188" href="#t188">188</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_ylabel</span><span class="op">(</span><span class="str">"Canonical Alpha-Gamma (%)"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t189" href="#t189">189</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_title</span><span class="op">(</span><span class="str">"Nucleotide parameter: Canonical Alpha-Gamma"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t190" href="#t190">190</a></span><span class="t">        <span class="nam">fig</span><span class="op">.</span><span class="nam">savefig</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t191" href="#t191">191</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'out'</span><span class="op">]</span><span class="op">[</span><span class="str">'output_jpg_path'</span><span class="op">]</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t192" href="#t192">192</a></span><span class="t">            <span class="nam">format</span><span class="op">=</span><span class="str">"jpg"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t193" href="#t193">193</a></span><span class="t">        <span class="nam">plt</span><span class="op">.</span><span class="nam">close</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t194" href="#t194">194</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t195" href="#t195">195</a></span><span class="t">        <span class="com"># Remove temporary file(s)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t196" href="#t196">196</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_files</span><span class="op">.</span><span class="nam">extend</span><span class="op">(</span><span class="op">[</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t197" href="#t197">197</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"unique_dir"</span><span class="op">)</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t198" href="#t198">198</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t199" href="#t199">199</a></span><span class="t">        <span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t200" href="#t200">200</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">remove_tmp_files</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t201" href="#t201">201</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t202" href="#t202">202</a></span><span class="t">        <span class="key">return</span> <span class="num">0</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t203" href="#t203">203</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t204" href="#t204">204</a></span><span class="t">    <span class="key">def</span> <span class="nam">get_xlabels</span><span class="op">(</span><span class="nam">self</span><span class="op">,</span> <span class="nam">strand1</span><span class="op">,</span> <span class="nam">strand2</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t205" href="#t205">205</a></span><span class="t">        <span class="com"># get list of tetramers, except first and last two bases</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t206" href="#t206">206</a></span><span class="t">        <span class="nam">labelsW</span> <span class="op">=</span> <span class="nam">list</span><span class="op">(</span><span class="nam">strand1</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t207" href="#t207">207</a></span><span class="t">        <span class="nam">labelsW</span><span class="op">[</span><span class="num">0</span><span class="op">]</span> <span class="op">=</span> <span class="str">f"{labelsW[0]}5\'"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t208" href="#t208">208</a></span><span class="t">        <span class="nam">labelsW</span><span class="op">[</span><span class="op">-</span><span class="num">1</span><span class="op">]</span> <span class="op">=</span> <span class="str">f"{labelsW[-1]}3\'"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t209" href="#t209">209</a></span><span class="t">        <span class="nam">labelsW</span> <span class="op">=</span> <span class="op">[</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t210" href="#t210">210</a></span><span class="t">            <span class="str">f"{i}-{j}"</span> <span class="key">for</span> <span class="nam">i</span><span class="op">,</span> <span class="nam">j</span> <span class="key">in</span> <span class="nam">zip</span><span class="op">(</span><span class="nam">labelsW</span><span class="op">,</span> <span class="nam">range</span><span class="op">(</span><span class="num">1</span><span class="op">,</span> <span class="nam">len</span><span class="op">(</span><span class="nam">labelsW</span><span class="op">)</span><span class="op">+</span><span class="num">1</span><span class="op">)</span><span class="op">)</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t211" href="#t211">211</a></span><span class="t">        <span class="nam">labelsC</span> <span class="op">=</span> <span class="nam">list</span><span class="op">(</span><span class="nam">strand2</span><span class="op">)</span><span class="op">[</span><span class="op">:</span><span class="op">:</span><span class="op">-</span><span class="num">1</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t212" href="#t212">212</a></span><span class="t">        <span class="nam">labelsC</span><span class="op">[</span><span class="num">0</span><span class="op">]</span> <span class="op">=</span> <span class="str">f"{labelsC[0]}5\'"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t213" href="#t213">213</a></span><span class="t">        <span class="nam">labelsC</span><span class="op">[</span><span class="op">-</span><span class="num">1</span><span class="op">]</span> <span class="op">=</span> <span class="str">f"{labelsC[-1]}3\'"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t214" href="#t214">214</a></span><span class="t">        <span class="nam">labelsC</span> <span class="op">=</span> <span class="op">[</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t215" href="#t215">215</a></span><span class="t">            <span class="str">f"{i}-{j}"</span> <span class="key">for</span> <span class="nam">i</span><span class="op">,</span> <span class="nam">j</span> <span class="key">in</span> <span class="nam">zip</span><span class="op">(</span><span class="nam">labelsC</span><span class="op">,</span> <span class="nam">range</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">labelsC</span><span class="op">)</span><span class="op">,</span> <span class="num">0</span><span class="op">,</span> <span class="op">-</span><span class="num">1</span><span class="op">)</span><span class="op">)</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t216" href="#t216">216</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t217" href="#t217">217</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span> <span class="key">is</span> <span class="key">not</span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t218" href="#t218">218</a></span><span class="t">            <span class="nam">labelsC</span> <span class="op">=</span> <span class="op">[</span><span class="nam">labelsC</span><span class="op">[</span><span class="nam">i</span><span class="op">]</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t219" href="#t219">219</a></span><span class="t">            <span class="nam">labelsW</span> <span class="op">=</span> <span class="op">[</span><span class="nam">labelsW</span><span class="op">[</span><span class="nam">i</span><span class="op">]</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t220" href="#t220">220</a></span><span class="t">        <span class="nam">xlabels</span> <span class="op">=</span> <span class="nam">labelsW</span> <span class="op">+</span> <span class="op">[</span><span class="str">'-'</span><span class="op">]</span> <span class="op">+</span> <span class="nam">labelsC</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t221" href="#t221">221</a></span><span class="t">        <span class="key">return</span> <span class="nam">xlabels</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t222" href="#t222">222</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t223" href="#t223">223</a></span><span class="t">    <span class="key">def</span> <span class="nam">check_alpha_gamma</span><span class="op">(</span><span class="nam">self</span><span class="op">,</span> <span class="nam">alphaC</span><span class="op">,</span> <span class="nam">gammaC</span><span class="op">,</span> <span class="nam">alphaW</span><span class="op">,</span> <span class="nam">gammaW</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t224" href="#t224">224</a></span><span class="t">        <span class="nam">separator_df</span> <span class="op">=</span> <span class="nam">pd</span><span class="op">.</span><span class="nam">DataFrame</span><span class="op">(</span><span class="op">{</span><span class="str">"-"</span><span class="op">:</span> <span class="nam">np</span><span class="op">.</span><span class="nam">nan</span><span class="op">}</span><span class="op">,</span> <span class="nam">index</span><span class="op">=</span><span class="nam">range</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">gammaW</span><span class="op">)</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t225" href="#t225">225</a></span><span class="t">        <span class="nam">gamma</span> <span class="op">=</span> <span class="nam">pd</span><span class="op">.</span><span class="nam">concat</span><span class="op">(</span><span class="op">[</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t226" href="#t226">226</a></span><span class="t">            <span class="nam">gammaW</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t227" href="#t227">227</a></span><span class="t">            <span class="nam">separator_df</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t228" href="#t228">228</a></span><span class="t">            <span class="nam">gammaC</span><span class="op">[</span><span class="nam">gammaC</span><span class="op">.</span><span class="nam">columns</span><span class="op">[</span><span class="op">:</span><span class="op">:</span><span class="op">-</span><span class="num">1</span><span class="op">]</span><span class="op">]</span><span class="op">]</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t229" href="#t229">229</a></span><span class="t">            <span class="nam">axis</span><span class="op">=</span><span class="num">1</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t230" href="#t230">230</a></span><span class="t">        <span class="nam">alpha</span> <span class="op">=</span> <span class="nam">pd</span><span class="op">.</span><span class="nam">concat</span><span class="op">(</span><span class="op">[</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t231" href="#t231">231</a></span><span class="t">            <span class="nam">alphaW</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t232" href="#t232">232</a></span><span class="t">            <span class="nam">separator_df</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t233" href="#t233">233</a></span><span class="t">            <span class="nam">alphaC</span><span class="op">[</span><span class="nam">alphaC</span><span class="op">.</span><span class="nam">columns</span><span class="op">[</span><span class="op">:</span><span class="op">:</span><span class="op">-</span><span class="num">1</span><span class="op">]</span><span class="op">]</span><span class="op">]</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t234" href="#t234">234</a></span><span class="t">            <span class="nam">axis</span><span class="op">=</span><span class="num">1</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t235" href="#t235">235</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t236" href="#t236">236</a></span><span class="t">        <span class="nam">alpha_filter</span> <span class="op">=</span> <span class="nam">np</span><span class="op">.</span><span class="nam">logical_and</span><span class="op">(</span><span class="nam">alpha</span> <span class="op">></span> <span class="num">240</span><span class="op">,</span> <span class="nam">alpha</span> <span class="op">&lt;</span> <span class="num">360</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t237" href="#t237">237</a></span><span class="t">        <span class="nam">gamma_filter</span> <span class="op">=</span> <span class="nam">np</span><span class="op">.</span><span class="nam">logical_and</span><span class="op">(</span><span class="nam">gamma</span> <span class="op">></span> <span class="num">0</span><span class="op">,</span> <span class="nam">gamma</span> <span class="op">&lt;</span> <span class="num">120</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t238" href="#t238">238</a></span><span class="t">        <span class="nam">canonical_alpha_gamma</span> <span class="op">=</span> <span class="nam">np</span><span class="op">.</span><span class="nam">logical_and</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t239" href="#t239">239</a></span><span class="t">            <span class="nam">alpha_filter</span><span class="op">,</span> <span class="nam">gamma_filter</span><span class="op">)</span><span class="op">.</span><span class="nam">mean</span><span class="op">(</span><span class="op">)</span> <span class="op">*</span> <span class="num">100</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t240" href="#t240">240</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t241" href="#t241">241</a></span><span class="t">        <span class="key">return</span> <span class="nam">canonical_alpha_gamma</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t242" href="#t242">242</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t243" href="#t243">243</a></span><span class="t">    <span class="key">def</span> <span class="nam">fix_angles</span><span class="op">(</span><span class="nam">self</span><span class="op">,</span> <span class="nam">dataset</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t244" href="#t244">244</a></span><span class="t">        <span class="nam">values</span> <span class="op">=</span> <span class="nam">np</span><span class="op">.</span><span class="nam">where</span><span class="op">(</span><span class="nam">dataset</span> <span class="op">&lt;</span> <span class="num">0</span><span class="op">,</span> <span class="nam">dataset</span> <span class="op">+</span> <span class="num">360</span><span class="op">,</span> <span class="nam">dataset</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t245" href="#t245">245</a></span><span class="t">        <span class="nam">values</span> <span class="op">=</span> <span class="nam">np</span><span class="op">.</span><span class="nam">where</span><span class="op">(</span><span class="nam">values</span> <span class="op">></span> <span class="num">360</span><span class="op">,</span> <span class="nam">values</span> <span class="op">-</span> <span class="num">360</span><span class="op">,</span> <span class="nam">values</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t246" href="#t246">246</a></span><span class="t">        <span class="nam">dataset</span> <span class="op">=</span> <span class="nam">pd</span><span class="op">.</span><span class="nam">DataFrame</span><span class="op">(</span><span class="nam">values</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t247" href="#t247">247</a></span><span class="t">        <span class="key">return</span> <span class="nam">dataset</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t248" href="#t248">248</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t249" href="#t249">249</a></span><span class="t"><span class="key">def</span> <span class="nam">canonicalag</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t250" href="#t250">250</a></span><span class="t">        <span class="nam">input_alphaC_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span> <span class="nam">input_alphaW_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t251" href="#t251">251</a></span><span class="t">        <span class="nam">input_gammaC_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span> <span class="nam">input_gammaW_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t252" href="#t252">252</a></span><span class="t">        <span class="nam">output_csv_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span> <span class="nam">output_jpg_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t253" href="#t253">253</a></span><span class="t">        <span class="nam">properties</span><span class="op">:</span> <span class="nam">dict</span> <span class="op">=</span> <span class="key">None</span><span class="op">,</span> <span class="op">**</span><span class="nam">kwargs</span><span class="op">)</span> <span class="op">-></span> <span class="nam">int</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t254" href="#t254">254</a></span><span class="t">    <span class="str">"""Create :class:`CanonicalAG &lt;dna.backbone.canonicalag.CanonicalAG>` class and</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t255" href="#t255">255</a></span><span class="t"><span class="str">    execute the: meth: `launch() &lt;dna.backbone.canonicalag.CanonicalAG.launch>` method. """</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t256" href="#t256">256</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t257" href="#t257">257</a></span><span class="t">    <span class="key">return</span> <span class="nam">CanonicalAG</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t258" href="#t258">258</a></span><span class="t">        <span class="nam">input_alphaC_path</span><span class="op">=</span><span class="nam">input_alphaC_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t259" href="#t259">259</a></span><span class="t">        <span class="nam">input_alphaW_path</span><span class="op">=</span><span class="nam">input_alphaW_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t260" href="#t260">260</a></span><span class="t">        <span class="nam">input_gammaC_path</span><span class="op">=</span><span class="nam">input_gammaC_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t261" href="#t261">261</a></span><span class="t">        <span class="nam">input_gammaW_path</span><span class="op">=</span><span class="nam">input_gammaW_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t262" href="#t262">262</a></span><span class="t">        <span class="nam">output_csv_path</span><span class="op">=</span><span class="nam">output_csv_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t263" href="#t263">263</a></span><span class="t">        <span class="nam">output_jpg_path</span><span class="op">=</span><span class="nam">output_jpg_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t264" href="#t264">264</a></span><span class="t">        <span class="nam">properties</span><span class="op">=</span><span class="nam">properties</span><span class="op">,</span> <span class="op">**</span><span class="nam">kwargs</span><span class="op">)</span><span class="op">.</span><span class="nam">launch</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t265" href="#t265">265</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t249" href="#t249">249</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t250" href="#t250">250</a></span><span class="t"><span class="key">def</span> <span class="nam">canonicalag</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t251" href="#t251">251</a></span><span class="t">        <span class="nam">input_alphaC_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span> <span class="nam">input_alphaW_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t252" href="#t252">252</a></span><span class="t">        <span class="nam">input_gammaC_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span> <span class="nam">input_gammaW_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t253" href="#t253">253</a></span><span class="t">        <span class="nam">output_csv_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span> <span class="nam">output_jpg_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t254" href="#t254">254</a></span><span class="t">        <span class="nam">properties</span><span class="op">:</span> <span class="nam">dict</span> <span class="op">=</span> <span class="key">None</span><span class="op">,</span> <span class="op">**</span><span class="nam">kwargs</span><span class="op">)</span> <span class="op">-></span> <span class="nam">int</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t255" href="#t255">255</a></span><span class="t">    <span class="str">"""Create :class:`CanonicalAG &lt;dna.backbone.canonicalag.CanonicalAG>` class and</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t256" href="#t256">256</a></span><span class="t"><span class="str">    execute the: meth: `launch() &lt;dna.backbone.canonicalag.CanonicalAG.launch>` method. """</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t257" href="#t257">257</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t258" href="#t258">258</a></span><span class="t">    <span class="key">return</span> <span class="nam">CanonicalAG</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t259" href="#t259">259</a></span><span class="t">        <span class="nam">input_alphaC_path</span><span class="op">=</span><span class="nam">input_alphaC_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t260" href="#t260">260</a></span><span class="t">        <span class="nam">input_alphaW_path</span><span class="op">=</span><span class="nam">input_alphaW_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t261" href="#t261">261</a></span><span class="t">        <span class="nam">input_gammaC_path</span><span class="op">=</span><span class="nam">input_gammaC_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t262" href="#t262">262</a></span><span class="t">        <span class="nam">input_gammaW_path</span><span class="op">=</span><span class="nam">input_gammaW_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t263" href="#t263">263</a></span><span class="t">        <span class="nam">output_csv_path</span><span class="op">=</span><span class="nam">output_csv_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t264" href="#t264">264</a></span><span class="t">        <span class="nam">output_jpg_path</span><span class="op">=</span><span class="nam">output_jpg_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t265" href="#t265">265</a></span><span class="t">        <span class="nam">properties</span><span class="op">=</span><span class="nam">properties</span><span class="op">,</span> <span class="op">**</span><span class="nam">kwargs</span><span class="op">)</span><span class="op">.</span><span class="nam">launch</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t266" href="#t266">266</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t267" href="#t267">267</a></span><span class="t"><span class="key">def</span> <span class="nam">main</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t268" href="#t268">268</a></span><span class="t">    <span class="str">"""Command line execution of this building block. Please check the command line documentation."""</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t269" href="#t269">269</a></span><span class="t">    <span class="nam">parser</span> <span class="op">=</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">ArgumentParser</span><span class="op">(</span><span class="nam">description</span><span class="op">=</span><span class="str">'Calculate Canonical Alpha/Gamma distributions.'</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t270" href="#t270">270</a></span><span class="t">                                     <span class="nam">formatter_class</span><span class="op">=</span><span class="key">lambda</span> <span class="nam">prog</span><span class="op">:</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">RawTextHelpFormatter</span><span class="op">(</span><span class="nam">prog</span><span class="op">,</span> <span class="nam">width</span><span class="op">=</span><span class="num">99999</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t271" href="#t271">271</a></span><span class="t">    <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--config'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">False</span><span class="op">,</span> <span class="nam">help</span><span class="op">=</span><span class="str">'Configuration file'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t272" href="#t272">272</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t273" href="#t273">273</a></span><span class="t">    <span class="nam">required_args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument_group</span><span class="op">(</span><span class="str">'required arguments'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t274" href="#t274">274</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--input_alphaC_path'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t275" href="#t275">275</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Helical parameter &lt;alphaC> input ser file path. Accepted formats: ser.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t276" href="#t276">276</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--input_alphaW_path'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t277" href="#t277">277</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Helical parameter &lt;alphaW> input ser file path. Accepted formats: ser.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t278" href="#t278">278</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--input_gammaC_path'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t279" href="#t279">279</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Helical parameter &lt;gammaC> input ser file path. Accepted formats: ser.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t280" href="#t280">280</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--input_gammaW_path'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t281" href="#t281">281</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Helical parameter &lt;gammaW> input ser file path. Accepted formats: ser.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t282" href="#t282">282</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--output_csv_path'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t283" href="#t283">283</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Path to output csv file. Accepted formats: csv.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t284" href="#t284">284</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--output_jpg_path'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t285" href="#t285">285</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Path to output jpg file. Accepted formats: jpg.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t286" href="#t286">286</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t287" href="#t287">287</a></span><span class="t">    <span class="nam">args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">parse_args</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t288" href="#t288">288</a></span><span class="t">    <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="op">=</span> <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="key">or</span> <span class="str">"{}"</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t289" href="#t289">289</a></span><span class="t">    <span class="nam">properties</span> <span class="op">=</span> <span class="nam">settings</span><span class="op">.</span><span class="nam">ConfReader</span><span class="op">(</span><span class="nam">config</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">config</span><span class="op">)</span><span class="op">.</span><span class="nam">get_prop_dic</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t290" href="#t290">290</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t291" href="#t291">291</a></span><span class="t">    <span class="nam">canonicalag</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t292" href="#t292">292</a></span><span class="t">        <span class="nam">input_alphaC_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_alphaC_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t293" href="#t293">293</a></span><span class="t">        <span class="nam">input_alphaW_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_alphaW_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t294" href="#t294">294</a></span><span class="t">        <span class="nam">input_gammaC_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_gammaC_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t295" href="#t295">295</a></span><span class="t">        <span class="nam">input_gammaW_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_gammaW_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t296" href="#t296">296</a></span><span class="t">        <span class="nam">output_csv_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">output_csv_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t297" href="#t297">297</a></span><span class="t">        <span class="nam">output_jpg_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">output_jpg_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t298" href="#t298">298</a></span><span class="t">        <span class="nam">properties</span><span class="op">=</span><span class="nam">properties</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t299" href="#t299">299</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t267" href="#t267">267</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t268" href="#t268">268</a></span><span class="t"><span class="key">def</span> <span class="nam">main</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t269" href="#t269">269</a></span><span class="t">    <span class="str">"""Command line execution of this building block. Please check the command line documentation."""</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t270" href="#t270">270</a></span><span class="t">    <span class="nam">parser</span> <span class="op">=</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">ArgumentParser</span><span class="op">(</span><span class="nam">description</span><span class="op">=</span><span class="str">'Calculate Canonical Alpha/Gamma distributions.'</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t271" href="#t271">271</a></span><span class="t">                                     <span class="nam">formatter_class</span><span class="op">=</span><span class="key">lambda</span> <span class="nam">prog</span><span class="op">:</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">RawTextHelpFormatter</span><span class="op">(</span><span class="nam">prog</span><span class="op">,</span> <span class="nam">width</span><span class="op">=</span><span class="num">99999</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t272" href="#t272">272</a></span><span class="t">    <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--config'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">False</span><span class="op">,</span> <span class="nam">help</span><span class="op">=</span><span class="str">'Configuration file'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t273" href="#t273">273</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t274" href="#t274">274</a></span><span class="t">    <span class="nam">required_args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument_group</span><span class="op">(</span><span class="str">'required arguments'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t275" href="#t275">275</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--input_alphaC_path'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t276" href="#t276">276</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Helical parameter &lt;alphaC> input ser file path. Accepted formats: ser.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t277" href="#t277">277</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--input_alphaW_path'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t278" href="#t278">278</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Helical parameter &lt;alphaW> input ser file path. Accepted formats: ser.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t279" href="#t279">279</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--input_gammaC_path'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t280" href="#t280">280</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Helical parameter &lt;gammaC> input ser file path. Accepted formats: ser.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t281" href="#t281">281</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--input_gammaW_path'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t282" href="#t282">282</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Helical parameter &lt;gammaW> input ser file path. Accepted formats: ser.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t283" href="#t283">283</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--output_csv_path'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t284" href="#t284">284</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Path to output csv file. Accepted formats: csv.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t285" href="#t285">285</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--output_jpg_path'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t286" href="#t286">286</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Path to output jpg file. Accepted formats: jpg.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t287" href="#t287">287</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t288" href="#t288">288</a></span><span class="t">    <span class="nam">args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">parse_args</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t289" href="#t289">289</a></span><span class="t">    <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="op">=</span> <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="key">or</span> <span class="str">"{}"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t290" href="#t290">290</a></span><span class="t">    <span class="nam">properties</span> <span class="op">=</span> <span class="nam">settings</span><span class="op">.</span><span class="nam">ConfReader</span><span class="op">(</span><span class="nam">config</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">config</span><span class="op">)</span><span class="op">.</span><span class="nam">get_prop_dic</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t291" href="#t291">291</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t292" href="#t292">292</a></span><span class="t">    <span class="nam">canonicalag</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t293" href="#t293">293</a></span><span class="t">        <span class="nam">input_alphaC_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_alphaC_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t294" href="#t294">294</a></span><span class="t">        <span class="nam">input_alphaW_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_alphaW_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t295" href="#t295">295</a></span><span class="t">        <span class="nam">input_gammaC_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_gammaC_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t296" href="#t296">296</a></span><span class="t">        <span class="nam">input_gammaW_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_gammaW_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t297" href="#t297">297</a></span><span class="t">        <span class="nam">output_csv_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">output_csv_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t298" href="#t298">298</a></span><span class="t">        <span class="nam">output_jpg_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">output_jpg_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t299" href="#t299">299</a></span><span class="t">        <span class="nam">properties</span><span class="op">=</span><span class="nam">properties</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t300" href="#t300">300</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t301" href="#t301">301</a></span><span class="t"><span class="key">if</span> <span class="nam">__name__</span> <span class="op">==</span> <span class="str">'__main__'</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t302" href="#t302">302</a></span><span class="t">    <span class="nam">main</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t301" href="#t301">301</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t302" href="#t302">302</a></span><span class="t"><span class="key">if</span> <span class="nam">__name__</span> <span class="op">==</span> <span class="str">'__main__'</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t303" href="#t303">303</a></span><span class="t">    <span class="nam">main</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
 </main>
 <footer>
     <div class="content">
@@ -391,7 +392,7 @@ <h2>
             <a class="nav" href="z_159731231e5c9c9d_puckering_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.5.1">coverage.py v7.5.1</a>,
-            created at 2024-05-07 09:06 +0000
+            created at 2024-05-24 09:29 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_159731231e5c9c9d_puckering_py.html b/coverage/z_159731231e5c9c9d_puckering_py.html
index a0c6efac..6775f3a5 100644
--- a/coverage/z_159731231e5c9c9d_puckering_py.html
+++ b/coverage/z_159731231e5c9c9d_puckering_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_74fa14c6d0e940a4___init___py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.5.1">coverage.py v7.5.1</a>,
-            created at 2024-05-07 09:06 +0000
+            created at 2024-05-24 09:29 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -101,271 +101,272 @@ <h2>
     <p class="pln"><span class="n"><a id="t19" href="#t19">19</a></span><span class="t">    <span class="str">"""</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t20" href="#t20">20</a></span><span class="t"><span class="str">    | biobb_dna Puckering</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t21" href="#t21">21</a></span><span class="t"><span class="str">    | Calculate Puckering from phase parameters.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t22" href="#t22">22</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t23" href="#t23">23</a></span><span class="t"><span class="str">    Args:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t24" href="#t24">24</a></span><span class="t"><span class="str">        input_phaseC_path (str): Path to .ser file for helical parameter 'phaseC'. File type: input. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/backbone/canal_output_phaseC.ser>`_. Accepted formats: ser (edam:format_2330).</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t25" href="#t25">25</a></span><span class="t"><span class="str">        input_phaseW_path (str): Path to .ser file for helical parameter 'phaseW'. File type: input. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/backbone/canal_output_phaseW.ser>`_. Accepted formats: ser (edam:format_2330).</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t26" href="#t26">26</a></span><span class="t"><span class="str">        output_csv_path (str): Path to .csv file where output is saved. File type: output. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/reference/backbone/puckering_ref.csv>`_. Accepted formats: csv (edam:format_3752).</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t27" href="#t27">27</a></span><span class="t"><span class="str">        output_jpg_path (str): Path to .jpg file where output is saved. File type: output. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/reference/backbone/puckering_ref.jpg>`_. Accepted formats: jpg (edam:format_3579).</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t28" href="#t28">28</a></span><span class="t"><span class="str">        properties (dict):</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t29" href="#t29">29</a></span><span class="t"><span class="str">            * **sequence** (*str*) - (None) Nucleic acid sequence corresponding to the input .ser file. Length of sequence is expected to be the same as the total number of columns in the .ser file, minus the index column (even if later on a subset of columns is selected with the *seqpos* option).</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t30" href="#t30">30</a></span><span class="t"><span class="str">            * **helpar_name** (*str*) - (None) helical parameter name.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t31" href="#t31">31</a></span><span class="t"><span class="str">            * **stride** (*int*) - (1000) granularity of the number of snapshots for plotting time series.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t32" href="#t32">32</a></span><span class="t"><span class="str">            * **seqpos** (*list*) - (None) list of sequence positions (columns indices starting by 0) to analyze.  If not specified it will analyse the complete sequence.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t33" href="#t33">33</a></span><span class="t"><span class="str">            * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t34" href="#t34">34</a></span><span class="t"><span class="str">            * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t35" href="#t35">35</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t36" href="#t36">36</a></span><span class="t"><span class="str">    Examples:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t37" href="#t37">37</a></span><span class="t"><span class="str">        This is a use example of how to use the building block from Python::</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t38" href="#t38">38</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t39" href="#t39">39</a></span><span class="t"><span class="str">            from biobb_dna.backbone.puckering import puckering</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t40" href="#t40">40</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t41" href="#t41">41</a></span><span class="t"><span class="str">            prop = {</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t42" href="#t42">42</a></span><span class="t"><span class="str">                'sequence': 'GCAT',</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t43" href="#t43">43</a></span><span class="t"><span class="str">            }</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t44" href="#t44">44</a></span><span class="t"><span class="str">            puckering(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t45" href="#t45">45</a></span><span class="t"><span class="str">                input_phaseC_path='/path/to/phaseC.ser',</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t46" href="#t46">46</a></span><span class="t"><span class="str">                input_phaseW_path='/path/to/phaseW.ser',</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t47" href="#t47">47</a></span><span class="t"><span class="str">                output_csv_path='/path/to/table/output.csv',</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t48" href="#t48">48</a></span><span class="t"><span class="str">                output_jpg_path='/path/to/table/output.jpg',</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t49" href="#t49">49</a></span><span class="t"><span class="str">                properties=prop)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t50" href="#t50">50</a></span><span class="t"><span class="str">    Info:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t51" href="#t51">51</a></span><span class="t"><span class="str">        * wrapped_software:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t52" href="#t52">52</a></span><span class="t"><span class="str">            * name: In house</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t53" href="#t53">53</a></span><span class="t"><span class="str">            * license: Apache-2.0</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t54" href="#t54">54</a></span><span class="t"><span class="str">        * ontology:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t55" href="#t55">55</a></span><span class="t"><span class="str">            * name: EDAM</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t56" href="#t56">56</a></span><span class="t"><span class="str">            * schema: http://edamontology.org/EDAM.owl</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t57" href="#t57">57</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t58" href="#t58">58</a></span><span class="t"><span class="str">    """</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t59" href="#t59">59</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t60" href="#t60">60</a></span><span class="t">    <span class="key">def</span> <span class="nam">__init__</span><span class="op">(</span><span class="nam">self</span><span class="op">,</span> <span class="nam">input_phaseC_path</span><span class="op">,</span> <span class="nam">input_phaseW_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t61" href="#t61">61</a></span><span class="t">                 <span class="nam">output_csv_path</span><span class="op">,</span> <span class="nam">output_jpg_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t62" href="#t62">62</a></span><span class="t">                 <span class="nam">properties</span><span class="op">=</span><span class="key">None</span><span class="op">,</span> <span class="op">**</span><span class="nam">kwargs</span><span class="op">)</span> <span class="op">-></span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t63" href="#t63">63</a></span><span class="t">        <span class="nam">properties</span> <span class="op">=</span> <span class="nam">properties</span> <span class="key">or</span> <span class="op">{</span><span class="op">}</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t64" href="#t64">64</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t65" href="#t65">65</a></span><span class="t">        <span class="com"># Call parent class constructor</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t66" href="#t66">66</a></span><span class="t">        <span class="nam">super</span><span class="op">(</span><span class="op">)</span><span class="op">.</span><span class="nam">__init__</span><span class="op">(</span><span class="nam">properties</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t67" href="#t67">67</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">locals_var_dict</span> <span class="op">=</span> <span class="nam">locals</span><span class="op">(</span><span class="op">)</span><span class="op">.</span><span class="nam">copy</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t68" href="#t68">68</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t69" href="#t69">69</a></span><span class="t">        <span class="com"># Input/Output files</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t70" href="#t70">70</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span> <span class="op">=</span> <span class="op">{</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t71" href="#t71">71</a></span><span class="t">            <span class="str">'in'</span><span class="op">:</span> <span class="op">{</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t72" href="#t72">72</a></span><span class="t">                <span class="str">'input_phaseC_path'</span><span class="op">:</span> <span class="nam">input_phaseC_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t73" href="#t73">73</a></span><span class="t">                <span class="str">'input_phaseW_path'</span><span class="op">:</span> <span class="nam">input_phaseW_path</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t74" href="#t74">74</a></span><span class="t">            <span class="op">}</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t75" href="#t75">75</a></span><span class="t">            <span class="str">'out'</span><span class="op">:</span> <span class="op">{</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t76" href="#t76">76</a></span><span class="t">                <span class="str">'output_csv_path'</span><span class="op">:</span> <span class="nam">output_csv_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t77" href="#t77">77</a></span><span class="t">                <span class="str">'output_jpg_path'</span><span class="op">:</span> <span class="nam">output_jpg_path</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t78" href="#t78">78</a></span><span class="t">            <span class="op">}</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t79" href="#t79">79</a></span><span class="t">        <span class="op">}</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t80" href="#t80">80</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t81" href="#t81">81</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">properties</span> <span class="op">=</span> <span class="nam">properties</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t82" href="#t82">82</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"sequence"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t83" href="#t83">83</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">stride</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t84" href="#t84">84</a></span><span class="t">            <span class="str">"stride"</span><span class="op">,</span> <span class="num">1000</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t85" href="#t85">85</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t86" href="#t86">86</a></span><span class="t">            <span class="str">"seqpos"</span><span class="op">,</span> <span class="key">None</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t87" href="#t87">87</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t88" href="#t88">88</a></span><span class="t">        <span class="com"># Check the properties</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t89" href="#t89">89</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_properties</span><span class="op">(</span><span class="nam">properties</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t90" href="#t90">90</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_arguments</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t91" href="#t91">91</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t92" href="#t92">92</a></span><span class="t">    <span class="op">@</span><span class="nam">launchlogger</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t93" href="#t93">93</a></span><span class="t">    <span class="key">def</span> <span class="nam">launch</span><span class="op">(</span><span class="nam">self</span><span class="op">)</span> <span class="op">-></span> <span class="nam">int</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t94" href="#t94">94</a></span><span class="t">        <span class="str">"""Execute the :class:`Puckering &lt;backbone.puckering.Puckering>` object."""</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t95" href="#t95">95</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t96" href="#t96">96</a></span><span class="t">        <span class="com"># Setup Biobb</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t97" href="#t97">97</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">check_restart</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t98" href="#t98">98</a></span><span class="t">            <span class="key">return</span> <span class="num">0</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t99" href="#t99">99</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">stage_files</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t100" href="#t100">100</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t101" href="#t101">101</a></span><span class="t">        <span class="com"># check sequence</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t102" href="#t102">102</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span> <span class="key">is</span> <span class="key">None</span> <span class="key">or</span> <span class="nam">len</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span><span class="op">)</span> <span class="op">&lt;</span> <span class="num">2</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t103" href="#t103">103</a></span><span class="t">            <span class="key">raise</span> <span class="nam">ValueError</span><span class="op">(</span><span class="str">"sequence is null or too short!"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t104" href="#t104">104</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t105" href="#t105">105</a></span><span class="t">        <span class="com"># check seqpos</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t106" href="#t106">106</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span> <span class="key">is</span> <span class="key">not</span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t107" href="#t107">107</a></span><span class="t">            <span class="key">if</span> <span class="op">(</span><span class="nam">max</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">)</span> <span class="op">></span> <span class="nam">len</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span><span class="op">)</span> <span class="op">-</span> <span class="num">2</span><span class="op">)</span> <span class="key">or</span> <span class="op">(</span><span class="nam">min</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">)</span> <span class="op">&lt;</span> <span class="num">1</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t108" href="#t108">108</a></span><span class="t">                <span class="key">raise</span> <span class="nam">ValueError</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t109" href="#t109">109</a></span><span class="t">                    <span class="str">f"seqpos values must be between 1 and {len(self.sequence) - 2}"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t110" href="#t110">110</a></span><span class="t">            <span class="key">if</span> <span class="key">not</span> <span class="op">(</span><span class="nam">isinstance</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">,</span> <span class="nam">list</span><span class="op">)</span> <span class="key">and</span> <span class="nam">len</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">)</span> <span class="op">></span> <span class="num">1</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t111" href="#t111">111</a></span><span class="t">                <span class="key">raise</span> <span class="nam">ValueError</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t112" href="#t112">112</a></span><span class="t">                    <span class="str">"seqpos must be a list of at least two integers"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t113" href="#t113">113</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t114" href="#t114">114</a></span><span class="t">        <span class="com"># Creating temporary folder</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t115" href="#t115">115</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span> <span class="op">=</span> <span class="nam">fu</span><span class="op">.</span><span class="nam">create_unique_dir</span><span class="op">(</span><span class="nam">prefix</span><span class="op">=</span><span class="str">"backbone_"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t116" href="#t116">116</a></span><span class="t">        <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="str">'Creating %s temporary folder'</span> <span class="op">%</span> <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t117" href="#t117">117</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t118" href="#t118">118</a></span><span class="t">        <span class="com"># Copy input_file_path1 to temporary folder</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t119" href="#t119">119</a></span><span class="t">        <span class="nam">shutil</span><span class="op">.</span><span class="nam">copy</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'input_phaseC_path'</span><span class="op">]</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t120" href="#t120">120</a></span><span class="t">        <span class="nam">shutil</span><span class="op">.</span><span class="nam">copy</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'input_phaseW_path'</span><span class="op">]</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t121" href="#t121">121</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t122" href="#t122">122</a></span><span class="t">        <span class="com"># read input files</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t123" href="#t123">123</a></span><span class="t">        <span class="nam">phaseC</span> <span class="op">=</span> <span class="nam">read_series</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t124" href="#t124">124</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'input_phaseC_path'</span><span class="op">]</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t125" href="#t125">125</a></span><span class="t">            <span class="nam">usecols</span><span class="op">=</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t126" href="#t126">126</a></span><span class="t">        <span class="nam">phaseW</span> <span class="op">=</span> <span class="nam">read_series</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t127" href="#t127">127</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'input_phaseW_path'</span><span class="op">]</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t128" href="#t128">128</a></span><span class="t">            <span class="nam">usecols</span><span class="op">=</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t129" href="#t129">129</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t130" href="#t130">130</a></span><span class="t">        <span class="com"># fix angle range so its not negative</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t131" href="#t131">131</a></span><span class="t">        <span class="nam">phaseC</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">fix_angles</span><span class="op">(</span><span class="nam">phaseC</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t132" href="#t132">132</a></span><span class="t">        <span class="nam">phaseW</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">fix_angles</span><span class="op">(</span><span class="nam">phaseW</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t133" href="#t133">133</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t134" href="#t134">134</a></span><span class="t">        <span class="com"># calculate difference between epsil and zeta parameters</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t135" href="#t135">135</a></span><span class="t">        <span class="nam">xlabels</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">get_xlabels</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t136" href="#t136">136</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t137" href="#t137">137</a></span><span class="t">            <span class="nam">inverse_complement</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t138" href="#t138">138</a></span><span class="t">        <span class="nam">Npop</span><span class="op">,</span> <span class="nam">Epop</span><span class="op">,</span> <span class="nam">Wpop</span><span class="op">,</span> <span class="nam">Spop</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">check_puckering</span><span class="op">(</span><span class="nam">phaseC</span><span class="op">,</span> <span class="nam">phaseW</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t139" href="#t139">139</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t140" href="#t140">140</a></span><span class="t">        <span class="com"># save plot</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t141" href="#t141">141</a></span><span class="t">        <span class="nam">fig</span><span class="op">,</span> <span class="nam">axs</span> <span class="op">=</span> <span class="nam">plt</span><span class="op">.</span><span class="nam">subplots</span><span class="op">(</span><span class="num">1</span><span class="op">,</span> <span class="num">1</span><span class="op">,</span> <span class="nam">dpi</span><span class="op">=</span><span class="num">300</span><span class="op">,</span> <span class="nam">tight_layout</span><span class="op">=</span><span class="key">True</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t142" href="#t142">142</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">bar</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t143" href="#t143">143</a></span><span class="t">            <span class="nam">range</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">xlabels</span><span class="op">)</span><span class="op">)</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t144" href="#t144">144</a></span><span class="t">            <span class="nam">Npop</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t145" href="#t145">145</a></span><span class="t">            <span class="nam">label</span><span class="op">=</span><span class="str">"North"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t146" href="#t146">146</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">bar</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t147" href="#t147">147</a></span><span class="t">            <span class="nam">range</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">xlabels</span><span class="op">)</span><span class="op">)</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t148" href="#t148">148</a></span><span class="t">            <span class="nam">Epop</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t149" href="#t149">149</a></span><span class="t">            <span class="nam">bottom</span><span class="op">=</span><span class="nam">Npop</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t150" href="#t150">150</a></span><span class="t">            <span class="nam">label</span><span class="op">=</span><span class="str">"East"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t151" href="#t151">151</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">bar</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t152" href="#t152">152</a></span><span class="t">            <span class="nam">range</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">xlabels</span><span class="op">)</span><span class="op">)</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t153" href="#t153">153</a></span><span class="t">            <span class="nam">Spop</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t154" href="#t154">154</a></span><span class="t">            <span class="nam">bottom</span><span class="op">=</span><span class="nam">Npop</span><span class="op">+</span><span class="nam">Epop</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t155" href="#t155">155</a></span><span class="t">            <span class="nam">label</span><span class="op">=</span><span class="str">"South"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t156" href="#t156">156</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">bar</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t157" href="#t157">157</a></span><span class="t">            <span class="nam">range</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">xlabels</span><span class="op">)</span><span class="op">)</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t158" href="#t158">158</a></span><span class="t">            <span class="nam">Wpop</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t159" href="#t159">159</a></span><span class="t">            <span class="nam">bottom</span><span class="op">=</span><span class="nam">Npop</span><span class="op">+</span><span class="nam">Epop</span><span class="op">+</span><span class="nam">Spop</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t160" href="#t160">160</a></span><span class="t">            <span class="nam">label</span><span class="op">=</span><span class="str">"West"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t161" href="#t161">161</a></span><span class="t">        <span class="com"># empty bar to divide both sequences</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t162" href="#t162">162</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">bar</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t163" href="#t163">163</a></span><span class="t">            <span class="op">[</span><span class="nam">len</span><span class="op">(</span><span class="nam">phaseC</span><span class="op">.</span><span class="nam">columns</span><span class="op">)</span><span class="op">]</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t164" href="#t164">164</a></span><span class="t">            <span class="op">[</span><span class="num">100</span><span class="op">]</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t165" href="#t165">165</a></span><span class="t">            <span class="nam">color</span><span class="op">=</span><span class="str">'white'</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t166" href="#t166">166</a></span><span class="t">            <span class="nam">label</span><span class="op">=</span><span class="key">None</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t167" href="#t167">167</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">legend</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t168" href="#t168">168</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_xticks</span><span class="op">(</span><span class="nam">range</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">xlabels</span><span class="op">)</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t169" href="#t169">169</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_xticklabels</span><span class="op">(</span><span class="nam">xlabels</span><span class="op">,</span> <span class="nam">rotation</span><span class="op">=</span><span class="num">90</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t170" href="#t170">170</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_xlabel</span><span class="op">(</span><span class="str">"Nucleotide Sequence"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t171" href="#t171">171</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_ylabel</span><span class="op">(</span><span class="str">"Puckering (%)"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t172" href="#t172">172</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_title</span><span class="op">(</span><span class="str">"Nucleotide parameter: Puckering"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t173" href="#t173">173</a></span><span class="t">        <span class="nam">fig</span><span class="op">.</span><span class="nam">savefig</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t174" href="#t174">174</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'out'</span><span class="op">]</span><span class="op">[</span><span class="str">'output_jpg_path'</span><span class="op">]</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t175" href="#t175">175</a></span><span class="t">            <span class="nam">format</span><span class="op">=</span><span class="str">"jpg"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t176" href="#t176">176</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t177" href="#t177">177</a></span><span class="t">        <span class="com"># save table</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t178" href="#t178">178</a></span><span class="t">        <span class="nam">populations</span> <span class="op">=</span> <span class="nam">pd</span><span class="op">.</span><span class="nam">DataFrame</span><span class="op">(</span><span class="op">{</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t179" href="#t179">179</a></span><span class="t">            <span class="str">"Nucleotide"</span><span class="op">:</span> <span class="nam">xlabels</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t180" href="#t180">180</a></span><span class="t">            <span class="str">"North"</span><span class="op">:</span> <span class="nam">Npop</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t181" href="#t181">181</a></span><span class="t">            <span class="str">"East"</span><span class="op">:</span> <span class="nam">Epop</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t182" href="#t182">182</a></span><span class="t">            <span class="str">"West"</span><span class="op">:</span> <span class="nam">Wpop</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t183" href="#t183">183</a></span><span class="t">            <span class="str">"South"</span><span class="op">:</span> <span class="nam">Spop</span><span class="op">}</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t184" href="#t184">184</a></span><span class="t">        <span class="nam">populations</span><span class="op">.</span><span class="nam">to_csv</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t185" href="#t185">185</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'out'</span><span class="op">]</span><span class="op">[</span><span class="str">'output_csv_path'</span><span class="op">]</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t186" href="#t186">186</a></span><span class="t">            <span class="nam">index</span><span class="op">=</span><span class="key">False</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t187" href="#t187">187</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t188" href="#t188">188</a></span><span class="t">        <span class="nam">plt</span><span class="op">.</span><span class="nam">close</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t189" href="#t189">189</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t190" href="#t190">190</a></span><span class="t">        <span class="com"># Remove temporary file(s)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t191" href="#t191">191</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_files</span><span class="op">.</span><span class="nam">extend</span><span class="op">(</span><span class="op">[</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t192" href="#t192">192</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"unique_dir"</span><span class="op">)</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t193" href="#t193">193</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t194" href="#t194">194</a></span><span class="t">        <span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t195" href="#t195">195</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">remove_tmp_files</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t196" href="#t196">196</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t197" href="#t197">197</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_arguments</span><span class="op">(</span><span class="nam">output_files_created</span><span class="op">=</span><span class="key">True</span><span class="op">,</span> <span class="nam">raise_exception</span><span class="op">=</span><span class="key">False</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t198" href="#t198">198</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t199" href="#t199">199</a></span><span class="t">        <span class="key">return</span> <span class="num">0</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t200" href="#t200">200</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t201" href="#t201">201</a></span><span class="t">    <span class="key">def</span> <span class="nam">get_xlabels</span><span class="op">(</span><span class="nam">self</span><span class="op">,</span> <span class="nam">strand1</span><span class="op">,</span> <span class="nam">strand2</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t202" href="#t202">202</a></span><span class="t">        <span class="com"># get list of tetramers, except first and last two bases</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t203" href="#t203">203</a></span><span class="t">        <span class="nam">labelsW</span> <span class="op">=</span> <span class="nam">list</span><span class="op">(</span><span class="nam">strand1</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t204" href="#t204">204</a></span><span class="t">        <span class="nam">labelsW</span><span class="op">[</span><span class="num">0</span><span class="op">]</span> <span class="op">=</span> <span class="str">f"{labelsW[0]}5\'"</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t205" href="#t205">205</a></span><span class="t">        <span class="nam">labelsW</span><span class="op">[</span><span class="op">-</span><span class="num">1</span><span class="op">]</span> <span class="op">=</span> <span class="str">f"{labelsW[-1]}3\'"</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t206" href="#t206">206</a></span><span class="t">        <span class="nam">labelsW</span> <span class="op">=</span> <span class="op">[</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t207" href="#t207">207</a></span><span class="t">            <span class="str">f"{i}-{j}"</span> <span class="key">for</span> <span class="nam">i</span><span class="op">,</span> <span class="nam">j</span> <span class="key">in</span> <span class="nam">zip</span><span class="op">(</span><span class="nam">labelsW</span><span class="op">,</span> <span class="nam">range</span><span class="op">(</span><span class="num">1</span><span class="op">,</span> <span class="nam">len</span><span class="op">(</span><span class="nam">labelsW</span><span class="op">)</span><span class="op">+</span><span class="num">1</span><span class="op">)</span><span class="op">)</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t208" href="#t208">208</a></span><span class="t">        <span class="nam">labelsC</span> <span class="op">=</span> <span class="nam">list</span><span class="op">(</span><span class="nam">strand2</span><span class="op">)</span><span class="op">[</span><span class="op">:</span><span class="op">:</span><span class="op">-</span><span class="num">1</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t209" href="#t209">209</a></span><span class="t">        <span class="nam">labelsC</span><span class="op">[</span><span class="num">0</span><span class="op">]</span> <span class="op">=</span> <span class="str">f"{labelsC[0]}5\'"</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t210" href="#t210">210</a></span><span class="t">        <span class="nam">labelsC</span><span class="op">[</span><span class="op">-</span><span class="num">1</span><span class="op">]</span> <span class="op">=</span> <span class="str">f"{labelsC[-1]}3\'"</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t211" href="#t211">211</a></span><span class="t">        <span class="nam">labelsC</span> <span class="op">=</span> <span class="op">[</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t212" href="#t212">212</a></span><span class="t">            <span class="str">f"{i}-{j}"</span> <span class="key">for</span> <span class="nam">i</span><span class="op">,</span> <span class="nam">j</span> <span class="key">in</span> <span class="nam">zip</span><span class="op">(</span><span class="nam">labelsC</span><span class="op">,</span> <span class="nam">range</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">labelsC</span><span class="op">)</span><span class="op">,</span> <span class="num">0</span><span class="op">,</span> <span class="op">-</span><span class="num">1</span><span class="op">)</span><span class="op">)</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t213" href="#t213">213</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t214" href="#t214">214</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span> <span class="key">is</span> <span class="key">not</span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t215" href="#t215">215</a></span><span class="t">            <span class="nam">labelsC</span> <span class="op">=</span> <span class="op">[</span><span class="nam">labelsC</span><span class="op">[</span><span class="nam">i</span><span class="op">]</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t216" href="#t216">216</a></span><span class="t">            <span class="nam">labelsW</span> <span class="op">=</span> <span class="op">[</span><span class="nam">labelsW</span><span class="op">[</span><span class="nam">i</span><span class="op">]</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t217" href="#t217">217</a></span><span class="t">        <span class="nam">xlabels</span> <span class="op">=</span> <span class="nam">labelsW</span> <span class="op">+</span> <span class="op">[</span><span class="str">'-'</span><span class="op">]</span> <span class="op">+</span> <span class="nam">labelsC</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t218" href="#t218">218</a></span><span class="t">        <span class="key">return</span> <span class="nam">xlabels</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t219" href="#t219">219</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t220" href="#t220">220</a></span><span class="t">    <span class="key">def</span> <span class="nam">check_puckering</span><span class="op">(</span><span class="nam">self</span><span class="op">,</span> <span class="nam">phaseC</span><span class="op">,</span> <span class="nam">phaseW</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t221" href="#t221">221</a></span><span class="t">        <span class="nam">separator_df</span> <span class="op">=</span> <span class="nam">pd</span><span class="op">.</span><span class="nam">DataFrame</span><span class="op">(</span><span class="op">{</span><span class="str">"-"</span><span class="op">:</span> <span class="nam">np</span><span class="op">.</span><span class="nam">nan</span><span class="op">}</span><span class="op">,</span> <span class="nam">index</span><span class="op">=</span><span class="nam">range</span><span class="op">(</span><span class="num">1</span><span class="op">,</span> <span class="nam">len</span><span class="op">(</span><span class="nam">phaseC</span><span class="op">)</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t222" href="#t222">222</a></span><span class="t">        <span class="nam">phase</span> <span class="op">=</span> <span class="nam">pd</span><span class="op">.</span><span class="nam">concat</span><span class="op">(</span><span class="op">[</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t223" href="#t223">223</a></span><span class="t">            <span class="nam">phaseW</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t224" href="#t224">224</a></span><span class="t">            <span class="nam">separator_df</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t225" href="#t225">225</a></span><span class="t">            <span class="nam">phaseC</span><span class="op">[</span><span class="nam">phaseC</span><span class="op">.</span><span class="nam">columns</span><span class="op">[</span><span class="op">:</span><span class="op">:</span><span class="op">-</span><span class="num">1</span><span class="op">]</span><span class="op">]</span><span class="op">]</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t226" href="#t226">226</a></span><span class="t">            <span class="nam">axis</span><span class="op">=</span><span class="num">1</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t227" href="#t227">227</a></span><span class="t">        <span class="com"># phase.columns = columns</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t228" href="#t228">228</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t229" href="#t229">229</a></span><span class="t">        <span class="nam">Npop</span> <span class="op">=</span> <span class="nam">np</span><span class="op">.</span><span class="nam">logical_or</span><span class="op">(</span><span class="nam">phase</span> <span class="op">></span> <span class="num">315</span><span class="op">,</span> <span class="nam">phase</span> <span class="op">&lt;</span> <span class="num">45</span><span class="op">)</span><span class="op">.</span><span class="nam">mean</span><span class="op">(</span><span class="op">)</span> <span class="op">*</span> <span class="num">100</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t230" href="#t230">230</a></span><span class="t">        <span class="nam">Epop</span> <span class="op">=</span> <span class="nam">np</span><span class="op">.</span><span class="nam">logical_and</span><span class="op">(</span><span class="nam">phase</span> <span class="op">></span> <span class="num">45</span><span class="op">,</span> <span class="nam">phase</span> <span class="op">&lt;</span> <span class="num">135</span><span class="op">)</span><span class="op">.</span><span class="nam">mean</span><span class="op">(</span><span class="op">)</span> <span class="op">*</span> <span class="num">100</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t231" href="#t231">231</a></span><span class="t">        <span class="nam">Wpop</span> <span class="op">=</span> <span class="nam">np</span><span class="op">.</span><span class="nam">logical_and</span><span class="op">(</span><span class="nam">phase</span> <span class="op">></span> <span class="num">225</span><span class="op">,</span> <span class="nam">phase</span> <span class="op">&lt;</span> <span class="num">315</span><span class="op">)</span><span class="op">.</span><span class="nam">mean</span><span class="op">(</span><span class="op">)</span> <span class="op">*</span> <span class="num">100</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t232" href="#t232">232</a></span><span class="t">        <span class="nam">Spop</span> <span class="op">=</span> <span class="nam">np</span><span class="op">.</span><span class="nam">logical_and</span><span class="op">(</span><span class="nam">phase</span> <span class="op">></span> <span class="num">135</span><span class="op">,</span> <span class="nam">phase</span> <span class="op">&lt;</span> <span class="num">225</span><span class="op">)</span><span class="op">.</span><span class="nam">mean</span><span class="op">(</span><span class="op">)</span> <span class="op">*</span> <span class="num">100</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t233" href="#t233">233</a></span><span class="t">        <span class="key">return</span> <span class="nam">Npop</span><span class="op">,</span> <span class="nam">Epop</span><span class="op">,</span> <span class="nam">Wpop</span><span class="op">,</span> <span class="nam">Spop</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t234" href="#t234">234</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t235" href="#t235">235</a></span><span class="t">    <span class="key">def</span> <span class="nam">fix_angles</span><span class="op">(</span><span class="nam">self</span><span class="op">,</span> <span class="nam">dataset</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t236" href="#t236">236</a></span><span class="t">        <span class="nam">values</span> <span class="op">=</span> <span class="nam">np</span><span class="op">.</span><span class="nam">where</span><span class="op">(</span><span class="nam">dataset</span> <span class="op">&lt;</span> <span class="num">0</span><span class="op">,</span> <span class="nam">dataset</span> <span class="op">+</span> <span class="num">360</span><span class="op">,</span> <span class="nam">dataset</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t237" href="#t237">237</a></span><span class="t">        <span class="com"># values = np.where(values > 360, values - 360, values)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t238" href="#t238">238</a></span><span class="t">        <span class="nam">dataset</span> <span class="op">=</span> <span class="nam">pd</span><span class="op">.</span><span class="nam">DataFrame</span><span class="op">(</span><span class="nam">values</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t239" href="#t239">239</a></span><span class="t">        <span class="key">return</span> <span class="nam">dataset</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t240" href="#t240">240</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t22" href="#t22">22</a></span><span class="t"><span class="str">    | Calculate North/East/West/South distribution of sugar puckering backbone torsions.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t23" href="#t23">23</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t24" href="#t24">24</a></span><span class="t"><span class="str">    Args:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t25" href="#t25">25</a></span><span class="t"><span class="str">        input_phaseC_path (str): Path to .ser file for helical parameter 'phaseC'. File type: input. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/backbone/canal_output_phaseC.ser>`_. Accepted formats: ser (edam:format_2330).</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t26" href="#t26">26</a></span><span class="t"><span class="str">        input_phaseW_path (str): Path to .ser file for helical parameter 'phaseW'. File type: input. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/backbone/canal_output_phaseW.ser>`_. Accepted formats: ser (edam:format_2330).</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t27" href="#t27">27</a></span><span class="t"><span class="str">        output_csv_path (str): Path to .csv file where output is saved. File type: output. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/reference/backbone/puckering_ref.csv>`_. Accepted formats: csv (edam:format_3752).</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t28" href="#t28">28</a></span><span class="t"><span class="str">        output_jpg_path (str): Path to .jpg file where output is saved. File type: output. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/reference/backbone/puckering_ref.jpg>`_. Accepted formats: jpg (edam:format_3579).</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t29" href="#t29">29</a></span><span class="t"><span class="str">        properties (dict):</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t30" href="#t30">30</a></span><span class="t"><span class="str">            * **sequence** (*str*) - (None) Nucleic acid sequence corresponding to the input .ser file. Length of sequence is expected to be the same as the total number of columns in the .ser file, minus the index column (even if later on a subset of columns is selected with the *seqpos* option).</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t31" href="#t31">31</a></span><span class="t"><span class="str">            * **helpar_name** (*str*) - (None) helical parameter name.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t32" href="#t32">32</a></span><span class="t"><span class="str">            * **stride** (*int*) - (1000) granularity of the number of snapshots for plotting time series.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t33" href="#t33">33</a></span><span class="t"><span class="str">            * **seqpos** (*list*) - (None) list of sequence positions (columns indices starting by 0) to analyze.  If not specified it will analyse the complete sequence.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t34" href="#t34">34</a></span><span class="t"><span class="str">            * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t35" href="#t35">35</a></span><span class="t"><span class="str">            * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t36" href="#t36">36</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t37" href="#t37">37</a></span><span class="t"><span class="str">    Examples:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t38" href="#t38">38</a></span><span class="t"><span class="str">        This is a use example of how to use the building block from Python::</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t39" href="#t39">39</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t40" href="#t40">40</a></span><span class="t"><span class="str">            from biobb_dna.backbone.puckering import puckering</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t41" href="#t41">41</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t42" href="#t42">42</a></span><span class="t"><span class="str">            prop = {</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t43" href="#t43">43</a></span><span class="t"><span class="str">                'sequence': 'GCAT',</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t44" href="#t44">44</a></span><span class="t"><span class="str">            }</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t45" href="#t45">45</a></span><span class="t"><span class="str">            puckering(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t46" href="#t46">46</a></span><span class="t"><span class="str">                input_phaseC_path='/path/to/phaseC.ser',</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t47" href="#t47">47</a></span><span class="t"><span class="str">                input_phaseW_path='/path/to/phaseW.ser',</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t48" href="#t48">48</a></span><span class="t"><span class="str">                output_csv_path='/path/to/table/output.csv',</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t49" href="#t49">49</a></span><span class="t"><span class="str">                output_jpg_path='/path/to/table/output.jpg',</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t50" href="#t50">50</a></span><span class="t"><span class="str">                properties=prop)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t51" href="#t51">51</a></span><span class="t"><span class="str">    Info:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t52" href="#t52">52</a></span><span class="t"><span class="str">        * wrapped_software:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t53" href="#t53">53</a></span><span class="t"><span class="str">            * name: In house</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t54" href="#t54">54</a></span><span class="t"><span class="str">            * license: Apache-2.0</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t55" href="#t55">55</a></span><span class="t"><span class="str">        * ontology:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t56" href="#t56">56</a></span><span class="t"><span class="str">            * name: EDAM</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t57" href="#t57">57</a></span><span class="t"><span class="str">            * schema: http://edamontology.org/EDAM.owl</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t58" href="#t58">58</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t59" href="#t59">59</a></span><span class="t"><span class="str">    """</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t60" href="#t60">60</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t61" href="#t61">61</a></span><span class="t">    <span class="key">def</span> <span class="nam">__init__</span><span class="op">(</span><span class="nam">self</span><span class="op">,</span> <span class="nam">input_phaseC_path</span><span class="op">,</span> <span class="nam">input_phaseW_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t62" href="#t62">62</a></span><span class="t">                 <span class="nam">output_csv_path</span><span class="op">,</span> <span class="nam">output_jpg_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t63" href="#t63">63</a></span><span class="t">                 <span class="nam">properties</span><span class="op">=</span><span class="key">None</span><span class="op">,</span> <span class="op">**</span><span class="nam">kwargs</span><span class="op">)</span> <span class="op">-></span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t64" href="#t64">64</a></span><span class="t">        <span class="nam">properties</span> <span class="op">=</span> <span class="nam">properties</span> <span class="key">or</span> <span class="op">{</span><span class="op">}</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t65" href="#t65">65</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t66" href="#t66">66</a></span><span class="t">        <span class="com"># Call parent class constructor</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t67" href="#t67">67</a></span><span class="t">        <span class="nam">super</span><span class="op">(</span><span class="op">)</span><span class="op">.</span><span class="nam">__init__</span><span class="op">(</span><span class="nam">properties</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t68" href="#t68">68</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">locals_var_dict</span> <span class="op">=</span> <span class="nam">locals</span><span class="op">(</span><span class="op">)</span><span class="op">.</span><span class="nam">copy</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t69" href="#t69">69</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t70" href="#t70">70</a></span><span class="t">        <span class="com"># Input/Output files</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t71" href="#t71">71</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span> <span class="op">=</span> <span class="op">{</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t72" href="#t72">72</a></span><span class="t">            <span class="str">'in'</span><span class="op">:</span> <span class="op">{</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t73" href="#t73">73</a></span><span class="t">                <span class="str">'input_phaseC_path'</span><span class="op">:</span> <span class="nam">input_phaseC_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t74" href="#t74">74</a></span><span class="t">                <span class="str">'input_phaseW_path'</span><span class="op">:</span> <span class="nam">input_phaseW_path</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t75" href="#t75">75</a></span><span class="t">            <span class="op">}</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t76" href="#t76">76</a></span><span class="t">            <span class="str">'out'</span><span class="op">:</span> <span class="op">{</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t77" href="#t77">77</a></span><span class="t">                <span class="str">'output_csv_path'</span><span class="op">:</span> <span class="nam">output_csv_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t78" href="#t78">78</a></span><span class="t">                <span class="str">'output_jpg_path'</span><span class="op">:</span> <span class="nam">output_jpg_path</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t79" href="#t79">79</a></span><span class="t">            <span class="op">}</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t80" href="#t80">80</a></span><span class="t">        <span class="op">}</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t81" href="#t81">81</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t82" href="#t82">82</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">properties</span> <span class="op">=</span> <span class="nam">properties</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t83" href="#t83">83</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"sequence"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t84" href="#t84">84</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">stride</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t85" href="#t85">85</a></span><span class="t">            <span class="str">"stride"</span><span class="op">,</span> <span class="num">1000</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t86" href="#t86">86</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t87" href="#t87">87</a></span><span class="t">            <span class="str">"seqpos"</span><span class="op">,</span> <span class="key">None</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t88" href="#t88">88</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t89" href="#t89">89</a></span><span class="t">        <span class="com"># Check the properties</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t90" href="#t90">90</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_properties</span><span class="op">(</span><span class="nam">properties</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t91" href="#t91">91</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_arguments</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t92" href="#t92">92</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t93" href="#t93">93</a></span><span class="t">    <span class="op">@</span><span class="nam">launchlogger</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t94" href="#t94">94</a></span><span class="t">    <span class="key">def</span> <span class="nam">launch</span><span class="op">(</span><span class="nam">self</span><span class="op">)</span> <span class="op">-></span> <span class="nam">int</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t95" href="#t95">95</a></span><span class="t">        <span class="str">"""Execute the :class:`Puckering &lt;backbone.puckering.Puckering>` object."""</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t96" href="#t96">96</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t97" href="#t97">97</a></span><span class="t">        <span class="com"># Setup Biobb</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t98" href="#t98">98</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">check_restart</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t99" href="#t99">99</a></span><span class="t">            <span class="key">return</span> <span class="num">0</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t100" href="#t100">100</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">stage_files</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t101" href="#t101">101</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t102" href="#t102">102</a></span><span class="t">        <span class="com"># check sequence</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t103" href="#t103">103</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span> <span class="key">is</span> <span class="key">None</span> <span class="key">or</span> <span class="nam">len</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span><span class="op">)</span> <span class="op">&lt;</span> <span class="num">2</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t104" href="#t104">104</a></span><span class="t">            <span class="key">raise</span> <span class="nam">ValueError</span><span class="op">(</span><span class="str">"sequence is null or too short!"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t105" href="#t105">105</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t106" href="#t106">106</a></span><span class="t">        <span class="com"># check seqpos</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t107" href="#t107">107</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span> <span class="key">is</span> <span class="key">not</span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t108" href="#t108">108</a></span><span class="t">            <span class="key">if</span> <span class="op">(</span><span class="nam">max</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">)</span> <span class="op">></span> <span class="nam">len</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span><span class="op">)</span> <span class="op">-</span> <span class="num">2</span><span class="op">)</span> <span class="key">or</span> <span class="op">(</span><span class="nam">min</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">)</span> <span class="op">&lt;</span> <span class="num">1</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t109" href="#t109">109</a></span><span class="t">                <span class="key">raise</span> <span class="nam">ValueError</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t110" href="#t110">110</a></span><span class="t">                    <span class="str">f"seqpos values must be between 1 and {len(self.sequence) - 2}"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t111" href="#t111">111</a></span><span class="t">            <span class="key">if</span> <span class="key">not</span> <span class="op">(</span><span class="nam">isinstance</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">,</span> <span class="nam">list</span><span class="op">)</span> <span class="key">and</span> <span class="nam">len</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">)</span> <span class="op">></span> <span class="num">1</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t112" href="#t112">112</a></span><span class="t">                <span class="key">raise</span> <span class="nam">ValueError</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t113" href="#t113">113</a></span><span class="t">                    <span class="str">"seqpos must be a list of at least two integers"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t114" href="#t114">114</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t115" href="#t115">115</a></span><span class="t">        <span class="com"># Creating temporary folder</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t116" href="#t116">116</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span> <span class="op">=</span> <span class="nam">fu</span><span class="op">.</span><span class="nam">create_unique_dir</span><span class="op">(</span><span class="nam">prefix</span><span class="op">=</span><span class="str">"backbone_"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t117" href="#t117">117</a></span><span class="t">        <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="str">'Creating %s temporary folder'</span> <span class="op">%</span> <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t118" href="#t118">118</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t119" href="#t119">119</a></span><span class="t">        <span class="com"># Copy input_file_path1 to temporary folder</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t120" href="#t120">120</a></span><span class="t">        <span class="nam">shutil</span><span class="op">.</span><span class="nam">copy</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'input_phaseC_path'</span><span class="op">]</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t121" href="#t121">121</a></span><span class="t">        <span class="nam">shutil</span><span class="op">.</span><span class="nam">copy</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'input_phaseW_path'</span><span class="op">]</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t122" href="#t122">122</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t123" href="#t123">123</a></span><span class="t">        <span class="com"># read input files</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t124" href="#t124">124</a></span><span class="t">        <span class="nam">phaseC</span> <span class="op">=</span> <span class="nam">read_series</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t125" href="#t125">125</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'input_phaseC_path'</span><span class="op">]</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t126" href="#t126">126</a></span><span class="t">            <span class="nam">usecols</span><span class="op">=</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t127" href="#t127">127</a></span><span class="t">        <span class="nam">phaseW</span> <span class="op">=</span> <span class="nam">read_series</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t128" href="#t128">128</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'input_phaseW_path'</span><span class="op">]</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t129" href="#t129">129</a></span><span class="t">            <span class="nam">usecols</span><span class="op">=</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t130" href="#t130">130</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t131" href="#t131">131</a></span><span class="t">        <span class="com"># fix angle range so its not negative</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t132" href="#t132">132</a></span><span class="t">        <span class="nam">phaseC</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">fix_angles</span><span class="op">(</span><span class="nam">phaseC</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t133" href="#t133">133</a></span><span class="t">        <span class="nam">phaseW</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">fix_angles</span><span class="op">(</span><span class="nam">phaseW</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t134" href="#t134">134</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t135" href="#t135">135</a></span><span class="t">        <span class="com"># calculate difference between epsil and zeta parameters</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t136" href="#t136">136</a></span><span class="t">        <span class="nam">xlabels</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">get_xlabels</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t137" href="#t137">137</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t138" href="#t138">138</a></span><span class="t">            <span class="nam">inverse_complement</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t139" href="#t139">139</a></span><span class="t">        <span class="nam">Npop</span><span class="op">,</span> <span class="nam">Epop</span><span class="op">,</span> <span class="nam">Wpop</span><span class="op">,</span> <span class="nam">Spop</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">check_puckering</span><span class="op">(</span><span class="nam">phaseC</span><span class="op">,</span> <span class="nam">phaseW</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t140" href="#t140">140</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t141" href="#t141">141</a></span><span class="t">        <span class="com"># save plot</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t142" href="#t142">142</a></span><span class="t">        <span class="nam">fig</span><span class="op">,</span> <span class="nam">axs</span> <span class="op">=</span> <span class="nam">plt</span><span class="op">.</span><span class="nam">subplots</span><span class="op">(</span><span class="num">1</span><span class="op">,</span> <span class="num">1</span><span class="op">,</span> <span class="nam">dpi</span><span class="op">=</span><span class="num">300</span><span class="op">,</span> <span class="nam">tight_layout</span><span class="op">=</span><span class="key">True</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t143" href="#t143">143</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">bar</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t144" href="#t144">144</a></span><span class="t">            <span class="nam">range</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">xlabels</span><span class="op">)</span><span class="op">)</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t145" href="#t145">145</a></span><span class="t">            <span class="nam">Npop</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t146" href="#t146">146</a></span><span class="t">            <span class="nam">label</span><span class="op">=</span><span class="str">"North"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t147" href="#t147">147</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">bar</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t148" href="#t148">148</a></span><span class="t">            <span class="nam">range</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">xlabels</span><span class="op">)</span><span class="op">)</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t149" href="#t149">149</a></span><span class="t">            <span class="nam">Epop</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t150" href="#t150">150</a></span><span class="t">            <span class="nam">bottom</span><span class="op">=</span><span class="nam">Npop</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t151" href="#t151">151</a></span><span class="t">            <span class="nam">label</span><span class="op">=</span><span class="str">"East"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t152" href="#t152">152</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">bar</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t153" href="#t153">153</a></span><span class="t">            <span class="nam">range</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">xlabels</span><span class="op">)</span><span class="op">)</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t154" href="#t154">154</a></span><span class="t">            <span class="nam">Spop</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t155" href="#t155">155</a></span><span class="t">            <span class="nam">bottom</span><span class="op">=</span><span class="nam">Npop</span><span class="op">+</span><span class="nam">Epop</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t156" href="#t156">156</a></span><span class="t">            <span class="nam">label</span><span class="op">=</span><span class="str">"South"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t157" href="#t157">157</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">bar</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t158" href="#t158">158</a></span><span class="t">            <span class="nam">range</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">xlabels</span><span class="op">)</span><span class="op">)</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t159" href="#t159">159</a></span><span class="t">            <span class="nam">Wpop</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t160" href="#t160">160</a></span><span class="t">            <span class="nam">bottom</span><span class="op">=</span><span class="nam">Npop</span><span class="op">+</span><span class="nam">Epop</span><span class="op">+</span><span class="nam">Spop</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t161" href="#t161">161</a></span><span class="t">            <span class="nam">label</span><span class="op">=</span><span class="str">"West"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t162" href="#t162">162</a></span><span class="t">        <span class="com"># empty bar to divide both sequences</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t163" href="#t163">163</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">bar</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t164" href="#t164">164</a></span><span class="t">            <span class="op">[</span><span class="nam">len</span><span class="op">(</span><span class="nam">phaseC</span><span class="op">.</span><span class="nam">columns</span><span class="op">)</span><span class="op">]</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t165" href="#t165">165</a></span><span class="t">            <span class="op">[</span><span class="num">100</span><span class="op">]</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t166" href="#t166">166</a></span><span class="t">            <span class="nam">color</span><span class="op">=</span><span class="str">'white'</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t167" href="#t167">167</a></span><span class="t">            <span class="nam">label</span><span class="op">=</span><span class="key">None</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t168" href="#t168">168</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">legend</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t169" href="#t169">169</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_xticks</span><span class="op">(</span><span class="nam">range</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">xlabels</span><span class="op">)</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t170" href="#t170">170</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_xticklabels</span><span class="op">(</span><span class="nam">xlabels</span><span class="op">,</span> <span class="nam">rotation</span><span class="op">=</span><span class="num">90</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t171" href="#t171">171</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_xlabel</span><span class="op">(</span><span class="str">"Nucleotide Sequence"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t172" href="#t172">172</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_ylabel</span><span class="op">(</span><span class="str">"Puckering (%)"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t173" href="#t173">173</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_title</span><span class="op">(</span><span class="str">"Nucleotide parameter: Puckering"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t174" href="#t174">174</a></span><span class="t">        <span class="nam">fig</span><span class="op">.</span><span class="nam">savefig</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t175" href="#t175">175</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'out'</span><span class="op">]</span><span class="op">[</span><span class="str">'output_jpg_path'</span><span class="op">]</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t176" href="#t176">176</a></span><span class="t">            <span class="nam">format</span><span class="op">=</span><span class="str">"jpg"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t177" href="#t177">177</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t178" href="#t178">178</a></span><span class="t">        <span class="com"># save table</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t179" href="#t179">179</a></span><span class="t">        <span class="nam">populations</span> <span class="op">=</span> <span class="nam">pd</span><span class="op">.</span><span class="nam">DataFrame</span><span class="op">(</span><span class="op">{</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t180" href="#t180">180</a></span><span class="t">            <span class="str">"Nucleotide"</span><span class="op">:</span> <span class="nam">xlabels</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t181" href="#t181">181</a></span><span class="t">            <span class="str">"North"</span><span class="op">:</span> <span class="nam">Npop</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t182" href="#t182">182</a></span><span class="t">            <span class="str">"East"</span><span class="op">:</span> <span class="nam">Epop</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t183" href="#t183">183</a></span><span class="t">            <span class="str">"West"</span><span class="op">:</span> <span class="nam">Wpop</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t184" href="#t184">184</a></span><span class="t">            <span class="str">"South"</span><span class="op">:</span> <span class="nam">Spop</span><span class="op">}</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t185" href="#t185">185</a></span><span class="t">        <span class="nam">populations</span><span class="op">.</span><span class="nam">to_csv</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t186" href="#t186">186</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'out'</span><span class="op">]</span><span class="op">[</span><span class="str">'output_csv_path'</span><span class="op">]</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t187" href="#t187">187</a></span><span class="t">            <span class="nam">index</span><span class="op">=</span><span class="key">False</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t188" href="#t188">188</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t189" href="#t189">189</a></span><span class="t">        <span class="nam">plt</span><span class="op">.</span><span class="nam">close</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t190" href="#t190">190</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t191" href="#t191">191</a></span><span class="t">        <span class="com"># Remove temporary file(s)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t192" href="#t192">192</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_files</span><span class="op">.</span><span class="nam">extend</span><span class="op">(</span><span class="op">[</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t193" href="#t193">193</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"unique_dir"</span><span class="op">)</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t194" href="#t194">194</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t195" href="#t195">195</a></span><span class="t">        <span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t196" href="#t196">196</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">remove_tmp_files</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t197" href="#t197">197</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t198" href="#t198">198</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_arguments</span><span class="op">(</span><span class="nam">output_files_created</span><span class="op">=</span><span class="key">True</span><span class="op">,</span> <span class="nam">raise_exception</span><span class="op">=</span><span class="key">False</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t199" href="#t199">199</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t200" href="#t200">200</a></span><span class="t">        <span class="key">return</span> <span class="num">0</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t201" href="#t201">201</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t202" href="#t202">202</a></span><span class="t">    <span class="key">def</span> <span class="nam">get_xlabels</span><span class="op">(</span><span class="nam">self</span><span class="op">,</span> <span class="nam">strand1</span><span class="op">,</span> <span class="nam">strand2</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t203" href="#t203">203</a></span><span class="t">        <span class="com"># get list of tetramers, except first and last two bases</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t204" href="#t204">204</a></span><span class="t">        <span class="nam">labelsW</span> <span class="op">=</span> <span class="nam">list</span><span class="op">(</span><span class="nam">strand1</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t205" href="#t205">205</a></span><span class="t">        <span class="nam">labelsW</span><span class="op">[</span><span class="num">0</span><span class="op">]</span> <span class="op">=</span> <span class="str">f"{labelsW[0]}5\'"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t206" href="#t206">206</a></span><span class="t">        <span class="nam">labelsW</span><span class="op">[</span><span class="op">-</span><span class="num">1</span><span class="op">]</span> <span class="op">=</span> <span class="str">f"{labelsW[-1]}3\'"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t207" href="#t207">207</a></span><span class="t">        <span class="nam">labelsW</span> <span class="op">=</span> <span class="op">[</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t208" href="#t208">208</a></span><span class="t">            <span class="str">f"{i}-{j}"</span> <span class="key">for</span> <span class="nam">i</span><span class="op">,</span> <span class="nam">j</span> <span class="key">in</span> <span class="nam">zip</span><span class="op">(</span><span class="nam">labelsW</span><span class="op">,</span> <span class="nam">range</span><span class="op">(</span><span class="num">1</span><span class="op">,</span> <span class="nam">len</span><span class="op">(</span><span class="nam">labelsW</span><span class="op">)</span><span class="op">+</span><span class="num">1</span><span class="op">)</span><span class="op">)</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t209" href="#t209">209</a></span><span class="t">        <span class="nam">labelsC</span> <span class="op">=</span> <span class="nam">list</span><span class="op">(</span><span class="nam">strand2</span><span class="op">)</span><span class="op">[</span><span class="op">:</span><span class="op">:</span><span class="op">-</span><span class="num">1</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t210" href="#t210">210</a></span><span class="t">        <span class="nam">labelsC</span><span class="op">[</span><span class="num">0</span><span class="op">]</span> <span class="op">=</span> <span class="str">f"{labelsC[0]}5\'"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t211" href="#t211">211</a></span><span class="t">        <span class="nam">labelsC</span><span class="op">[</span><span class="op">-</span><span class="num">1</span><span class="op">]</span> <span class="op">=</span> <span class="str">f"{labelsC[-1]}3\'"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t212" href="#t212">212</a></span><span class="t">        <span class="nam">labelsC</span> <span class="op">=</span> <span class="op">[</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t213" href="#t213">213</a></span><span class="t">            <span class="str">f"{i}-{j}"</span> <span class="key">for</span> <span class="nam">i</span><span class="op">,</span> <span class="nam">j</span> <span class="key">in</span> <span class="nam">zip</span><span class="op">(</span><span class="nam">labelsC</span><span class="op">,</span> <span class="nam">range</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">labelsC</span><span class="op">)</span><span class="op">,</span> <span class="num">0</span><span class="op">,</span> <span class="op">-</span><span class="num">1</span><span class="op">)</span><span class="op">)</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t214" href="#t214">214</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t215" href="#t215">215</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span> <span class="key">is</span> <span class="key">not</span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t216" href="#t216">216</a></span><span class="t">            <span class="nam">labelsC</span> <span class="op">=</span> <span class="op">[</span><span class="nam">labelsC</span><span class="op">[</span><span class="nam">i</span><span class="op">]</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t217" href="#t217">217</a></span><span class="t">            <span class="nam">labelsW</span> <span class="op">=</span> <span class="op">[</span><span class="nam">labelsW</span><span class="op">[</span><span class="nam">i</span><span class="op">]</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t218" href="#t218">218</a></span><span class="t">        <span class="nam">xlabels</span> <span class="op">=</span> <span class="nam">labelsW</span> <span class="op">+</span> <span class="op">[</span><span class="str">'-'</span><span class="op">]</span> <span class="op">+</span> <span class="nam">labelsC</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t219" href="#t219">219</a></span><span class="t">        <span class="key">return</span> <span class="nam">xlabels</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t220" href="#t220">220</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t221" href="#t221">221</a></span><span class="t">    <span class="key">def</span> <span class="nam">check_puckering</span><span class="op">(</span><span class="nam">self</span><span class="op">,</span> <span class="nam">phaseC</span><span class="op">,</span> <span class="nam">phaseW</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t222" href="#t222">222</a></span><span class="t">        <span class="nam">separator_df</span> <span class="op">=</span> <span class="nam">pd</span><span class="op">.</span><span class="nam">DataFrame</span><span class="op">(</span><span class="op">{</span><span class="str">"-"</span><span class="op">:</span> <span class="nam">np</span><span class="op">.</span><span class="nam">nan</span><span class="op">}</span><span class="op">,</span> <span class="nam">index</span><span class="op">=</span><span class="nam">range</span><span class="op">(</span><span class="num">1</span><span class="op">,</span> <span class="nam">len</span><span class="op">(</span><span class="nam">phaseC</span><span class="op">)</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t223" href="#t223">223</a></span><span class="t">        <span class="nam">phase</span> <span class="op">=</span> <span class="nam">pd</span><span class="op">.</span><span class="nam">concat</span><span class="op">(</span><span class="op">[</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t224" href="#t224">224</a></span><span class="t">            <span class="nam">phaseW</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t225" href="#t225">225</a></span><span class="t">            <span class="nam">separator_df</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t226" href="#t226">226</a></span><span class="t">            <span class="nam">phaseC</span><span class="op">[</span><span class="nam">phaseC</span><span class="op">.</span><span class="nam">columns</span><span class="op">[</span><span class="op">:</span><span class="op">:</span><span class="op">-</span><span class="num">1</span><span class="op">]</span><span class="op">]</span><span class="op">]</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t227" href="#t227">227</a></span><span class="t">            <span class="nam">axis</span><span class="op">=</span><span class="num">1</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t228" href="#t228">228</a></span><span class="t">        <span class="com"># phase.columns = columns</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t229" href="#t229">229</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t230" href="#t230">230</a></span><span class="t">        <span class="nam">Npop</span> <span class="op">=</span> <span class="nam">np</span><span class="op">.</span><span class="nam">logical_or</span><span class="op">(</span><span class="nam">phase</span> <span class="op">></span> <span class="num">315</span><span class="op">,</span> <span class="nam">phase</span> <span class="op">&lt;</span> <span class="num">45</span><span class="op">)</span><span class="op">.</span><span class="nam">mean</span><span class="op">(</span><span class="op">)</span> <span class="op">*</span> <span class="num">100</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t231" href="#t231">231</a></span><span class="t">        <span class="nam">Epop</span> <span class="op">=</span> <span class="nam">np</span><span class="op">.</span><span class="nam">logical_and</span><span class="op">(</span><span class="nam">phase</span> <span class="op">></span> <span class="num">45</span><span class="op">,</span> <span class="nam">phase</span> <span class="op">&lt;</span> <span class="num">135</span><span class="op">)</span><span class="op">.</span><span class="nam">mean</span><span class="op">(</span><span class="op">)</span> <span class="op">*</span> <span class="num">100</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t232" href="#t232">232</a></span><span class="t">        <span class="nam">Wpop</span> <span class="op">=</span> <span class="nam">np</span><span class="op">.</span><span class="nam">logical_and</span><span class="op">(</span><span class="nam">phase</span> <span class="op">></span> <span class="num">225</span><span class="op">,</span> <span class="nam">phase</span> <span class="op">&lt;</span> <span class="num">315</span><span class="op">)</span><span class="op">.</span><span class="nam">mean</span><span class="op">(</span><span class="op">)</span> <span class="op">*</span> <span class="num">100</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t233" href="#t233">233</a></span><span class="t">        <span class="nam">Spop</span> <span class="op">=</span> <span class="nam">np</span><span class="op">.</span><span class="nam">logical_and</span><span class="op">(</span><span class="nam">phase</span> <span class="op">></span> <span class="num">135</span><span class="op">,</span> <span class="nam">phase</span> <span class="op">&lt;</span> <span class="num">225</span><span class="op">)</span><span class="op">.</span><span class="nam">mean</span><span class="op">(</span><span class="op">)</span> <span class="op">*</span> <span class="num">100</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t234" href="#t234">234</a></span><span class="t">        <span class="key">return</span> <span class="nam">Npop</span><span class="op">,</span> <span class="nam">Epop</span><span class="op">,</span> <span class="nam">Wpop</span><span class="op">,</span> <span class="nam">Spop</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t235" href="#t235">235</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t236" href="#t236">236</a></span><span class="t">    <span class="key">def</span> <span class="nam">fix_angles</span><span class="op">(</span><span class="nam">self</span><span class="op">,</span> <span class="nam">dataset</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t237" href="#t237">237</a></span><span class="t">        <span class="nam">values</span> <span class="op">=</span> <span class="nam">np</span><span class="op">.</span><span class="nam">where</span><span class="op">(</span><span class="nam">dataset</span> <span class="op">&lt;</span> <span class="num">0</span><span class="op">,</span> <span class="nam">dataset</span> <span class="op">+</span> <span class="num">360</span><span class="op">,</span> <span class="nam">dataset</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t238" href="#t238">238</a></span><span class="t">        <span class="com"># values = np.where(values > 360, values - 360, values)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t239" href="#t239">239</a></span><span class="t">        <span class="nam">dataset</span> <span class="op">=</span> <span class="nam">pd</span><span class="op">.</span><span class="nam">DataFrame</span><span class="op">(</span><span class="nam">values</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t240" href="#t240">240</a></span><span class="t">        <span class="key">return</span> <span class="nam">dataset</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t241" href="#t241">241</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t242" href="#t242">242</a></span><span class="t"><span class="key">def</span> <span class="nam">puckering</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t243" href="#t243">243</a></span><span class="t">        <span class="nam">input_phaseC_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span> <span class="nam">input_phaseW_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t244" href="#t244">244</a></span><span class="t">        <span class="nam">output_csv_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span> <span class="nam">output_jpg_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t245" href="#t245">245</a></span><span class="t">        <span class="nam">properties</span><span class="op">:</span> <span class="nam">dict</span> <span class="op">=</span> <span class="key">None</span><span class="op">,</span> <span class="op">**</span><span class="nam">kwargs</span><span class="op">)</span> <span class="op">-></span> <span class="nam">int</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t246" href="#t246">246</a></span><span class="t">    <span class="str">"""Create :class:`Puckering &lt;dna.backbone.puckering.Puckering>` class and</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t247" href="#t247">247</a></span><span class="t"><span class="str">    execute the: meth: `launch() &lt;dna.backbone.puckering.Puckering.launch>` method. """</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t248" href="#t248">248</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t249" href="#t249">249</a></span><span class="t">    <span class="key">return</span> <span class="nam">Puckering</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t250" href="#t250">250</a></span><span class="t">        <span class="nam">input_phaseC_path</span><span class="op">=</span><span class="nam">input_phaseC_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t251" href="#t251">251</a></span><span class="t">        <span class="nam">input_phaseW_path</span><span class="op">=</span><span class="nam">input_phaseW_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t252" href="#t252">252</a></span><span class="t">        <span class="nam">output_csv_path</span><span class="op">=</span><span class="nam">output_csv_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t253" href="#t253">253</a></span><span class="t">        <span class="nam">output_jpg_path</span><span class="op">=</span><span class="nam">output_jpg_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t254" href="#t254">254</a></span><span class="t">        <span class="nam">properties</span><span class="op">=</span><span class="nam">properties</span><span class="op">,</span> <span class="op">**</span><span class="nam">kwargs</span><span class="op">)</span><span class="op">.</span><span class="nam">launch</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t255" href="#t255">255</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t242" href="#t242">242</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t243" href="#t243">243</a></span><span class="t"><span class="key">def</span> <span class="nam">puckering</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t244" href="#t244">244</a></span><span class="t">        <span class="nam">input_phaseC_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span> <span class="nam">input_phaseW_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t245" href="#t245">245</a></span><span class="t">        <span class="nam">output_csv_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span> <span class="nam">output_jpg_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t246" href="#t246">246</a></span><span class="t">        <span class="nam">properties</span><span class="op">:</span> <span class="nam">dict</span> <span class="op">=</span> <span class="key">None</span><span class="op">,</span> <span class="op">**</span><span class="nam">kwargs</span><span class="op">)</span> <span class="op">-></span> <span class="nam">int</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t247" href="#t247">247</a></span><span class="t">    <span class="str">"""Create :class:`Puckering &lt;dna.backbone.puckering.Puckering>` class and</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t248" href="#t248">248</a></span><span class="t"><span class="str">    execute the: meth: `launch() &lt;dna.backbone.puckering.Puckering.launch>` method. """</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t249" href="#t249">249</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t250" href="#t250">250</a></span><span class="t">    <span class="key">return</span> <span class="nam">Puckering</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t251" href="#t251">251</a></span><span class="t">        <span class="nam">input_phaseC_path</span><span class="op">=</span><span class="nam">input_phaseC_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t252" href="#t252">252</a></span><span class="t">        <span class="nam">input_phaseW_path</span><span class="op">=</span><span class="nam">input_phaseW_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t253" href="#t253">253</a></span><span class="t">        <span class="nam">output_csv_path</span><span class="op">=</span><span class="nam">output_csv_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t254" href="#t254">254</a></span><span class="t">        <span class="nam">output_jpg_path</span><span class="op">=</span><span class="nam">output_jpg_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t255" href="#t255">255</a></span><span class="t">        <span class="nam">properties</span><span class="op">=</span><span class="nam">properties</span><span class="op">,</span> <span class="op">**</span><span class="nam">kwargs</span><span class="op">)</span><span class="op">.</span><span class="nam">launch</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t256" href="#t256">256</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t257" href="#t257">257</a></span><span class="t"><span class="key">def</span> <span class="nam">main</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t258" href="#t258">258</a></span><span class="t">    <span class="str">"""Command line execution of this building block. Please check the command line documentation."""</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t259" href="#t259">259</a></span><span class="t">    <span class="nam">parser</span> <span class="op">=</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">ArgumentParser</span><span class="op">(</span><span class="nam">description</span><span class="op">=</span><span class="str">'Calculate North/East/West/South distribution of sugar puckering backbone torsions.'</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t260" href="#t260">260</a></span><span class="t">                                     <span class="nam">formatter_class</span><span class="op">=</span><span class="key">lambda</span> <span class="nam">prog</span><span class="op">:</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">RawTextHelpFormatter</span><span class="op">(</span><span class="nam">prog</span><span class="op">,</span> <span class="nam">width</span><span class="op">=</span><span class="num">99999</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t261" href="#t261">261</a></span><span class="t">    <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--config'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">False</span><span class="op">,</span> <span class="nam">help</span><span class="op">=</span><span class="str">'Configuration file'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t262" href="#t262">262</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t263" href="#t263">263</a></span><span class="t">    <span class="nam">required_args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument_group</span><span class="op">(</span><span class="str">'required arguments'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t264" href="#t264">264</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--input_phaseC_path'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t265" href="#t265">265</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Helical parameter &lt;alphaC> input ser file path. Accepted formats: ser.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t266" href="#t266">266</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--input_phaseW_path'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t267" href="#t267">267</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Helical parameter &lt;alphaW> input ser file path. Accepted formats: ser.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t268" href="#t268">268</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--output_csv_path'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t269" href="#t269">269</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Path to output csv file. Accepted formats: csv.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t270" href="#t270">270</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--output_jpg_path'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t271" href="#t271">271</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Path to output jpg file. Accepted formats: jpg.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t272" href="#t272">272</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t273" href="#t273">273</a></span><span class="t">    <span class="nam">args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">parse_args</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t274" href="#t274">274</a></span><span class="t">    <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="op">=</span> <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="key">or</span> <span class="str">"{}"</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t275" href="#t275">275</a></span><span class="t">    <span class="nam">properties</span> <span class="op">=</span> <span class="nam">settings</span><span class="op">.</span><span class="nam">ConfReader</span><span class="op">(</span><span class="nam">config</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">config</span><span class="op">)</span><span class="op">.</span><span class="nam">get_prop_dic</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t276" href="#t276">276</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t277" href="#t277">277</a></span><span class="t">    <span class="nam">puckering</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t278" href="#t278">278</a></span><span class="t">        <span class="nam">input_phaseC_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_phaseC_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t279" href="#t279">279</a></span><span class="t">        <span class="nam">input_phaseW_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_phaseW_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t280" href="#t280">280</a></span><span class="t">        <span class="nam">output_csv_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">output_csv_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t281" href="#t281">281</a></span><span class="t">        <span class="nam">output_jpg_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">output_jpg_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t282" href="#t282">282</a></span><span class="t">        <span class="nam">properties</span><span class="op">=</span><span class="nam">properties</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t283" href="#t283">283</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t257" href="#t257">257</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t258" href="#t258">258</a></span><span class="t"><span class="key">def</span> <span class="nam">main</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t259" href="#t259">259</a></span><span class="t">    <span class="str">"""Command line execution of this building block. Please check the command line documentation."""</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t260" href="#t260">260</a></span><span class="t">    <span class="nam">parser</span> <span class="op">=</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">ArgumentParser</span><span class="op">(</span><span class="nam">description</span><span class="op">=</span><span class="str">'Calculate North/East/West/South distribution of sugar puckering backbone torsions.'</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t261" href="#t261">261</a></span><span class="t">                                     <span class="nam">formatter_class</span><span class="op">=</span><span class="key">lambda</span> <span class="nam">prog</span><span class="op">:</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">RawTextHelpFormatter</span><span class="op">(</span><span class="nam">prog</span><span class="op">,</span> <span class="nam">width</span><span class="op">=</span><span class="num">99999</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t262" href="#t262">262</a></span><span class="t">    <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--config'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">False</span><span class="op">,</span> <span class="nam">help</span><span class="op">=</span><span class="str">'Configuration file'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t263" href="#t263">263</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t264" href="#t264">264</a></span><span class="t">    <span class="nam">required_args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument_group</span><span class="op">(</span><span class="str">'required arguments'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t265" href="#t265">265</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--input_phaseC_path'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t266" href="#t266">266</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Helical parameter &lt;alphaC> input ser file path. Accepted formats: ser.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t267" href="#t267">267</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--input_phaseW_path'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t268" href="#t268">268</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Helical parameter &lt;alphaW> input ser file path. Accepted formats: ser.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t269" href="#t269">269</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--output_csv_path'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t270" href="#t270">270</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Path to output csv file. Accepted formats: csv.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t271" href="#t271">271</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--output_jpg_path'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t272" href="#t272">272</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Path to output jpg file. Accepted formats: jpg.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t273" href="#t273">273</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t274" href="#t274">274</a></span><span class="t">    <span class="nam">args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">parse_args</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t275" href="#t275">275</a></span><span class="t">    <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="op">=</span> <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="key">or</span> <span class="str">"{}"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t276" href="#t276">276</a></span><span class="t">    <span class="nam">properties</span> <span class="op">=</span> <span class="nam">settings</span><span class="op">.</span><span class="nam">ConfReader</span><span class="op">(</span><span class="nam">config</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">config</span><span class="op">)</span><span class="op">.</span><span class="nam">get_prop_dic</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t277" href="#t277">277</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t278" href="#t278">278</a></span><span class="t">    <span class="nam">puckering</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t279" href="#t279">279</a></span><span class="t">        <span class="nam">input_phaseC_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_phaseC_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t280" href="#t280">280</a></span><span class="t">        <span class="nam">input_phaseW_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_phaseW_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t281" href="#t281">281</a></span><span class="t">        <span class="nam">output_csv_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">output_csv_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t282" href="#t282">282</a></span><span class="t">        <span class="nam">output_jpg_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">output_jpg_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t283" href="#t283">283</a></span><span class="t">        <span class="nam">properties</span><span class="op">=</span><span class="nam">properties</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t284" href="#t284">284</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t285" href="#t285">285</a></span><span class="t"><span class="key">if</span> <span class="nam">__name__</span> <span class="op">==</span> <span class="str">'__main__'</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t286" href="#t286">286</a></span><span class="t">    <span class="nam">main</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t285" href="#t285">285</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t286" href="#t286">286</a></span><span class="t"><span class="key">if</span> <span class="nam">__name__</span> <span class="op">==</span> <span class="str">'__main__'</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t287" href="#t287">287</a></span><span class="t">    <span class="nam">main</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
 </main>
 <footer>
     <div class="content">
@@ -375,7 +376,7 @@ <h2>
             <a class="nav" href="z_74fa14c6d0e940a4___init___py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.5.1">coverage.py v7.5.1</a>,
-            created at 2024-05-07 09:06 +0000
+            created at 2024-05-24 09:29 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_3afbcd666ed82c91___init___py.html b/coverage/z_3afbcd666ed82c91___init___py.html
index 0142d2b7..1b6c8efb 100644
--- a/coverage/z_3afbcd666ed82c91___init___py.html
+++ b/coverage/z_3afbcd666ed82c91___init___py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_3afbcd666ed82c91_dna_averages_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.5.1">coverage.py v7.5.1</a>,
-            created at 2024-05-07 09:06 +0000
+            created at 2024-05-24 09:29 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -91,7 +91,7 @@ <h2>
             <a class="nav" href="z_3afbcd666ed82c91_dna_averages_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.5.1">coverage.py v7.5.1</a>,
-            created at 2024-05-07 09:06 +0000
+            created at 2024-05-24 09:29 +0000
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 </footer>
diff --git a/coverage/z_3afbcd666ed82c91_dna_averages_py.html b/coverage/z_3afbcd666ed82c91_dna_averages_py.html
index f6a918ac..2fc9037b 100644
--- a/coverage/z_3afbcd666ed82c91_dna_averages_py.html
+++ b/coverage/z_3afbcd666ed82c91_dna_averages_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_3afbcd666ed82c91_dna_bimodality_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.5.1">coverage.py v7.5.1</a>,
-            created at 2024-05-07 09:06 +0000
+            created at 2024-05-24 09:29 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -101,244 +101,245 @@ <h2>
     <p class="pln"><span class="n"><a id="t19" href="#t19">19</a></span><span class="t">    <span class="str">"""</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t20" href="#t20">20</a></span><span class="t"><span class="str">    | biobb_dna HelParAverages</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t21" href="#t21">21</a></span><span class="t"><span class="str">    | Load .ser file for a given helical parameter and read each column corresponding to a base calculating average over each one.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t22" href="#t22">22</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t23" href="#t23">23</a></span><span class="t"><span class="str">    Args:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t24" href="#t24">24</a></span><span class="t"><span class="str">        input_ser_path (str): Path to .ser file for helical parameter. File is expected to be a table, with the first column being an index and the rest the helical parameter values for each base/basepair. File type: input. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/dna/canal_output_shift.ser>`_. Accepted formats: ser (edam:format_2330).</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t25" href="#t25">25</a></span><span class="t"><span class="str">        output_csv_path (str): Path to .csv file where output is saved. File type: output. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/reference/dna/shift_avg.csv>`_. Accepted formats: csv (edam:format_3752).</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t26" href="#t26">26</a></span><span class="t"><span class="str">        output_jpg_path (str): Path to .jpg file where output is saved. File type: output. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/reference/dna/shift_avg.jpg>`_. Accepted formats: jpg (edam:format_3579).</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t27" href="#t27">27</a></span><span class="t"><span class="str">        properties (dict):</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t28" href="#t28">28</a></span><span class="t"><span class="str">            * **sequence** (*str*) - (None) Nucleic acid sequence corresponding to the input .ser file. Length of sequence is expected to be the same as the total number of columns in the .ser file, minus the index column (even if later on a subset of columns is selected with the *seqpos* option).</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t29" href="#t29">29</a></span><span class="t"><span class="str">            * **helpar_name** (*str*) - (Optional) helical parameter name.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t30" href="#t30">30</a></span><span class="t"><span class="str">            * **stride** (*int*) - (1000) granularity of the number of snapshots for plotting time series.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t31" href="#t31">31</a></span><span class="t"><span class="str">            * **seqpos** (*list*) - (None) list of sequence positions (columns indices starting by 0) to analyze.  If not specified it will analyse the complete sequence.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t32" href="#t32">32</a></span><span class="t"><span class="str">            * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t33" href="#t33">33</a></span><span class="t"><span class="str">            * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t34" href="#t34">34</a></span><span class="t"><span class="str">    Examples:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t35" href="#t35">35</a></span><span class="t"><span class="str">        This is a use example of how to use the building block from Python::</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t36" href="#t36">36</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t37" href="#t37">37</a></span><span class="t"><span class="str">            from biobb_dna.dna.dna_averages import dna_averages</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t38" href="#t38">38</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t39" href="#t39">39</a></span><span class="t"><span class="str">            prop = {</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t40" href="#t40">40</a></span><span class="t"><span class="str">                'helpar_name': 'twist',</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t41" href="#t41">41</a></span><span class="t"><span class="str">                'seqpos': [1,2],</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t42" href="#t42">42</a></span><span class="t"><span class="str">                'sequence': 'GCAT'</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t43" href="#t43">43</a></span><span class="t"><span class="str">            }</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t44" href="#t44">44</a></span><span class="t"><span class="str">            dna_averages(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t45" href="#t45">45</a></span><span class="t"><span class="str">                input_ser_path='/path/to/twist.ser',</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t46" href="#t46">46</a></span><span class="t"><span class="str">                output_csv_path='/path/to/table/output.csv',</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t47" href="#t47">47</a></span><span class="t"><span class="str">                output_jpg_path='/path/to/table/output.jpg',</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t48" href="#t48">48</a></span><span class="t"><span class="str">                properties=prop)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t49" href="#t49">49</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t50" href="#t50">50</a></span><span class="t"><span class="str">    Info:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t51" href="#t51">51</a></span><span class="t"><span class="str">        * wrapped_software:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t52" href="#t52">52</a></span><span class="t"><span class="str">            * name: In house</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t53" href="#t53">53</a></span><span class="t"><span class="str">            * license: Apache-2.0</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t54" href="#t54">54</a></span><span class="t"><span class="str">        * ontology:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t55" href="#t55">55</a></span><span class="t"><span class="str">            * name: EDAM</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t56" href="#t56">56</a></span><span class="t"><span class="str">            * schema: http://edamontology.org/EDAM.owl</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t57" href="#t57">57</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t58" href="#t58">58</a></span><span class="t"><span class="str">    """</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t59" href="#t59">59</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t60" href="#t60">60</a></span><span class="t">    <span class="key">def</span> <span class="nam">__init__</span><span class="op">(</span><span class="nam">self</span><span class="op">,</span> <span class="nam">input_ser_path</span><span class="op">,</span> <span class="nam">output_csv_path</span><span class="op">,</span> <span class="nam">output_jpg_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t61" href="#t61">61</a></span><span class="t">                 <span class="nam">properties</span><span class="op">=</span><span class="key">None</span><span class="op">,</span> <span class="op">**</span><span class="nam">kwargs</span><span class="op">)</span> <span class="op">-></span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t62" href="#t62">62</a></span><span class="t">        <span class="nam">properties</span> <span class="op">=</span> <span class="nam">properties</span> <span class="key">or</span> <span class="op">{</span><span class="op">}</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t63" href="#t63">63</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t64" href="#t64">64</a></span><span class="t">        <span class="com"># Call parent class constructor</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t65" href="#t65">65</a></span><span class="t">        <span class="nam">super</span><span class="op">(</span><span class="op">)</span><span class="op">.</span><span class="nam">__init__</span><span class="op">(</span><span class="nam">properties</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t66" href="#t66">66</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">locals_var_dict</span> <span class="op">=</span> <span class="nam">locals</span><span class="op">(</span><span class="op">)</span><span class="op">.</span><span class="nam">copy</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t67" href="#t67">67</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t68" href="#t68">68</a></span><span class="t">        <span class="com"># Input/Output files</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t69" href="#t69">69</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span> <span class="op">=</span> <span class="op">{</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t70" href="#t70">70</a></span><span class="t">            <span class="str">'in'</span><span class="op">:</span> <span class="op">{</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t71" href="#t71">71</a></span><span class="t">                <span class="str">'input_ser_path'</span><span class="op">:</span> <span class="nam">input_ser_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t72" href="#t72">72</a></span><span class="t">            <span class="op">}</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t73" href="#t73">73</a></span><span class="t">            <span class="str">'out'</span><span class="op">:</span> <span class="op">{</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t74" href="#t74">74</a></span><span class="t">                <span class="str">'output_csv_path'</span><span class="op">:</span> <span class="nam">output_csv_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t75" href="#t75">75</a></span><span class="t">                <span class="str">'output_jpg_path'</span><span class="op">:</span> <span class="nam">output_jpg_path</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t76" href="#t76">76</a></span><span class="t">            <span class="op">}</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t77" href="#t77">77</a></span><span class="t">        <span class="op">}</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t78" href="#t78">78</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t79" href="#t79">79</a></span><span class="t">        <span class="com"># Properties specific for BB</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t80" href="#t80">80</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">properties</span> <span class="op">=</span> <span class="nam">properties</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t81" href="#t81">81</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"sequence"</span><span class="op">,</span> <span class="key">None</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t82" href="#t82">82</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">stride</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t83" href="#t83">83</a></span><span class="t">            <span class="str">"stride"</span><span class="op">,</span> <span class="num">1000</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t84" href="#t84">84</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t85" href="#t85">85</a></span><span class="t">            <span class="str">"seqpos"</span><span class="op">,</span> <span class="key">None</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t86" href="#t86">86</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">helpar_name</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t87" href="#t87">87</a></span><span class="t">            <span class="str">"helpar_name"</span><span class="op">,</span> <span class="key">None</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t88" href="#t88">88</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t89" href="#t89">89</a></span><span class="t">        <span class="com"># Check the properties</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t90" href="#t90">90</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_properties</span><span class="op">(</span><span class="nam">properties</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t91" href="#t91">91</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_arguments</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t92" href="#t92">92</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t93" href="#t93">93</a></span><span class="t">    <span class="op">@</span><span class="nam">launchlogger</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t94" href="#t94">94</a></span><span class="t">    <span class="key">def</span> <span class="nam">launch</span><span class="op">(</span><span class="nam">self</span><span class="op">)</span> <span class="op">-></span> <span class="nam">int</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t95" href="#t95">95</a></span><span class="t">        <span class="str">"""Execute the :class:`HelParAverages &lt;dna.averages.HelParAverages>` object."""</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t96" href="#t96">96</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t97" href="#t97">97</a></span><span class="t">        <span class="com"># Setup Biobb</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t98" href="#t98">98</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">check_restart</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t99" href="#t99">99</a></span><span class="t">            <span class="key">return</span> <span class="num">0</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t100" href="#t100">100</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">stage_files</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t101" href="#t101">101</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t102" href="#t102">102</a></span><span class="t">        <span class="com"># check sequence</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t103" href="#t103">103</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span> <span class="key">is</span> <span class="key">None</span> <span class="key">or</span> <span class="nam">len</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span><span class="op">)</span> <span class="op">&lt;</span> <span class="num">2</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t104" href="#t104">104</a></span><span class="t">            <span class="key">raise</span> <span class="nam">ValueError</span><span class="op">(</span><span class="str">"sequence is null or too short!"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t105" href="#t105">105</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t106" href="#t106">106</a></span><span class="t">        <span class="com"># get helical parameter from filename if not specified</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t107" href="#t107">107</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">helpar_name</span> <span class="key">is</span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t108" href="#t108">108</a></span><span class="t">            <span class="key">for</span> <span class="nam">hp</span> <span class="key">in</span> <span class="nam">constants</span><span class="op">.</span><span class="nam">helical_parameters</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t109" href="#t109">109</a></span><span class="t">                <span class="nam">ser_name</span> <span class="op">=</span> <span class="nam">Path</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t110" href="#t110">110</a></span><span class="t">                    <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'input_ser_path'</span><span class="op">]</span><span class="op">)</span><span class="op">.</span><span class="nam">name</span><span class="op">.</span><span class="nam">lower</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t111" href="#t111">111</a></span><span class="t">                <span class="key">if</span> <span class="nam">hp</span><span class="op">.</span><span class="nam">lower</span><span class="op">(</span><span class="op">)</span> <span class="key">in</span> <span class="nam">ser_name</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t112" href="#t112">112</a></span><span class="t">                    <span class="nam">self</span><span class="op">.</span><span class="nam">helpar_name</span> <span class="op">=</span> <span class="nam">hp</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t113" href="#t113">113</a></span><span class="t">            <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">helpar_name</span> <span class="key">is</span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t114" href="#t114">114</a></span><span class="t">                <span class="key">raise</span> <span class="nam">ValueError</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t115" href="#t115">115</a></span><span class="t">                    <span class="str">"Helical parameter name can't be inferred from file, "</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t116" href="#t116">116</a></span><span class="t">                    <span class="str">"so it must be specified!"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t117" href="#t117">117</a></span><span class="t">        <span class="key">else</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t118" href="#t118">118</a></span><span class="t">            <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">helpar_name</span> <span class="key">not</span> <span class="key">in</span> <span class="nam">constants</span><span class="op">.</span><span class="nam">helical_parameters</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t119" href="#t119">119</a></span><span class="t">                <span class="key">raise</span> <span class="nam">ValueError</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t120" href="#t120">120</a></span><span class="t">                    <span class="str">"Helical parameter name is invalid! "</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t121" href="#t121">121</a></span><span class="t">                    <span class="str">f"Options: {constants.helical_parameters}"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t122" href="#t122">122</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t123" href="#t123">123</a></span><span class="t">        <span class="com"># get base length and unit from helical parameter name</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t124" href="#t124">124</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">helpar_name</span><span class="op">.</span><span class="nam">lower</span><span class="op">(</span><span class="op">)</span> <span class="key">in</span> <span class="nam">constants</span><span class="op">.</span><span class="nam">hp_basepairs</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t125" href="#t125">125</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">baselen</span> <span class="op">=</span> <span class="num">1</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t126" href="#t126">126</a></span><span class="t">        <span class="key">elif</span> <span class="nam">self</span><span class="op">.</span><span class="nam">helpar_name</span><span class="op">.</span><span class="nam">lower</span><span class="op">(</span><span class="op">)</span> <span class="key">in</span> <span class="nam">constants</span><span class="op">.</span><span class="nam">hp_singlebases</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t127" href="#t127">127</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">baselen</span> <span class="op">=</span> <span class="num">0</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t128" href="#t128">128</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">helpar_name</span> <span class="key">in</span> <span class="nam">constants</span><span class="op">.</span><span class="nam">hp_angular</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t129" href="#t129">129</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">hp_unit</span> <span class="op">=</span> <span class="str">"Degrees"</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t130" href="#t130">130</a></span><span class="t">        <span class="key">else</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t131" href="#t131">131</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">hp_unit</span> <span class="op">=</span> <span class="str">"Angstroms"</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t132" href="#t132">132</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t133" href="#t133">133</a></span><span class="t">        <span class="com"># check seqpos</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t134" href="#t134">134</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span> <span class="key">is</span> <span class="key">not</span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t135" href="#t135">135</a></span><span class="t">            <span class="key">if</span> <span class="op">(</span><span class="nam">max</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">)</span> <span class="op">></span> <span class="nam">len</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span><span class="op">)</span> <span class="op">-</span> <span class="num">2</span><span class="op">)</span> <span class="key">or</span> <span class="op">(</span><span class="nam">min</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">)</span> <span class="op">&lt;</span> <span class="num">1</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t136" href="#t136">136</a></span><span class="t">                <span class="key">raise</span> <span class="nam">ValueError</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t137" href="#t137">137</a></span><span class="t">                    <span class="str">f"seqpos values must be between 1 and {len(self.sequence) - 2}"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t138" href="#t138">138</a></span><span class="t">            <span class="key">if</span> <span class="key">not</span> <span class="op">(</span><span class="nam">isinstance</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">,</span> <span class="nam">list</span><span class="op">)</span> <span class="key">and</span> <span class="nam">len</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">)</span> <span class="op">></span> <span class="num">1</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t139" href="#t139">139</a></span><span class="t">                <span class="key">raise</span> <span class="nam">ValueError</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t140" href="#t140">140</a></span><span class="t">                    <span class="str">"seqpos must be a list of at least two integers"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t141" href="#t141">141</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t142" href="#t142">142</a></span><span class="t">        <span class="com"># Creating temporary folder</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t143" href="#t143">143</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span> <span class="op">=</span> <span class="nam">fu</span><span class="op">.</span><span class="nam">create_unique_dir</span><span class="op">(</span><span class="nam">prefix</span><span class="op">=</span><span class="str">"averages_"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t144" href="#t144">144</a></span><span class="t">        <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="str">'Creating %s temporary folder'</span> <span class="op">%</span> <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t145" href="#t145">145</a></span><span class="t">        <span class="com"># Copy input_file_path1 to temporary folder</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t146" href="#t146">146</a></span><span class="t">        <span class="nam">shutil</span><span class="op">.</span><span class="nam">copy</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'input_ser_path'</span><span class="op">]</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t147" href="#t147">147</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t148" href="#t148">148</a></span><span class="t">        <span class="com"># read input .ser file</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t149" href="#t149">149</a></span><span class="t">        <span class="nam">ser_data</span> <span class="op">=</span> <span class="nam">read_series</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t150" href="#t150">150</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'input_ser_path'</span><span class="op">]</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t151" href="#t151">151</a></span><span class="t">            <span class="nam">usecols</span><span class="op">=</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t152" href="#t152">152</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span> <span class="key">is</span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t153" href="#t153">153</a></span><span class="t">            <span class="nam">ser_data</span> <span class="op">=</span> <span class="nam">ser_data</span><span class="op">[</span><span class="nam">ser_data</span><span class="op">.</span><span class="nam">columns</span><span class="op">[</span><span class="num">1</span><span class="op">:</span><span class="op">-</span><span class="num">1</span><span class="op">]</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t154" href="#t154">154</a></span><span class="t">            <span class="com"># discard first and last base(pairs) from sequence</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t155" href="#t155">155</a></span><span class="t">            <span class="nam">sequence</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span><span class="op">[</span><span class="num">1</span><span class="op">:</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t156" href="#t156">156</a></span><span class="t">            <span class="nam">xlabels</span> <span class="op">=</span> <span class="op">[</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t157" href="#t157">157</a></span><span class="t">                <span class="str">f"{sequence[i:i+1+self.baselen]}"</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t158" href="#t158">158</a></span><span class="t">                <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">range</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">ser_data</span><span class="op">.</span><span class="nam">columns</span><span class="op">)</span> <span class="op">-</span> <span class="nam">self</span><span class="op">.</span><span class="nam">baselen</span><span class="op">)</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t159" href="#t159">159</a></span><span class="t">        <span class="key">else</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t160" href="#t160">160</a></span><span class="t">            <span class="nam">sequence</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t161" href="#t161">161</a></span><span class="t">            <span class="nam">xlabels</span> <span class="op">=</span> <span class="op">[</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t162" href="#t162">162</a></span><span class="t">                <span class="str">f"{sequence[i:i+1+self.baselen]}"</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t163" href="#t163">163</a></span><span class="t">                <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t164" href="#t164">164</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t165" href="#t165">165</a></span><span class="t">        <span class="com"># rename duplicated subunits</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t166" href="#t166">166</a></span><span class="t">        <span class="key">while</span> <span class="nam">any</span><span class="op">(</span><span class="nam">ser_data</span><span class="op">.</span><span class="nam">columns</span><span class="op">.</span><span class="nam">duplicated</span><span class="op">(</span><span class="op">)</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t167" href="#t167">167</a></span><span class="t">            <span class="nam">ser_data</span><span class="op">.</span><span class="nam">columns</span> <span class="op">=</span> <span class="op">[</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t168" href="#t168">168</a></span><span class="t">                <span class="nam">name</span> <span class="key">if</span> <span class="key">not</span> <span class="nam">duplicated</span> <span class="key">else</span> <span class="nam">name</span> <span class="op">+</span> <span class="str">"_dup"</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t169" href="#t169">169</a></span><span class="t">                <span class="key">for</span> <span class="nam">duplicated</span><span class="op">,</span> <span class="nam">name</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t170" href="#t170">170</a></span><span class="t">                <span class="key">in</span> <span class="nam">zip</span><span class="op">(</span><span class="nam">ser_data</span><span class="op">.</span><span class="nam">columns</span><span class="op">.</span><span class="nam">duplicated</span><span class="op">(</span><span class="op">)</span><span class="op">,</span> <span class="nam">ser_data</span><span class="op">.</span><span class="nam">columns</span><span class="op">)</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t171" href="#t171">171</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t172" href="#t172">172</a></span><span class="t">        <span class="com"># write output files for all selected bases</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t173" href="#t173">173</a></span><span class="t">        <span class="nam">means</span> <span class="op">=</span> <span class="nam">ser_data</span><span class="op">.</span><span class="nam">mean</span><span class="op">(</span><span class="nam">axis</span><span class="op">=</span><span class="num">0</span><span class="op">)</span><span class="op">.</span><span class="nam">iloc</span><span class="op">[</span><span class="op">:</span><span class="nam">len</span><span class="op">(</span><span class="nam">xlabels</span><span class="op">)</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t174" href="#t174">174</a></span><span class="t">        <span class="nam">stds</span> <span class="op">=</span> <span class="nam">ser_data</span><span class="op">.</span><span class="nam">std</span><span class="op">(</span><span class="nam">axis</span><span class="op">=</span><span class="num">0</span><span class="op">)</span><span class="op">.</span><span class="nam">iloc</span><span class="op">[</span><span class="op">:</span><span class="nam">len</span><span class="op">(</span><span class="nam">xlabels</span><span class="op">)</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t175" href="#t175">175</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t176" href="#t176">176</a></span><span class="t">        <span class="com"># save plot</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t177" href="#t177">177</a></span><span class="t">        <span class="nam">fig</span><span class="op">,</span> <span class="nam">axs</span> <span class="op">=</span> <span class="nam">plt</span><span class="op">.</span><span class="nam">subplots</span><span class="op">(</span><span class="num">1</span><span class="op">,</span> <span class="num">1</span><span class="op">,</span> <span class="nam">dpi</span><span class="op">=</span><span class="num">300</span><span class="op">,</span> <span class="nam">tight_layout</span><span class="op">=</span><span class="key">True</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t178" href="#t178">178</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">errorbar</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t179" href="#t179">179</a></span><span class="t">            <span class="nam">means</span><span class="op">.</span><span class="nam">index</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t180" href="#t180">180</a></span><span class="t">            <span class="nam">means</span><span class="op">.</span><span class="nam">to_numpy</span><span class="op">(</span><span class="op">)</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t181" href="#t181">181</a></span><span class="t">            <span class="nam">yerr</span><span class="op">=</span><span class="nam">stds</span><span class="op">.</span><span class="nam">to_numpy</span><span class="op">(</span><span class="op">)</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t182" href="#t182">182</a></span><span class="t">            <span class="nam">marker</span><span class="op">=</span><span class="str">"o"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t183" href="#t183">183</a></span><span class="t">            <span class="nam">capsize</span><span class="op">=</span><span class="num">5</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t184" href="#t184">184</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_xticks</span><span class="op">(</span><span class="nam">means</span><span class="op">.</span><span class="nam">index</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t185" href="#t185">185</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_xticklabels</span><span class="op">(</span><span class="nam">xlabels</span><span class="op">,</span> <span class="nam">rotation</span><span class="op">=</span><span class="num">90</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t186" href="#t186">186</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_xlabel</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t187" href="#t187">187</a></span><span class="t">            <span class="str">"Sequence Base Pair "</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t188" href="#t188">188</a></span><span class="t">            <span class="str">f"{'Step' if self.baselen==1 else ''}"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t189" href="#t189">189</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_ylabel</span><span class="op">(</span><span class="str">f"{self.helpar_name.capitalize()} ({self.hp_unit})"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t190" href="#t190">190</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_title</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t191" href="#t191">191</a></span><span class="t">            <span class="str">"Base Pair "</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t192" href="#t192">192</a></span><span class="t">            <span class="str">f"{'Step' if self.baselen==1 else ''} "</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t193" href="#t193">193</a></span><span class="t">            <span class="str">f"Helical Parameter: {self.helpar_name.capitalize()}"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t194" href="#t194">194</a></span><span class="t">        <span class="nam">fig</span><span class="op">.</span><span class="nam">savefig</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t195" href="#t195">195</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'out'</span><span class="op">]</span><span class="op">[</span><span class="str">'output_jpg_path'</span><span class="op">]</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t196" href="#t196">196</a></span><span class="t">            <span class="nam">format</span><span class="op">=</span><span class="str">"jpg"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t197" href="#t197">197</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t198" href="#t198">198</a></span><span class="t">        <span class="com"># save table</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t199" href="#t199">199</a></span><span class="t">        <span class="nam">dataset</span> <span class="op">=</span> <span class="nam">pd</span><span class="op">.</span><span class="nam">DataFrame</span><span class="op">(</span><span class="op">{</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t200" href="#t200">200</a></span><span class="t">            <span class="str">f"Base Pair {'Step' if self.baselen==1 else ''}"</span><span class="op">:</span> <span class="nam">xlabels</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t201" href="#t201">201</a></span><span class="t">            <span class="str">"mean"</span><span class="op">:</span> <span class="nam">means</span><span class="op">.</span><span class="nam">to_numpy</span><span class="op">(</span><span class="op">)</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t202" href="#t202">202</a></span><span class="t">            <span class="str">"std"</span><span class="op">:</span> <span class="nam">stds</span><span class="op">.</span><span class="nam">to_numpy</span><span class="op">(</span><span class="op">)</span><span class="op">}</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t203" href="#t203">203</a></span><span class="t">        <span class="nam">dataset</span><span class="op">.</span><span class="nam">to_csv</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t204" href="#t204">204</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'out'</span><span class="op">]</span><span class="op">[</span><span class="str">'output_csv_path'</span><span class="op">]</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t205" href="#t205">205</a></span><span class="t">            <span class="nam">index</span><span class="op">=</span><span class="key">False</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t206" href="#t206">206</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t207" href="#t207">207</a></span><span class="t">        <span class="nam">plt</span><span class="op">.</span><span class="nam">close</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t208" href="#t208">208</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t209" href="#t209">209</a></span><span class="t">        <span class="com"># Remove temporary file(s)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t210" href="#t210">210</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_files</span><span class="op">.</span><span class="nam">extend</span><span class="op">(</span><span class="op">[</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t211" href="#t211">211</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"unique_dir"</span><span class="op">)</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t212" href="#t212">212</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t213" href="#t213">213</a></span><span class="t">        <span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t214" href="#t214">214</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">remove_tmp_files</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t215" href="#t215">215</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t216" href="#t216">216</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_arguments</span><span class="op">(</span><span class="nam">output_files_created</span><span class="op">=</span><span class="key">True</span><span class="op">,</span> <span class="nam">raise_exception</span><span class="op">=</span><span class="key">False</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t217" href="#t217">217</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t218" href="#t218">218</a></span><span class="t">        <span class="key">return</span> <span class="num">0</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t219" href="#t219">219</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t22" href="#t22">22</a></span><span class="t"><span class="str">    | Calculate average values for each base pair and save them in a .csv file.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t23" href="#t23">23</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t24" href="#t24">24</a></span><span class="t"><span class="str">    Args:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t25" href="#t25">25</a></span><span class="t"><span class="str">        input_ser_path (str): Path to .ser file for helical parameter. File is expected to be a table, with the first column being an index and the rest the helical parameter values for each base/basepair. File type: input. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/dna/canal_output_shift.ser>`_. Accepted formats: ser (edam:format_2330).</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t26" href="#t26">26</a></span><span class="t"><span class="str">        output_csv_path (str): Path to .csv file where output is saved. File type: output. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/reference/dna/shift_avg.csv>`_. Accepted formats: csv (edam:format_3752).</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t27" href="#t27">27</a></span><span class="t"><span class="str">        output_jpg_path (str): Path to .jpg file where output is saved. File type: output. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/reference/dna/shift_avg.jpg>`_. Accepted formats: jpg (edam:format_3579).</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t28" href="#t28">28</a></span><span class="t"><span class="str">        properties (dict):</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t29" href="#t29">29</a></span><span class="t"><span class="str">            * **sequence** (*str*) - (None) Nucleic acid sequence corresponding to the input .ser file. Length of sequence is expected to be the same as the total number of columns in the .ser file, minus the index column (even if later on a subset of columns is selected with the *seqpos* option).</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t30" href="#t30">30</a></span><span class="t"><span class="str">            * **helpar_name** (*str*) - (Optional) helical parameter name.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t31" href="#t31">31</a></span><span class="t"><span class="str">            * **stride** (*int*) - (1000) granularity of the number of snapshots for plotting time series.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t32" href="#t32">32</a></span><span class="t"><span class="str">            * **seqpos** (*list*) - (None) list of sequence positions (columns indices starting by 0) to analyze.  If not specified it will analyse the complete sequence.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t33" href="#t33">33</a></span><span class="t"><span class="str">            * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t34" href="#t34">34</a></span><span class="t"><span class="str">            * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t35" href="#t35">35</a></span><span class="t"><span class="str">    Examples:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t36" href="#t36">36</a></span><span class="t"><span class="str">        This is a use example of how to use the building block from Python::</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t37" href="#t37">37</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t38" href="#t38">38</a></span><span class="t"><span class="str">            from biobb_dna.dna.dna_averages import dna_averages</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t39" href="#t39">39</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t40" href="#t40">40</a></span><span class="t"><span class="str">            prop = {</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t41" href="#t41">41</a></span><span class="t"><span class="str">                'helpar_name': 'twist',</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t42" href="#t42">42</a></span><span class="t"><span class="str">                'seqpos': [1,2],</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t43" href="#t43">43</a></span><span class="t"><span class="str">                'sequence': 'GCAT'</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t44" href="#t44">44</a></span><span class="t"><span class="str">            }</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t45" href="#t45">45</a></span><span class="t"><span class="str">            dna_averages(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t46" href="#t46">46</a></span><span class="t"><span class="str">                input_ser_path='/path/to/twist.ser',</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t47" href="#t47">47</a></span><span class="t"><span class="str">                output_csv_path='/path/to/table/output.csv',</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t48" href="#t48">48</a></span><span class="t"><span class="str">                output_jpg_path='/path/to/table/output.jpg',</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t49" href="#t49">49</a></span><span class="t"><span class="str">                properties=prop)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t50" href="#t50">50</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t51" href="#t51">51</a></span><span class="t"><span class="str">    Info:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t52" href="#t52">52</a></span><span class="t"><span class="str">        * wrapped_software:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t53" href="#t53">53</a></span><span class="t"><span class="str">            * name: In house</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t54" href="#t54">54</a></span><span class="t"><span class="str">            * license: Apache-2.0</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t55" href="#t55">55</a></span><span class="t"><span class="str">        * ontology:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t56" href="#t56">56</a></span><span class="t"><span class="str">            * name: EDAM</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t57" href="#t57">57</a></span><span class="t"><span class="str">            * schema: http://edamontology.org/EDAM.owl</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t58" href="#t58">58</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t59" href="#t59">59</a></span><span class="t"><span class="str">    """</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t60" href="#t60">60</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t61" href="#t61">61</a></span><span class="t">    <span class="key">def</span> <span class="nam">__init__</span><span class="op">(</span><span class="nam">self</span><span class="op">,</span> <span class="nam">input_ser_path</span><span class="op">,</span> <span class="nam">output_csv_path</span><span class="op">,</span> <span class="nam">output_jpg_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t62" href="#t62">62</a></span><span class="t">                 <span class="nam">properties</span><span class="op">=</span><span class="key">None</span><span class="op">,</span> <span class="op">**</span><span class="nam">kwargs</span><span class="op">)</span> <span class="op">-></span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t63" href="#t63">63</a></span><span class="t">        <span class="nam">properties</span> <span class="op">=</span> <span class="nam">properties</span> <span class="key">or</span> <span class="op">{</span><span class="op">}</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t64" href="#t64">64</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t65" href="#t65">65</a></span><span class="t">        <span class="com"># Call parent class constructor</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t66" href="#t66">66</a></span><span class="t">        <span class="nam">super</span><span class="op">(</span><span class="op">)</span><span class="op">.</span><span class="nam">__init__</span><span class="op">(</span><span class="nam">properties</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t67" href="#t67">67</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">locals_var_dict</span> <span class="op">=</span> <span class="nam">locals</span><span class="op">(</span><span class="op">)</span><span class="op">.</span><span class="nam">copy</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t68" href="#t68">68</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t69" href="#t69">69</a></span><span class="t">        <span class="com"># Input/Output files</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t70" href="#t70">70</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span> <span class="op">=</span> <span class="op">{</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t71" href="#t71">71</a></span><span class="t">            <span class="str">'in'</span><span class="op">:</span> <span class="op">{</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t72" href="#t72">72</a></span><span class="t">                <span class="str">'input_ser_path'</span><span class="op">:</span> <span class="nam">input_ser_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t73" href="#t73">73</a></span><span class="t">            <span class="op">}</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t74" href="#t74">74</a></span><span class="t">            <span class="str">'out'</span><span class="op">:</span> <span class="op">{</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t75" href="#t75">75</a></span><span class="t">                <span class="str">'output_csv_path'</span><span class="op">:</span> <span class="nam">output_csv_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t76" href="#t76">76</a></span><span class="t">                <span class="str">'output_jpg_path'</span><span class="op">:</span> <span class="nam">output_jpg_path</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t77" href="#t77">77</a></span><span class="t">            <span class="op">}</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t78" href="#t78">78</a></span><span class="t">        <span class="op">}</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t79" href="#t79">79</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t80" href="#t80">80</a></span><span class="t">        <span class="com"># Properties specific for BB</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t81" href="#t81">81</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">properties</span> <span class="op">=</span> <span class="nam">properties</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t82" href="#t82">82</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"sequence"</span><span class="op">,</span> <span class="key">None</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t83" href="#t83">83</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">stride</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t84" href="#t84">84</a></span><span class="t">            <span class="str">"stride"</span><span class="op">,</span> <span class="num">1000</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t85" href="#t85">85</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t86" href="#t86">86</a></span><span class="t">            <span class="str">"seqpos"</span><span class="op">,</span> <span class="key">None</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t87" href="#t87">87</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">helpar_name</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t88" href="#t88">88</a></span><span class="t">            <span class="str">"helpar_name"</span><span class="op">,</span> <span class="key">None</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t89" href="#t89">89</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t90" href="#t90">90</a></span><span class="t">        <span class="com"># Check the properties</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t91" href="#t91">91</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_properties</span><span class="op">(</span><span class="nam">properties</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t92" href="#t92">92</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_arguments</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t93" href="#t93">93</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t94" href="#t94">94</a></span><span class="t">    <span class="op">@</span><span class="nam">launchlogger</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t95" href="#t95">95</a></span><span class="t">    <span class="key">def</span> <span class="nam">launch</span><span class="op">(</span><span class="nam">self</span><span class="op">)</span> <span class="op">-></span> <span class="nam">int</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t96" href="#t96">96</a></span><span class="t">        <span class="str">"""Execute the :class:`HelParAverages &lt;dna.averages.HelParAverages>` object."""</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t97" href="#t97">97</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t98" href="#t98">98</a></span><span class="t">        <span class="com"># Setup Biobb</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t99" href="#t99">99</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">check_restart</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t100" href="#t100">100</a></span><span class="t">            <span class="key">return</span> <span class="num">0</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t101" href="#t101">101</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">stage_files</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t102" href="#t102">102</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t103" href="#t103">103</a></span><span class="t">        <span class="com"># check sequence</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t104" href="#t104">104</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span> <span class="key">is</span> <span class="key">None</span> <span class="key">or</span> <span class="nam">len</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span><span class="op">)</span> <span class="op">&lt;</span> <span class="num">2</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t105" href="#t105">105</a></span><span class="t">            <span class="key">raise</span> <span class="nam">ValueError</span><span class="op">(</span><span class="str">"sequence is null or too short!"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t106" href="#t106">106</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t107" href="#t107">107</a></span><span class="t">        <span class="com"># get helical parameter from filename if not specified</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t108" href="#t108">108</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">helpar_name</span> <span class="key">is</span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t109" href="#t109">109</a></span><span class="t">            <span class="key">for</span> <span class="nam">hp</span> <span class="key">in</span> <span class="nam">constants</span><span class="op">.</span><span class="nam">helical_parameters</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t110" href="#t110">110</a></span><span class="t">                <span class="nam">ser_name</span> <span class="op">=</span> <span class="nam">Path</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t111" href="#t111">111</a></span><span class="t">                    <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'input_ser_path'</span><span class="op">]</span><span class="op">)</span><span class="op">.</span><span class="nam">name</span><span class="op">.</span><span class="nam">lower</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t112" href="#t112">112</a></span><span class="t">                <span class="key">if</span> <span class="nam">hp</span><span class="op">.</span><span class="nam">lower</span><span class="op">(</span><span class="op">)</span> <span class="key">in</span> <span class="nam">ser_name</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t113" href="#t113">113</a></span><span class="t">                    <span class="nam">self</span><span class="op">.</span><span class="nam">helpar_name</span> <span class="op">=</span> <span class="nam">hp</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t114" href="#t114">114</a></span><span class="t">            <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">helpar_name</span> <span class="key">is</span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t115" href="#t115">115</a></span><span class="t">                <span class="key">raise</span> <span class="nam">ValueError</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t116" href="#t116">116</a></span><span class="t">                    <span class="str">"Helical parameter name can't be inferred from file, "</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t117" href="#t117">117</a></span><span class="t">                    <span class="str">"so it must be specified!"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t118" href="#t118">118</a></span><span class="t">        <span class="key">else</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t119" href="#t119">119</a></span><span class="t">            <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">helpar_name</span> <span class="key">not</span> <span class="key">in</span> <span class="nam">constants</span><span class="op">.</span><span class="nam">helical_parameters</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t120" href="#t120">120</a></span><span class="t">                <span class="key">raise</span> <span class="nam">ValueError</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t121" href="#t121">121</a></span><span class="t">                    <span class="str">"Helical parameter name is invalid! "</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t122" href="#t122">122</a></span><span class="t">                    <span class="str">f"Options: {constants.helical_parameters}"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t123" href="#t123">123</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t124" href="#t124">124</a></span><span class="t">        <span class="com"># get base length and unit from helical parameter name</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t125" href="#t125">125</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">helpar_name</span><span class="op">.</span><span class="nam">lower</span><span class="op">(</span><span class="op">)</span> <span class="key">in</span> <span class="nam">constants</span><span class="op">.</span><span class="nam">hp_basepairs</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t126" href="#t126">126</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">baselen</span> <span class="op">=</span> <span class="num">1</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t127" href="#t127">127</a></span><span class="t">        <span class="key">elif</span> <span class="nam">self</span><span class="op">.</span><span class="nam">helpar_name</span><span class="op">.</span><span class="nam">lower</span><span class="op">(</span><span class="op">)</span> <span class="key">in</span> <span class="nam">constants</span><span class="op">.</span><span class="nam">hp_singlebases</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t128" href="#t128">128</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">baselen</span> <span class="op">=</span> <span class="num">0</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t129" href="#t129">129</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">helpar_name</span> <span class="key">in</span> <span class="nam">constants</span><span class="op">.</span><span class="nam">hp_angular</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t130" href="#t130">130</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">hp_unit</span> <span class="op">=</span> <span class="str">"Degrees"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t131" href="#t131">131</a></span><span class="t">        <span class="key">else</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t132" href="#t132">132</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">hp_unit</span> <span class="op">=</span> <span class="str">"Angstroms"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t133" href="#t133">133</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t134" href="#t134">134</a></span><span class="t">        <span class="com"># check seqpos</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t135" href="#t135">135</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span> <span class="key">is</span> <span class="key">not</span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t136" href="#t136">136</a></span><span class="t">            <span class="key">if</span> <span class="op">(</span><span class="nam">max</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">)</span> <span class="op">></span> <span class="nam">len</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span><span class="op">)</span> <span class="op">-</span> <span class="num">2</span><span class="op">)</span> <span class="key">or</span> <span class="op">(</span><span class="nam">min</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">)</span> <span class="op">&lt;</span> <span class="num">1</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t137" href="#t137">137</a></span><span class="t">                <span class="key">raise</span> <span class="nam">ValueError</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t138" href="#t138">138</a></span><span class="t">                    <span class="str">f"seqpos values must be between 1 and {len(self.sequence) - 2}"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t139" href="#t139">139</a></span><span class="t">            <span class="key">if</span> <span class="key">not</span> <span class="op">(</span><span class="nam">isinstance</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">,</span> <span class="nam">list</span><span class="op">)</span> <span class="key">and</span> <span class="nam">len</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">)</span> <span class="op">></span> <span class="num">1</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t140" href="#t140">140</a></span><span class="t">                <span class="key">raise</span> <span class="nam">ValueError</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t141" href="#t141">141</a></span><span class="t">                    <span class="str">"seqpos must be a list of at least two integers"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t142" href="#t142">142</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t143" href="#t143">143</a></span><span class="t">        <span class="com"># Creating temporary folder</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t144" href="#t144">144</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span> <span class="op">=</span> <span class="nam">fu</span><span class="op">.</span><span class="nam">create_unique_dir</span><span class="op">(</span><span class="nam">prefix</span><span class="op">=</span><span class="str">"averages_"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t145" href="#t145">145</a></span><span class="t">        <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="str">'Creating %s temporary folder'</span> <span class="op">%</span> <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t146" href="#t146">146</a></span><span class="t">        <span class="com"># Copy input_file_path1 to temporary folder</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t147" href="#t147">147</a></span><span class="t">        <span class="nam">shutil</span><span class="op">.</span><span class="nam">copy</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'input_ser_path'</span><span class="op">]</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t148" href="#t148">148</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t149" href="#t149">149</a></span><span class="t">        <span class="com"># read input .ser file</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t150" href="#t150">150</a></span><span class="t">        <span class="nam">ser_data</span> <span class="op">=</span> <span class="nam">read_series</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t151" href="#t151">151</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'input_ser_path'</span><span class="op">]</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t152" href="#t152">152</a></span><span class="t">            <span class="nam">usecols</span><span class="op">=</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t153" href="#t153">153</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span> <span class="key">is</span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t154" href="#t154">154</a></span><span class="t">            <span class="nam">ser_data</span> <span class="op">=</span> <span class="nam">ser_data</span><span class="op">[</span><span class="nam">ser_data</span><span class="op">.</span><span class="nam">columns</span><span class="op">[</span><span class="num">1</span><span class="op">:</span><span class="op">-</span><span class="num">1</span><span class="op">]</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t155" href="#t155">155</a></span><span class="t">            <span class="com"># discard first and last base(pairs) from sequence</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t156" href="#t156">156</a></span><span class="t">            <span class="nam">sequence</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span><span class="op">[</span><span class="num">1</span><span class="op">:</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t157" href="#t157">157</a></span><span class="t">            <span class="nam">xlabels</span> <span class="op">=</span> <span class="op">[</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t158" href="#t158">158</a></span><span class="t">                <span class="str">f"{sequence[i:i+1+self.baselen]}"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t159" href="#t159">159</a></span><span class="t">                <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">range</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">ser_data</span><span class="op">.</span><span class="nam">columns</span><span class="op">)</span> <span class="op">-</span> <span class="nam">self</span><span class="op">.</span><span class="nam">baselen</span><span class="op">)</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t160" href="#t160">160</a></span><span class="t">        <span class="key">else</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t161" href="#t161">161</a></span><span class="t">            <span class="nam">sequence</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t162" href="#t162">162</a></span><span class="t">            <span class="nam">xlabels</span> <span class="op">=</span> <span class="op">[</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t163" href="#t163">163</a></span><span class="t">                <span class="str">f"{sequence[i:i+1+self.baselen]}"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t164" href="#t164">164</a></span><span class="t">                <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t165" href="#t165">165</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t166" href="#t166">166</a></span><span class="t">        <span class="com"># rename duplicated subunits</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t167" href="#t167">167</a></span><span class="t">        <span class="key">while</span> <span class="nam">any</span><span class="op">(</span><span class="nam">ser_data</span><span class="op">.</span><span class="nam">columns</span><span class="op">.</span><span class="nam">duplicated</span><span class="op">(</span><span class="op">)</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t168" href="#t168">168</a></span><span class="t">            <span class="nam">ser_data</span><span class="op">.</span><span class="nam">columns</span> <span class="op">=</span> <span class="op">[</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t169" href="#t169">169</a></span><span class="t">                <span class="nam">name</span> <span class="key">if</span> <span class="key">not</span> <span class="nam">duplicated</span> <span class="key">else</span> <span class="nam">name</span> <span class="op">+</span> <span class="str">"_dup"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t170" href="#t170">170</a></span><span class="t">                <span class="key">for</span> <span class="nam">duplicated</span><span class="op">,</span> <span class="nam">name</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t171" href="#t171">171</a></span><span class="t">                <span class="key">in</span> <span class="nam">zip</span><span class="op">(</span><span class="nam">ser_data</span><span class="op">.</span><span class="nam">columns</span><span class="op">.</span><span class="nam">duplicated</span><span class="op">(</span><span class="op">)</span><span class="op">,</span> <span class="nam">ser_data</span><span class="op">.</span><span class="nam">columns</span><span class="op">)</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t172" href="#t172">172</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t173" href="#t173">173</a></span><span class="t">        <span class="com"># write output files for all selected bases</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t174" href="#t174">174</a></span><span class="t">        <span class="nam">means</span> <span class="op">=</span> <span class="nam">ser_data</span><span class="op">.</span><span class="nam">mean</span><span class="op">(</span><span class="nam">axis</span><span class="op">=</span><span class="num">0</span><span class="op">)</span><span class="op">.</span><span class="nam">iloc</span><span class="op">[</span><span class="op">:</span><span class="nam">len</span><span class="op">(</span><span class="nam">xlabels</span><span class="op">)</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t175" href="#t175">175</a></span><span class="t">        <span class="nam">stds</span> <span class="op">=</span> <span class="nam">ser_data</span><span class="op">.</span><span class="nam">std</span><span class="op">(</span><span class="nam">axis</span><span class="op">=</span><span class="num">0</span><span class="op">)</span><span class="op">.</span><span class="nam">iloc</span><span class="op">[</span><span class="op">:</span><span class="nam">len</span><span class="op">(</span><span class="nam">xlabels</span><span class="op">)</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t176" href="#t176">176</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t177" href="#t177">177</a></span><span class="t">        <span class="com"># save plot</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t178" href="#t178">178</a></span><span class="t">        <span class="nam">fig</span><span class="op">,</span> <span class="nam">axs</span> <span class="op">=</span> <span class="nam">plt</span><span class="op">.</span><span class="nam">subplots</span><span class="op">(</span><span class="num">1</span><span class="op">,</span> <span class="num">1</span><span class="op">,</span> <span class="nam">dpi</span><span class="op">=</span><span class="num">300</span><span class="op">,</span> <span class="nam">tight_layout</span><span class="op">=</span><span class="key">True</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t179" href="#t179">179</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">errorbar</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t180" href="#t180">180</a></span><span class="t">            <span class="nam">means</span><span class="op">.</span><span class="nam">index</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t181" href="#t181">181</a></span><span class="t">            <span class="nam">means</span><span class="op">.</span><span class="nam">to_numpy</span><span class="op">(</span><span class="op">)</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t182" href="#t182">182</a></span><span class="t">            <span class="nam">yerr</span><span class="op">=</span><span class="nam">stds</span><span class="op">.</span><span class="nam">to_numpy</span><span class="op">(</span><span class="op">)</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t183" href="#t183">183</a></span><span class="t">            <span class="nam">marker</span><span class="op">=</span><span class="str">"o"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t184" href="#t184">184</a></span><span class="t">            <span class="nam">capsize</span><span class="op">=</span><span class="num">5</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t185" href="#t185">185</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_xticks</span><span class="op">(</span><span class="nam">means</span><span class="op">.</span><span class="nam">index</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t186" href="#t186">186</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_xticklabels</span><span class="op">(</span><span class="nam">xlabels</span><span class="op">,</span> <span class="nam">rotation</span><span class="op">=</span><span class="num">90</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t187" href="#t187">187</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_xlabel</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t188" href="#t188">188</a></span><span class="t">            <span class="str">"Sequence Base Pair "</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t189" href="#t189">189</a></span><span class="t">            <span class="str">f"{'Step' if self.baselen==1 else ''}"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t190" href="#t190">190</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_ylabel</span><span class="op">(</span><span class="str">f"{self.helpar_name.capitalize()} ({self.hp_unit})"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t191" href="#t191">191</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_title</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t192" href="#t192">192</a></span><span class="t">            <span class="str">"Base Pair "</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t193" href="#t193">193</a></span><span class="t">            <span class="str">f"{'Step' if self.baselen==1 else ''} "</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t194" href="#t194">194</a></span><span class="t">            <span class="str">f"Helical Parameter: {self.helpar_name.capitalize()}"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t195" href="#t195">195</a></span><span class="t">        <span class="nam">fig</span><span class="op">.</span><span class="nam">savefig</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t196" href="#t196">196</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'out'</span><span class="op">]</span><span class="op">[</span><span class="str">'output_jpg_path'</span><span class="op">]</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t197" href="#t197">197</a></span><span class="t">            <span class="nam">format</span><span class="op">=</span><span class="str">"jpg"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t198" href="#t198">198</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t199" href="#t199">199</a></span><span class="t">        <span class="com"># save table</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t200" href="#t200">200</a></span><span class="t">        <span class="nam">dataset</span> <span class="op">=</span> <span class="nam">pd</span><span class="op">.</span><span class="nam">DataFrame</span><span class="op">(</span><span class="op">{</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t201" href="#t201">201</a></span><span class="t">            <span class="str">f"Base Pair {'Step' if self.baselen==1 else ''}"</span><span class="op">:</span> <span class="nam">xlabels</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t202" href="#t202">202</a></span><span class="t">            <span class="str">"mean"</span><span class="op">:</span> <span class="nam">means</span><span class="op">.</span><span class="nam">to_numpy</span><span class="op">(</span><span class="op">)</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t203" href="#t203">203</a></span><span class="t">            <span class="str">"std"</span><span class="op">:</span> <span class="nam">stds</span><span class="op">.</span><span class="nam">to_numpy</span><span class="op">(</span><span class="op">)</span><span class="op">}</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t204" href="#t204">204</a></span><span class="t">        <span class="nam">dataset</span><span class="op">.</span><span class="nam">to_csv</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t205" href="#t205">205</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'out'</span><span class="op">]</span><span class="op">[</span><span class="str">'output_csv_path'</span><span class="op">]</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t206" href="#t206">206</a></span><span class="t">            <span class="nam">index</span><span class="op">=</span><span class="key">False</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t207" href="#t207">207</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t208" href="#t208">208</a></span><span class="t">        <span class="nam">plt</span><span class="op">.</span><span class="nam">close</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t209" href="#t209">209</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t210" href="#t210">210</a></span><span class="t">        <span class="com"># Remove temporary file(s)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t211" href="#t211">211</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_files</span><span class="op">.</span><span class="nam">extend</span><span class="op">(</span><span class="op">[</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t212" href="#t212">212</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"unique_dir"</span><span class="op">)</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t213" href="#t213">213</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t214" href="#t214">214</a></span><span class="t">        <span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t215" href="#t215">215</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">remove_tmp_files</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t216" href="#t216">216</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t217" href="#t217">217</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_arguments</span><span class="op">(</span><span class="nam">output_files_created</span><span class="op">=</span><span class="key">True</span><span class="op">,</span> <span class="nam">raise_exception</span><span class="op">=</span><span class="key">False</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t218" href="#t218">218</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t219" href="#t219">219</a></span><span class="t">        <span class="key">return</span> <span class="num">0</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t220" href="#t220">220</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t221" href="#t221">221</a></span><span class="t"><span class="key">def</span> <span class="nam">dna_averages</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t222" href="#t222">222</a></span><span class="t">        <span class="nam">input_ser_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span> <span class="nam">output_csv_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span> <span class="nam">output_jpg_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t223" href="#t223">223</a></span><span class="t">        <span class="nam">properties</span><span class="op">:</span> <span class="nam">dict</span> <span class="op">=</span> <span class="key">None</span><span class="op">,</span> <span class="op">**</span><span class="nam">kwargs</span><span class="op">)</span> <span class="op">-></span> <span class="nam">int</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t224" href="#t224">224</a></span><span class="t">    <span class="str">"""Create :class:`HelParAverages &lt;dna.dna_averages.HelParAverages>` class and</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t225" href="#t225">225</a></span><span class="t"><span class="str">    execute the :meth:`launch() &lt;dna.dna_averages.HelParAverages.launch>` method."""</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t226" href="#t226">226</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t227" href="#t227">227</a></span><span class="t">    <span class="key">return</span> <span class="nam">HelParAverages</span><span class="op">(</span><span class="nam">input_ser_path</span><span class="op">=</span><span class="nam">input_ser_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t228" href="#t228">228</a></span><span class="t">                          <span class="nam">output_csv_path</span><span class="op">=</span><span class="nam">output_csv_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t229" href="#t229">229</a></span><span class="t">                          <span class="nam">output_jpg_path</span><span class="op">=</span><span class="nam">output_jpg_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t230" href="#t230">230</a></span><span class="t">                          <span class="nam">properties</span><span class="op">=</span><span class="nam">properties</span><span class="op">,</span> <span class="op">**</span><span class="nam">kwargs</span><span class="op">)</span><span class="op">.</span><span class="nam">launch</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t231" href="#t231">231</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t221" href="#t221">221</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t222" href="#t222">222</a></span><span class="t"><span class="key">def</span> <span class="nam">dna_averages</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t223" href="#t223">223</a></span><span class="t">        <span class="nam">input_ser_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span> <span class="nam">output_csv_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span> <span class="nam">output_jpg_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t224" href="#t224">224</a></span><span class="t">        <span class="nam">properties</span><span class="op">:</span> <span class="nam">dict</span> <span class="op">=</span> <span class="key">None</span><span class="op">,</span> <span class="op">**</span><span class="nam">kwargs</span><span class="op">)</span> <span class="op">-></span> <span class="nam">int</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t225" href="#t225">225</a></span><span class="t">    <span class="str">"""Create :class:`HelParAverages &lt;dna.dna_averages.HelParAverages>` class and</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t226" href="#t226">226</a></span><span class="t"><span class="str">    execute the :meth:`launch() &lt;dna.dna_averages.HelParAverages.launch>` method."""</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t227" href="#t227">227</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t228" href="#t228">228</a></span><span class="t">    <span class="key">return</span> <span class="nam">HelParAverages</span><span class="op">(</span><span class="nam">input_ser_path</span><span class="op">=</span><span class="nam">input_ser_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t229" href="#t229">229</a></span><span class="t">                          <span class="nam">output_csv_path</span><span class="op">=</span><span class="nam">output_csv_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t230" href="#t230">230</a></span><span class="t">                          <span class="nam">output_jpg_path</span><span class="op">=</span><span class="nam">output_jpg_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t231" href="#t231">231</a></span><span class="t">                          <span class="nam">properties</span><span class="op">=</span><span class="nam">properties</span><span class="op">,</span> <span class="op">**</span><span class="nam">kwargs</span><span class="op">)</span><span class="op">.</span><span class="nam">launch</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t232" href="#t232">232</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t233" href="#t233">233</a></span><span class="t"><span class="key">def</span> <span class="nam">main</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t234" href="#t234">234</a></span><span class="t">    <span class="str">"""Command line execution of this building block. Please check the command line documentation."""</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t235" href="#t235">235</a></span><span class="t">    <span class="nam">parser</span> <span class="op">=</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">ArgumentParser</span><span class="op">(</span><span class="nam">description</span><span class="op">=</span><span class="str">'Load helical parameter file and calculate average values for each base pair.'</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t236" href="#t236">236</a></span><span class="t">                                     <span class="nam">formatter_class</span><span class="op">=</span><span class="key">lambda</span> <span class="nam">prog</span><span class="op">:</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">RawTextHelpFormatter</span><span class="op">(</span><span class="nam">prog</span><span class="op">,</span> <span class="nam">width</span><span class="op">=</span><span class="num">99999</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t237" href="#t237">237</a></span><span class="t">    <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--config'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">False</span><span class="op">,</span> <span class="nam">help</span><span class="op">=</span><span class="str">'Configuration file'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t238" href="#t238">238</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t239" href="#t239">239</a></span><span class="t">    <span class="nam">required_args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument_group</span><span class="op">(</span><span class="str">'required arguments'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t240" href="#t240">240</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--input_ser_path'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t241" href="#t241">241</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Helical parameter input ser file path. Accepted formats: ser.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t242" href="#t242">242</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--output_csv_path'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t243" href="#t243">243</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Path to output csv file. Accepted formats: csv.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t244" href="#t244">244</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--output_jpg_path'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t245" href="#t245">245</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Path to output jpg file. Accepted formats: jpg.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t246" href="#t246">246</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t247" href="#t247">247</a></span><span class="t">    <span class="nam">args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">parse_args</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t248" href="#t248">248</a></span><span class="t">    <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="op">=</span> <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="key">or</span> <span class="str">"{}"</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t249" href="#t249">249</a></span><span class="t">    <span class="nam">properties</span> <span class="op">=</span> <span class="nam">settings</span><span class="op">.</span><span class="nam">ConfReader</span><span class="op">(</span><span class="nam">config</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">config</span><span class="op">)</span><span class="op">.</span><span class="nam">get_prop_dic</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t250" href="#t250">250</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t251" href="#t251">251</a></span><span class="t">    <span class="nam">dna_averages</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t252" href="#t252">252</a></span><span class="t">        <span class="nam">input_ser_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_ser_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t253" href="#t253">253</a></span><span class="t">        <span class="nam">output_csv_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">output_csv_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t254" href="#t254">254</a></span><span class="t">        <span class="nam">output_jpg_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">output_jpg_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t255" href="#t255">255</a></span><span class="t">        <span class="nam">properties</span><span class="op">=</span><span class="nam">properties</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t256" href="#t256">256</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t233" href="#t233">233</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t234" href="#t234">234</a></span><span class="t"><span class="key">def</span> <span class="nam">main</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t235" href="#t235">235</a></span><span class="t">    <span class="str">"""Command line execution of this building block. Please check the command line documentation."""</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t236" href="#t236">236</a></span><span class="t">    <span class="nam">parser</span> <span class="op">=</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">ArgumentParser</span><span class="op">(</span><span class="nam">description</span><span class="op">=</span><span class="str">'Load helical parameter file and calculate average values for each base pair.'</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t237" href="#t237">237</a></span><span class="t">                                     <span class="nam">formatter_class</span><span class="op">=</span><span class="key">lambda</span> <span class="nam">prog</span><span class="op">:</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">RawTextHelpFormatter</span><span class="op">(</span><span class="nam">prog</span><span class="op">,</span> <span class="nam">width</span><span class="op">=</span><span class="num">99999</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t238" href="#t238">238</a></span><span class="t">    <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--config'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">False</span><span class="op">,</span> <span class="nam">help</span><span class="op">=</span><span class="str">'Configuration file'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t239" href="#t239">239</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t240" href="#t240">240</a></span><span class="t">    <span class="nam">required_args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument_group</span><span class="op">(</span><span class="str">'required arguments'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t241" href="#t241">241</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--input_ser_path'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t242" href="#t242">242</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Helical parameter input ser file path. Accepted formats: ser.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t243" href="#t243">243</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--output_csv_path'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t244" href="#t244">244</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Path to output csv file. Accepted formats: csv.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t245" href="#t245">245</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--output_jpg_path'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t246" href="#t246">246</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Path to output jpg file. Accepted formats: jpg.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t247" href="#t247">247</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t248" href="#t248">248</a></span><span class="t">    <span class="nam">args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">parse_args</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t249" href="#t249">249</a></span><span class="t">    <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="op">=</span> <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="key">or</span> <span class="str">"{}"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t250" href="#t250">250</a></span><span class="t">    <span class="nam">properties</span> <span class="op">=</span> <span class="nam">settings</span><span class="op">.</span><span class="nam">ConfReader</span><span class="op">(</span><span class="nam">config</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">config</span><span class="op">)</span><span class="op">.</span><span class="nam">get_prop_dic</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t251" href="#t251">251</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t252" href="#t252">252</a></span><span class="t">    <span class="nam">dna_averages</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t253" href="#t253">253</a></span><span class="t">        <span class="nam">input_ser_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_ser_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t254" href="#t254">254</a></span><span class="t">        <span class="nam">output_csv_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">output_csv_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t255" href="#t255">255</a></span><span class="t">        <span class="nam">output_jpg_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">output_jpg_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t256" href="#t256">256</a></span><span class="t">        <span class="nam">properties</span><span class="op">=</span><span class="nam">properties</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t257" href="#t257">257</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t258" href="#t258">258</a></span><span class="t"><span class="key">if</span> <span class="nam">__name__</span> <span class="op">==</span> <span class="str">'__main__'</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t259" href="#t259">259</a></span><span class="t">    <span class="nam">main</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t258" href="#t258">258</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t259" href="#t259">259</a></span><span class="t"><span class="key">if</span> <span class="nam">__name__</span> <span class="op">==</span> <span class="str">'__main__'</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t260" href="#t260">260</a></span><span class="t">    <span class="nam">main</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
 </main>
 <footer>
     <div class="content">
@@ -348,7 +349,7 @@ <h2>
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             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.5.1">coverage.py v7.5.1</a>,
-            created at 2024-05-07 09:06 +0000
+            created at 2024-05-24 09:29 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_3afbcd666ed82c91_dna_bimodality_py.html b/coverage/z_3afbcd666ed82c91_dna_bimodality_py.html
index 66f909c7..2433657c 100644
--- a/coverage/z_3afbcd666ed82c91_dna_bimodality_py.html
+++ b/coverage/z_3afbcd666ed82c91_dna_bimodality_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_3afbcd666ed82c91_dna_timeseries_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.5.1">coverage.py v7.5.1</a>,
-            created at 2024-05-07 09:06 +0000
+            created at 2024-05-24 09:29 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -106,325 +106,326 @@ <h2>
     <p class="pln"><span class="n"><a id="t24" href="#t24">24</a></span><span class="t">    <span class="str">"""</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t25" href="#t25">25</a></span><span class="t"><span class="str">    | biobb_dna HelParBimodality</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t26" href="#t26">26</a></span><span class="t"><span class="str">    | Determine binormality/bimodality from a helical parameter series dataset.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t27" href="#t27">27</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t28" href="#t28">28</a></span><span class="t"><span class="str">    Args:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t29" href="#t29">29</a></span><span class="t"><span class="str">        input_csv_file (str): Path to .csv file with helical parameter series. If `input_zip_file` is passed, this should be just the filename of the .csv file inside .zip.  File type: input. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/dna/series_shift_AT.csv>`_. Accepted formats: csv (edam:format_3752).</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t30" href="#t30">30</a></span><span class="t"><span class="str">        input_zip_file (str) (Optional): .zip file containing the `input_csv_file` .csv file. File type: input. Accepted formats: zip (edam:format_3987).</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t31" href="#t31">31</a></span><span class="t"><span class="str">        output_csv_path (str): Path to .csv file where output is saved. File type: output. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/reference/dna/AT_shift_bimod.csv>`_. Accepted formats: csv (edam:format_3752).</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t32" href="#t32">32</a></span><span class="t"><span class="str">        output_jpg_path (str): Path to .jpg file where output is saved. File type: output. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/reference/dna/AT_shift_bimod.jpg>`_. Accepted formats: jpg (edam:format_3579).</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t33" href="#t33">33</a></span><span class="t"><span class="str">        properties (dict):</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t34" href="#t34">34</a></span><span class="t"><span class="str">            * **helpar_name** (*str*) - (Optional) helical parameter name.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t35" href="#t35">35</a></span><span class="t"><span class="str">            * **confidence_level** (*float*) - (5.0) Confidence level for Byes Factor test (in percentage).</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t36" href="#t36">36</a></span><span class="t"><span class="str">            * **max_iter** (*int*) - (400) Number of maximum iterations for EM algorithm.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t37" href="#t37">37</a></span><span class="t"><span class="str">            * **tol** (*float*) - (1e-5) Tolerance value for EM algorithm.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t38" href="#t38">38</a></span><span class="t"><span class="str">            * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t39" href="#t39">39</a></span><span class="t"><span class="str">            * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.1</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t40" href="#t40">40</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t41" href="#t41">41</a></span><span class="t"><span class="str">    Examples:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t42" href="#t42">42</a></span><span class="t"><span class="str">        This is a use example of how to use the building block from Python::</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t43" href="#t43">43</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t44" href="#t44">44</a></span><span class="t"><span class="str">            from biobb_dna.dna.dna_bimodality import dna_bimodality</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t45" href="#t45">45</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t46" href="#t46">46</a></span><span class="t"><span class="str">            prop = {</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t47" href="#t47">47</a></span><span class="t"><span class="str">                'max_iter': 500,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t48" href="#t48">48</a></span><span class="t"><span class="str">            }</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t49" href="#t49">49</a></span><span class="t"><span class="str">            dna_bimodality(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t50" href="#t50">50</a></span><span class="t"><span class="str">                input_csv_file='filename.csv',</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t51" href="#t51">51</a></span><span class="t"><span class="str">                input_zip_file='/path/to/input.zip',</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t52" href="#t52">52</a></span><span class="t"><span class="str">                output_csv_path='/path/to/output.csv',</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t53" href="#t53">53</a></span><span class="t"><span class="str">                output_jpg_path='/path/to/output.jpg',</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t54" href="#t54">54</a></span><span class="t"><span class="str">                properties=prop)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t55" href="#t55">55</a></span><span class="t"><span class="str">    Info:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t56" href="#t56">56</a></span><span class="t"><span class="str">        * wrapped_software:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t57" href="#t57">57</a></span><span class="t"><span class="str">            * name: In house</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t58" href="#t58">58</a></span><span class="t"><span class="str">            * license: Apache-2.0</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t59" href="#t59">59</a></span><span class="t"><span class="str">        * ontology:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t60" href="#t60">60</a></span><span class="t"><span class="str">            * name: EDAM</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t61" href="#t61">61</a></span><span class="t"><span class="str">            * schema: http://edamontology.org/EDAM.owl</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t62" href="#t62">62</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t63" href="#t63">63</a></span><span class="t"><span class="str">    """</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t64" href="#t64">64</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t65" href="#t65">65</a></span><span class="t">    <span class="key">def</span> <span class="nam">__init__</span><span class="op">(</span><span class="nam">self</span><span class="op">,</span> <span class="nam">input_csv_file</span><span class="op">,</span> <span class="nam">output_csv_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t66" href="#t66">66</a></span><span class="t">                 <span class="nam">output_jpg_path</span><span class="op">,</span> <span class="nam">input_zip_file</span><span class="op">=</span><span class="key">None</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t67" href="#t67">67</a></span><span class="t">                 <span class="nam">properties</span><span class="op">=</span><span class="key">None</span><span class="op">,</span> <span class="op">**</span><span class="nam">kwargs</span><span class="op">)</span> <span class="op">-></span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t68" href="#t68">68</a></span><span class="t">        <span class="nam">properties</span> <span class="op">=</span> <span class="nam">properties</span> <span class="key">or</span> <span class="op">{</span><span class="op">}</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t69" href="#t69">69</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t70" href="#t70">70</a></span><span class="t">        <span class="com"># Call parent class constructor</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t71" href="#t71">71</a></span><span class="t">        <span class="nam">super</span><span class="op">(</span><span class="op">)</span><span class="op">.</span><span class="nam">__init__</span><span class="op">(</span><span class="nam">properties</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t72" href="#t72">72</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">locals_var_dict</span> <span class="op">=</span> <span class="nam">locals</span><span class="op">(</span><span class="op">)</span><span class="op">.</span><span class="nam">copy</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t73" href="#t73">73</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t74" href="#t74">74</a></span><span class="t">        <span class="com"># Input/Output files</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t75" href="#t75">75</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span> <span class="op">=</span> <span class="op">{</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t76" href="#t76">76</a></span><span class="t">            <span class="str">'in'</span><span class="op">:</span> <span class="op">{</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t77" href="#t77">77</a></span><span class="t">                <span class="str">'input_csv_file'</span><span class="op">:</span> <span class="nam">input_csv_file</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t78" href="#t78">78</a></span><span class="t">                <span class="str">'input_zip_file'</span><span class="op">:</span> <span class="nam">input_zip_file</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t79" href="#t79">79</a></span><span class="t">            <span class="op">}</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t80" href="#t80">80</a></span><span class="t">            <span class="str">'out'</span><span class="op">:</span> <span class="op">{</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t81" href="#t81">81</a></span><span class="t">                <span class="str">'output_csv_path'</span><span class="op">:</span> <span class="nam">output_csv_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t82" href="#t82">82</a></span><span class="t">                <span class="str">'output_jpg_path'</span><span class="op">:</span> <span class="nam">output_jpg_path</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t83" href="#t83">83</a></span><span class="t">            <span class="op">}</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t84" href="#t84">84</a></span><span class="t">        <span class="op">}</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t85" href="#t85">85</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t86" href="#t86">86</a></span><span class="t">        <span class="com"># Properties specific for BB</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t87" href="#t87">87</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">confidence_level</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t88" href="#t88">88</a></span><span class="t">            <span class="str">"confidence_level"</span><span class="op">,</span> <span class="num">5.0</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t89" href="#t89">89</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">max_iter</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t90" href="#t90">90</a></span><span class="t">            <span class="str">"max_iter"</span><span class="op">,</span> <span class="num">400</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t91" href="#t91">91</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">tol</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t92" href="#t92">92</a></span><span class="t">            <span class="str">"tol"</span><span class="op">,</span> <span class="num">1e-5</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t93" href="#t93">93</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">helpar_name</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"helpar_name"</span><span class="op">,</span> <span class="key">None</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t94" href="#t94">94</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">properties</span> <span class="op">=</span> <span class="nam">properties</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t95" href="#t95">95</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t96" href="#t96">96</a></span><span class="t">        <span class="com"># Check the properties</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t97" href="#t97">97</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_properties</span><span class="op">(</span><span class="nam">properties</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t98" href="#t98">98</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_arguments</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t99" href="#t99">99</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t100" href="#t100">100</a></span><span class="t">    <span class="op">@</span><span class="nam">launchlogger</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t101" href="#t101">101</a></span><span class="t">    <span class="key">def</span> <span class="nam">launch</span><span class="op">(</span><span class="nam">self</span><span class="op">)</span> <span class="op">-></span> <span class="nam">int</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t102" href="#t102">102</a></span><span class="t">        <span class="str">"""Execute the :class:`HelParBimodality &lt;dna.dna_bimodality.HelParBimodality>` object."""</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t103" href="#t103">103</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t104" href="#t104">104</a></span><span class="t">        <span class="com"># Setup Biobb</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t105" href="#t105">105</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">check_restart</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t106" href="#t106">106</a></span><span class="t">            <span class="key">return</span> <span class="num">0</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t107" href="#t107">107</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">stage_files</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t108" href="#t108">108</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t109" href="#t109">109</a></span><span class="t">        <span class="com"># get helical parameter from filename if not specified</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t110" href="#t110">110</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">helpar_name</span> <span class="key">is</span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t111" href="#t111">111</a></span><span class="t">            <span class="key">for</span> <span class="nam">hp</span> <span class="key">in</span> <span class="nam">constants</span><span class="op">.</span><span class="nam">helical_parameters</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t112" href="#t112">112</a></span><span class="t">                <span class="nam">input_zip_path</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'input_zip_file'</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t113" href="#t113">113</a></span><span class="t">                <span class="key">if</span> <span class="nam">input_zip_path</span> <span class="key">is</span> <span class="key">not</span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t114" href="#t114">114</a></span><span class="t">                    <span class="nam">condition_2</span> <span class="op">=</span> <span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t115" href="#t115">115</a></span><span class="t">                        <span class="nam">hp</span><span class="op">.</span><span class="nam">lower</span><span class="op">(</span><span class="op">)</span> <span class="key">in</span> <span class="nam">Path</span><span class="op">(</span><span class="nam">input_zip_path</span><span class="op">)</span><span class="op">.</span><span class="nam">name</span><span class="op">.</span><span class="nam">lower</span><span class="op">(</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t116" href="#t116">116</a></span><span class="t">                <span class="key">else</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t117" href="#t117">117</a></span><span class="t">                    <span class="nam">condition_2</span> <span class="op">=</span> <span class="key">False</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t118" href="#t118">118</a></span><span class="t">                <span class="nam">condition_1</span> <span class="op">=</span> <span class="nam">hp</span><span class="op">.</span><span class="nam">lower</span><span class="op">(</span><span class="op">)</span> <span class="key">in</span> <span class="nam">Path</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t119" href="#t119">119</a></span><span class="t">                    <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'input_csv_file'</span><span class="op">]</span><span class="op">)</span><span class="op">.</span><span class="nam">name</span><span class="op">.</span><span class="nam">lower</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t120" href="#t120">120</a></span><span class="t">                <span class="key">if</span> <span class="op">(</span><span class="nam">condition_1</span> <span class="key">or</span> <span class="nam">condition_2</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t121" href="#t121">121</a></span><span class="t">                    <span class="nam">self</span><span class="op">.</span><span class="nam">helpar_name</span> <span class="op">=</span> <span class="nam">hp</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t122" href="#t122">122</a></span><span class="t">            <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">helpar_name</span> <span class="key">is</span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t123" href="#t123">123</a></span><span class="t">                <span class="key">raise</span> <span class="nam">ValueError</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t124" href="#t124">124</a></span><span class="t">                    <span class="str">"Helical parameter name can't be inferred from file, "</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t125" href="#t125">125</a></span><span class="t">                    <span class="str">"so it must be specified!"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t126" href="#t126">126</a></span><span class="t">        <span class="key">else</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t127" href="#t127">127</a></span><span class="t">            <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">helpar_name</span> <span class="key">not</span> <span class="key">in</span> <span class="nam">constants</span><span class="op">.</span><span class="nam">helical_parameters</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t128" href="#t128">128</a></span><span class="t">                <span class="key">raise</span> <span class="nam">ValueError</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t129" href="#t129">129</a></span><span class="t">                    <span class="str">"Helical parameter name is invalid! "</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t130" href="#t130">130</a></span><span class="t">                    <span class="str">f"Options: {constants.helical_parameters}"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t131" href="#t131">131</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t132" href="#t132">132</a></span><span class="t">        <span class="com"># get  unit from helical parameter name</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t133" href="#t133">133</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">helpar_name</span> <span class="key">in</span> <span class="nam">constants</span><span class="op">.</span><span class="nam">hp_angular</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t134" href="#t134">134</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">hp_unit</span> <span class="op">=</span> <span class="str">"Degrees"</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t135" href="#t135">135</a></span><span class="t">        <span class="key">else</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t136" href="#t136">136</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">hp_unit</span> <span class="op">=</span> <span class="str">"Angstroms"</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t137" href="#t137">137</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t138" href="#t138">138</a></span><span class="t">        <span class="com"># resolve output</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t139" href="#t139">139</a></span><span class="t">        <span class="nam">output_csv_path</span> <span class="op">=</span> <span class="nam">Path</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t140" href="#t140">140</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'out'</span><span class="op">]</span><span class="op">[</span><span class="str">'output_csv_path'</span><span class="op">]</span><span class="op">)</span><span class="op">.</span><span class="nam">resolve</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t141" href="#t141">141</a></span><span class="t">        <span class="nam">output_jpg_path</span> <span class="op">=</span> <span class="nam">Path</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t142" href="#t142">142</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'out'</span><span class="op">]</span><span class="op">[</span><span class="str">'output_jpg_path'</span><span class="op">]</span><span class="op">)</span><span class="op">.</span><span class="nam">resolve</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t143" href="#t143">143</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t144" href="#t144">144</a></span><span class="t">        <span class="com"># Creating temporary folder</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t145" href="#t145">145</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span> <span class="op">=</span> <span class="nam">fu</span><span class="op">.</span><span class="nam">create_unique_dir</span><span class="op">(</span><span class="nam">prefix</span><span class="op">=</span><span class="str">"bimodality_"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t146" href="#t146">146</a></span><span class="t">        <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="str">'Creating %s temporary folder'</span> <span class="op">%</span> <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t147" href="#t147">147</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t148" href="#t148">148</a></span><span class="t">        <span class="com"># read input</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t149" href="#t149">149</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'input_zip_file'</span><span class="op">]</span> <span class="key">is</span> <span class="key">not</span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t150" href="#t150">150</a></span><span class="t">            <span class="com"># Copy input_file_path1 to temporary folder</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t151" href="#t151">151</a></span><span class="t">            <span class="nam">shutil</span><span class="op">.</span><span class="nam">copy</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'input_zip_file'</span><span class="op">]</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t152" href="#t152">152</a></span><span class="t">            <span class="com"># if zipfile is specified, extract to temporary folder</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t153" href="#t153">153</a></span><span class="t">            <span class="key">with</span> <span class="nam">zipfile</span><span class="op">.</span><span class="nam">ZipFile</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t154" href="#t154">154</a></span><span class="t">                    <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'input_zip_file'</span><span class="op">]</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t155" href="#t155">155</a></span><span class="t">                    <span class="str">'r'</span><span class="op">)</span> <span class="key">as</span> <span class="nam">zip_ref</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t156" href="#t156">156</a></span><span class="t">                <span class="nam">zip_ref</span><span class="op">.</span><span class="nam">extractall</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t157" href="#t157">157</a></span><span class="t">        <span class="key">else</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t158" href="#t158">158</a></span><span class="t">            <span class="com"># copy input files to temporary folder</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t159" href="#t159">159</a></span><span class="t">            <span class="nam">shutil</span><span class="op">.</span><span class="nam">copy</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t160" href="#t160">160</a></span><span class="t">                <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'input_csv_file'</span><span class="op">]</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t161" href="#t161">161</a></span><span class="t">                <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t162" href="#t162">162</a></span><span class="t">        <span class="com"># change directory to temporary folder</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t163" href="#t163">163</a></span><span class="t">        <span class="nam">original_directory</span> <span class="op">=</span> <span class="nam">os</span><span class="op">.</span><span class="nam">getcwd</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t164" href="#t164">164</a></span><span class="t">        <span class="nam">os</span><span class="op">.</span><span class="nam">chdir</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t165" href="#t165">165</a></span><span class="t">        <span class="nam">data</span> <span class="op">=</span> <span class="nam">load_data</span><span class="op">(</span><span class="nam">Path</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'input_csv_file'</span><span class="op">]</span><span class="op">)</span><span class="op">.</span><span class="nam">name</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t166" href="#t166">166</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t167" href="#t167">167</a></span><span class="t">        <span class="nam">means</span><span class="op">,</span> <span class="nam">variances</span><span class="op">,</span> <span class="nam">bics</span><span class="op">,</span> <span class="nam">weights</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">fit_to_model</span><span class="op">(</span><span class="nam">data</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t168" href="#t168">168</a></span><span class="t">        <span class="nam">uninormal</span><span class="op">,</span> <span class="nam">binormal</span><span class="op">,</span> <span class="nam">insuf_ev</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">bayes_factor_criteria</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t169" href="#t169">169</a></span><span class="t">            <span class="nam">bics</span><span class="op">[</span><span class="num">0</span><span class="op">]</span><span class="op">,</span> <span class="nam">bics</span><span class="op">[</span><span class="num">1</span><span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t170" href="#t170">170</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t171" href="#t171">171</a></span><span class="t">        <span class="key">if</span> <span class="nam">binormal</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t172" href="#t172">172</a></span><span class="t">            <span class="nam">maxm</span> <span class="op">=</span> <span class="nam">np</span><span class="op">.</span><span class="nam">argmax</span><span class="op">(</span><span class="nam">means</span><span class="op">[</span><span class="num">1</span><span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t173" href="#t173">173</a></span><span class="t">            <span class="nam">minm</span> <span class="op">=</span> <span class="nam">np</span><span class="op">.</span><span class="nam">argmin</span><span class="op">(</span><span class="nam">means</span><span class="op">[</span><span class="num">1</span><span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t174" href="#t174">174</a></span><span class="t">            <span class="nam">mean1</span> <span class="op">=</span> <span class="nam">means</span><span class="op">[</span><span class="num">1</span><span class="op">]</span><span class="op">[</span><span class="nam">minm</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t175" href="#t175">175</a></span><span class="t">            <span class="nam">var1</span> <span class="op">=</span> <span class="nam">variances</span><span class="op">[</span><span class="num">1</span><span class="op">]</span><span class="op">[</span><span class="nam">minm</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t176" href="#t176">176</a></span><span class="t">            <span class="nam">w1</span> <span class="op">=</span> <span class="nam">weights</span><span class="op">[</span><span class="num">1</span><span class="op">]</span><span class="op">[</span><span class="nam">minm</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t177" href="#t177">177</a></span><span class="t">            <span class="nam">mean2</span> <span class="op">=</span> <span class="nam">means</span><span class="op">[</span><span class="num">1</span><span class="op">]</span><span class="op">[</span><span class="nam">maxm</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t178" href="#t178">178</a></span><span class="t">            <span class="nam">var2</span> <span class="op">=</span> <span class="nam">variances</span><span class="op">[</span><span class="num">1</span><span class="op">]</span><span class="op">[</span><span class="nam">maxm</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t179" href="#t179">179</a></span><span class="t">            <span class="nam">w2</span> <span class="op">=</span> <span class="nam">weights</span><span class="op">[</span><span class="num">1</span><span class="op">]</span><span class="op">[</span><span class="nam">maxm</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t180" href="#t180">180</a></span><span class="t">            <span class="nam">bimodal</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">helguero_theorem</span><span class="op">(</span><span class="nam">mean1</span><span class="op">,</span> <span class="nam">mean2</span><span class="op">,</span> <span class="nam">var1</span><span class="op">,</span> <span class="nam">var2</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t181" href="#t181">181</a></span><span class="t">        <span class="key">else</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t182" href="#t182">182</a></span><span class="t">            <span class="nam">mean1</span> <span class="op">=</span> <span class="nam">means</span><span class="op">[</span><span class="num">0</span><span class="op">]</span><span class="op">[</span><span class="num">0</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t183" href="#t183">183</a></span><span class="t">            <span class="nam">var1</span> <span class="op">=</span> <span class="nam">variances</span><span class="op">[</span><span class="num">0</span><span class="op">]</span><span class="op">[</span><span class="num">0</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t184" href="#t184">184</a></span><span class="t">            <span class="nam">w1</span> <span class="op">=</span> <span class="nam">weights</span><span class="op">[</span><span class="num">0</span><span class="op">]</span><span class="op">[</span><span class="num">0</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t185" href="#t185">185</a></span><span class="t">            <span class="nam">mean2</span><span class="op">,</span> <span class="nam">var2</span><span class="op">,</span> <span class="nam">w2</span> <span class="op">=</span> <span class="nam">np</span><span class="op">.</span><span class="nam">nan</span><span class="op">,</span> <span class="nam">np</span><span class="op">.</span><span class="nam">nan</span><span class="op">,</span> <span class="num">0</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t186" href="#t186">186</a></span><span class="t">            <span class="nam">bimodal</span> <span class="op">=</span> <span class="key">False</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t187" href="#t187">187</a></span><span class="t">        <span class="nam">info</span> <span class="op">=</span> <span class="nam">dict</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t188" href="#t188">188</a></span><span class="t">            <span class="nam">binormal</span><span class="op">=</span><span class="nam">binormal</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t189" href="#t189">189</a></span><span class="t">            <span class="nam">uninormal</span><span class="op">=</span><span class="nam">uninormal</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t190" href="#t190">190</a></span><span class="t">            <span class="nam">insuf_ev</span><span class="op">=</span><span class="nam">insuf_ev</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t191" href="#t191">191</a></span><span class="t">            <span class="nam">bimodal</span><span class="op">=</span><span class="nam">bimodal</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t192" href="#t192">192</a></span><span class="t">            <span class="nam">mean1</span><span class="op">=</span><span class="nam">mean1</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t193" href="#t193">193</a></span><span class="t">            <span class="nam">mean2</span><span class="op">=</span><span class="nam">mean2</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t194" href="#t194">194</a></span><span class="t">            <span class="nam">var1</span><span class="op">=</span><span class="nam">var1</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t195" href="#t195">195</a></span><span class="t">            <span class="nam">var2</span><span class="op">=</span><span class="nam">var2</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t196" href="#t196">196</a></span><span class="t">            <span class="nam">w1</span><span class="op">=</span><span class="nam">w1</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t197" href="#t197">197</a></span><span class="t">            <span class="nam">w2</span><span class="op">=</span><span class="nam">w2</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t198" href="#t198">198</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t199" href="#t199">199</a></span><span class="t">        <span class="com"># save tables</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t200" href="#t200">200</a></span><span class="t">        <span class="nam">pd</span><span class="op">.</span><span class="nam">DataFrame</span><span class="op">(</span><span class="nam">info</span><span class="op">,</span> <span class="nam">index</span><span class="op">=</span><span class="nam">data</span><span class="op">.</span><span class="nam">columns</span><span class="op">)</span><span class="op">.</span><span class="nam">to_csv</span><span class="op">(</span><span class="nam">output_csv_path</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t201" href="#t201">201</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t202" href="#t202">202</a></span><span class="t">        <span class="com"># make and save plot</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t203" href="#t203">203</a></span><span class="t">        <span class="nam">data_size</span> <span class="op">=</span> <span class="nam">len</span><span class="op">(</span><span class="nam">data</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t204" href="#t204">204</a></span><span class="t">        <span class="nam">synth1</span> <span class="op">=</span> <span class="nam">np</span><span class="op">.</span><span class="nam">random</span><span class="op">.</span><span class="nam">normal</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t205" href="#t205">205</a></span><span class="t">            <span class="nam">loc</span><span class="op">=</span><span class="nam">info</span><span class="op">[</span><span class="str">'mean1'</span><span class="op">]</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t206" href="#t206">206</a></span><span class="t">            <span class="nam">scale</span><span class="op">=</span><span class="nam">np</span><span class="op">.</span><span class="nam">sqrt</span><span class="op">(</span><span class="nam">info</span><span class="op">[</span><span class="str">'var1'</span><span class="op">]</span><span class="op">)</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t207" href="#t207">207</a></span><span class="t">            <span class="nam">size</span><span class="op">=</span><span class="nam">int</span><span class="op">(</span><span class="nam">data_size</span> <span class="op">*</span> <span class="nam">info</span><span class="op">[</span><span class="str">'w1'</span><span class="op">]</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t208" href="#t208">208</a></span><span class="t">        <span class="nam">synth2</span> <span class="op">=</span> <span class="nam">np</span><span class="op">.</span><span class="nam">random</span><span class="op">.</span><span class="nam">normal</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t209" href="#t209">209</a></span><span class="t">            <span class="nam">loc</span><span class="op">=</span><span class="nam">info</span><span class="op">[</span><span class="str">'mean2'</span><span class="op">]</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t210" href="#t210">210</a></span><span class="t">            <span class="nam">scale</span><span class="op">=</span><span class="nam">np</span><span class="op">.</span><span class="nam">sqrt</span><span class="op">(</span><span class="nam">info</span><span class="op">[</span><span class="str">'var2'</span><span class="op">]</span><span class="op">)</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t211" href="#t211">211</a></span><span class="t">            <span class="nam">size</span><span class="op">=</span><span class="nam">int</span><span class="op">(</span><span class="nam">data_size</span> <span class="op">*</span> <span class="nam">info</span><span class="op">[</span><span class="str">'w2'</span><span class="op">]</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t212" href="#t212">212</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t213" href="#t213">213</a></span><span class="t">        <span class="nam">plt</span><span class="op">.</span><span class="nam">figure</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t214" href="#t214">214</a></span><span class="t">        <span class="nam">alpha</span> <span class="op">=</span> <span class="num">0.7</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t215" href="#t215">215</a></span><span class="t">        <span class="nam">bins</span> <span class="op">=</span> <span class="num">100</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t216" href="#t216">216</a></span><span class="t">        <span class="key">if</span> <span class="nam">binormal</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t217" href="#t217">217</a></span><span class="t">            <span class="nam">label1</span> <span class="op">=</span> <span class="str">"Low State"</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t218" href="#t218">218</a></span><span class="t">        <span class="key">else</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t219" href="#t219">219</a></span><span class="t">            <span class="nam">label1</span> <span class="op">=</span> <span class="str">"Single State"</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t220" href="#t220">220</a></span><span class="t">        <span class="nam">out</span> <span class="op">=</span> <span class="nam">plt</span><span class="op">.</span><span class="nam">hist</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t221" href="#t221">221</a></span><span class="t">            <span class="nam">synth1</span><span class="op">,</span> <span class="nam">bins</span><span class="op">=</span><span class="nam">bins</span><span class="op">,</span> <span class="nam">alpha</span><span class="op">=</span><span class="nam">alpha</span><span class="op">,</span> <span class="nam">density</span><span class="op">=</span><span class="key">True</span><span class="op">,</span> <span class="nam">label</span><span class="op">=</span><span class="nam">label1</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t222" href="#t222">222</a></span><span class="t">        <span class="nam">ylim</span> <span class="op">=</span> <span class="nam">max</span><span class="op">(</span><span class="nam">out</span><span class="op">[</span><span class="num">0</span><span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t223" href="#t223">223</a></span><span class="t">        <span class="nam">plt</span><span class="op">.</span><span class="nam">vlines</span><span class="op">(</span><span class="nam">info</span><span class="op">[</span><span class="str">'mean1'</span><span class="op">]</span><span class="op">,</span> <span class="num">0</span><span class="op">,</span> <span class="nam">ylim</span><span class="op">,</span> <span class="nam">colors</span><span class="op">=</span><span class="str">"r"</span><span class="op">,</span> <span class="nam">linestyles</span><span class="op">=</span><span class="str">"dashed"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t224" href="#t224">224</a></span><span class="t">        <span class="key">if</span> <span class="nam">binormal</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t225" href="#t225">225</a></span><span class="t">            <span class="nam">out</span> <span class="op">=</span> <span class="nam">plt</span><span class="op">.</span><span class="nam">hist</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t226" href="#t226">226</a></span><span class="t">                <span class="nam">synth2</span><span class="op">,</span> <span class="nam">bins</span><span class="op">=</span><span class="nam">bins</span><span class="op">,</span> <span class="nam">alpha</span><span class="op">=</span><span class="nam">alpha</span><span class="op">,</span> <span class="nam">density</span><span class="op">=</span><span class="key">True</span><span class="op">,</span> <span class="nam">label</span><span class="op">=</span><span class="str">"high state"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t227" href="#t227">227</a></span><span class="t">            <span class="nam">ylim</span> <span class="op">=</span> <span class="nam">max</span><span class="op">(</span><span class="nam">out</span><span class="op">[</span><span class="num">0</span><span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t228" href="#t228">228</a></span><span class="t">            <span class="nam">plt</span><span class="op">.</span><span class="nam">vlines</span><span class="op">(</span><span class="nam">info</span><span class="op">[</span><span class="str">'mean2'</span><span class="op">]</span><span class="op">,</span> <span class="num">0</span><span class="op">,</span> <span class="nam">ylim</span><span class="op">,</span> <span class="nam">colors</span><span class="op">=</span><span class="str">"r"</span><span class="op">,</span> <span class="nam">linestyles</span><span class="op">=</span><span class="str">"dashed"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t229" href="#t229">229</a></span><span class="t">        <span class="nam">plt</span><span class="op">.</span><span class="nam">legend</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t230" href="#t230">230</a></span><span class="t">        <span class="nam">plt</span><span class="op">.</span><span class="nam">ylabel</span><span class="op">(</span><span class="str">"Density"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t231" href="#t231">231</a></span><span class="t">        <span class="nam">plt</span><span class="op">.</span><span class="nam">xlabel</span><span class="op">(</span><span class="str">f"{self.helpar_name.capitalize()} ({self.hp_unit})"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t232" href="#t232">232</a></span><span class="t">        <span class="nam">plt</span><span class="op">.</span><span class="nam">title</span><span class="op">(</span><span class="str">f"Distribution of {self.helpar_name} states"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t233" href="#t233">233</a></span><span class="t">        <span class="nam">plt</span><span class="op">.</span><span class="nam">savefig</span><span class="op">(</span><span class="nam">output_jpg_path</span><span class="op">,</span> <span class="nam">format</span><span class="op">=</span><span class="str">"jpg"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t234" href="#t234">234</a></span><span class="t">        <span class="nam">plt</span><span class="op">.</span><span class="nam">close</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t235" href="#t235">235</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t236" href="#t236">236</a></span><span class="t">        <span class="com"># change back to original directory</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t237" href="#t237">237</a></span><span class="t">        <span class="nam">os</span><span class="op">.</span><span class="nam">chdir</span><span class="op">(</span><span class="nam">original_directory</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t238" href="#t238">238</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t239" href="#t239">239</a></span><span class="t">        <span class="com"># Remove temporary file(s)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t240" href="#t240">240</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_files</span><span class="op">.</span><span class="nam">extend</span><span class="op">(</span><span class="op">[</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t241" href="#t241">241</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"unique_dir"</span><span class="op">)</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t242" href="#t242">242</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t243" href="#t243">243</a></span><span class="t">        <span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t244" href="#t244">244</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">remove_tmp_files</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t245" href="#t245">245</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t246" href="#t246">246</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_arguments</span><span class="op">(</span><span class="nam">output_files_created</span><span class="op">=</span><span class="key">True</span><span class="op">,</span> <span class="nam">raise_exception</span><span class="op">=</span><span class="key">False</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t247" href="#t247">247</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t248" href="#t248">248</a></span><span class="t">        <span class="key">return</span> <span class="num">0</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t249" href="#t249">249</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t250" href="#t250">250</a></span><span class="t">    <span class="key">def</span> <span class="nam">fit_to_model</span><span class="op">(</span><span class="nam">self</span><span class="op">,</span> <span class="nam">data</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t251" href="#t251">251</a></span><span class="t">        <span class="str">"""</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t252" href="#t252">252</a></span><span class="t"><span class="str">        Fit data to Gaussian Mixture models.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t253" href="#t253">253</a></span><span class="t"><span class="str">        Return dictionary with distribution data.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t254" href="#t254">254</a></span><span class="t"><span class="str">        """</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t255" href="#t255">255</a></span><span class="t">        <span class="nam">means</span> <span class="op">=</span> <span class="op">[</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t256" href="#t256">256</a></span><span class="t">        <span class="nam">variances</span> <span class="op">=</span> <span class="op">[</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t257" href="#t257">257</a></span><span class="t">        <span class="nam">bics</span> <span class="op">=</span> <span class="op">[</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t258" href="#t258">258</a></span><span class="t">        <span class="nam">weights</span> <span class="op">=</span> <span class="op">[</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t259" href="#t259">259</a></span><span class="t">        <span class="key">for</span> <span class="nam">n_components</span> <span class="key">in</span> <span class="op">(</span><span class="num">1</span><span class="op">,</span> <span class="num">2</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t260" href="#t260">260</a></span><span class="t">            <span class="nam">gmm</span> <span class="op">=</span> <span class="nam">GaussianMixture</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t261" href="#t261">261</a></span><span class="t">                <span class="nam">n_components</span><span class="op">=</span><span class="nam">n_components</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t262" href="#t262">262</a></span><span class="t">                <span class="nam">max_iter</span><span class="op">=</span><span class="nam">self</span><span class="op">.</span><span class="nam">max_iter</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t263" href="#t263">263</a></span><span class="t">                <span class="nam">tol</span><span class="op">=</span><span class="nam">self</span><span class="op">.</span><span class="nam">tol</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t264" href="#t264">264</a></span><span class="t">            <span class="nam">gmm</span> <span class="op">=</span> <span class="nam">gmm</span><span class="op">.</span><span class="nam">fit</span><span class="op">(</span><span class="nam">data</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t265" href="#t265">265</a></span><span class="t">            <span class="nam">m</span> <span class="op">=</span> <span class="nam">gmm</span><span class="op">.</span><span class="nam">means_</span><span class="op">.</span><span class="nam">flatten</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t266" href="#t266">266</a></span><span class="t">            <span class="nam">v</span> <span class="op">=</span> <span class="nam">gmm</span><span class="op">.</span><span class="nam">covariances_</span><span class="op">.</span><span class="nam">flatten</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t267" href="#t267">267</a></span><span class="t">            <span class="nam">b</span> <span class="op">=</span> <span class="nam">gmm</span><span class="op">.</span><span class="nam">bic</span><span class="op">(</span><span class="nam">data</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t268" href="#t268">268</a></span><span class="t">            <span class="nam">w</span> <span class="op">=</span> <span class="nam">gmm</span><span class="op">.</span><span class="nam">weights_</span><span class="op">.</span><span class="nam">flatten</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t269" href="#t269">269</a></span><span class="t">            <span class="nam">means</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="nam">m</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t270" href="#t270">270</a></span><span class="t">            <span class="nam">variances</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="nam">v</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t271" href="#t271">271</a></span><span class="t">            <span class="nam">bics</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="nam">b</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t272" href="#t272">272</a></span><span class="t">            <span class="nam">weights</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="nam">w</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t273" href="#t273">273</a></span><span class="t">        <span class="key">return</span> <span class="nam">means</span><span class="op">,</span> <span class="nam">variances</span><span class="op">,</span> <span class="nam">bics</span><span class="op">,</span> <span class="nam">weights</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t274" href="#t274">274</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t275" href="#t275">275</a></span><span class="t">    <span class="key">def</span> <span class="nam">bayes_factor_criteria</span><span class="op">(</span><span class="nam">self</span><span class="op">,</span> <span class="nam">bic1</span><span class="op">,</span> <span class="nam">bic2</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t276" href="#t276">276</a></span><span class="t">        <span class="nam">diff_bic</span> <span class="op">=</span> <span class="nam">bic2</span> <span class="op">-</span> <span class="nam">bic1</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t277" href="#t277">277</a></span><span class="t">        <span class="com"># probability of a two-component model</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t278" href="#t278">278</a></span><span class="t">        <span class="nam">p</span> <span class="op">=</span> <span class="num">1</span> <span class="op">/</span> <span class="op">(</span><span class="num">1</span> <span class="op">+</span> <span class="nam">np</span><span class="op">.</span><span class="nam">exp</span><span class="op">(</span><span class="num">0.5</span><span class="op">*</span><span class="nam">diff_bic</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t279" href="#t279">279</a></span><span class="t">        <span class="key">if</span> <span class="nam">p</span> <span class="op">==</span> <span class="nam">np</span><span class="op">.</span><span class="nam">nan</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t280" href="#t280">280</a></span><span class="t">            <span class="key">if</span> <span class="nam">bic1</span> <span class="op">==</span> <span class="nam">np</span><span class="op">.</span><span class="nam">nan</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t281" href="#t281">281</a></span><span class="t">                <span class="nam">p</span> <span class="op">=</span> <span class="num">1</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t282" href="#t282">282</a></span><span class="t">            <span class="key">elif</span> <span class="nam">bic2</span> <span class="op">==</span> <span class="nam">np</span><span class="op">.</span><span class="nam">nan</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t283" href="#t283">283</a></span><span class="t">                <span class="nam">p</span> <span class="op">=</span> <span class="num">0</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t284" href="#t284">284</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t285" href="#t285">285</a></span><span class="t">        <span class="nam">uninormal</span> <span class="op">=</span> <span class="nam">p</span> <span class="op">&lt;</span> <span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">confidence_level</span> <span class="op">/</span> <span class="num">100</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t286" href="#t286">286</a></span><span class="t">        <span class="nam">binormal</span> <span class="op">=</span> <span class="nam">p</span> <span class="op">></span> <span class="op">(</span><span class="num">1</span> <span class="op">-</span> <span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">confidence_level</span> <span class="op">/</span> <span class="num">100</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t287" href="#t287">287</a></span><span class="t">        <span class="nam">insuf_ev</span> <span class="op">=</span> <span class="key">True</span> <span class="key">if</span> <span class="op">(</span><span class="key">not</span> <span class="nam">uninormal</span> <span class="key">and</span> <span class="key">not</span> <span class="nam">binormal</span><span class="op">)</span> <span class="key">else</span> <span class="key">False</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t288" href="#t288">288</a></span><span class="t">        <span class="key">return</span> <span class="nam">uninormal</span><span class="op">,</span> <span class="nam">binormal</span><span class="op">,</span> <span class="nam">insuf_ev</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t289" href="#t289">289</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t290" href="#t290">290</a></span><span class="t">    <span class="key">def</span> <span class="nam">helguero_theorem</span><span class="op">(</span><span class="nam">self</span><span class="op">,</span> <span class="nam">mean1</span><span class="op">,</span> <span class="nam">mean2</span><span class="op">,</span> <span class="nam">var1</span><span class="op">,</span> <span class="nam">var2</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t291" href="#t291">291</a></span><span class="t">        <span class="nam">r</span> <span class="op">=</span> <span class="nam">var1</span> <span class="op">/</span> <span class="nam">var2</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t292" href="#t292">292</a></span><span class="t">        <span class="nam">separation_factor</span> <span class="op">=</span> <span class="nam">np</span><span class="op">.</span><span class="nam">sqrt</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t293" href="#t293">293</a></span><span class="t">            <span class="op">-</span><span class="num">2</span> <span class="op">+</span> <span class="num">3</span><span class="op">*</span><span class="nam">r</span> <span class="op">+</span> <span class="num">3</span><span class="op">*</span><span class="nam">r</span><span class="op">**</span><span class="num">2</span> <span class="op">-</span> <span class="num">2</span><span class="op">*</span><span class="nam">r</span><span class="op">**</span><span class="num">3</span> <span class="op">+</span> <span class="num">2</span><span class="op">*</span><span class="op">(</span><span class="num">1</span> <span class="op">-</span> <span class="nam">r</span> <span class="op">+</span> <span class="nam">r</span><span class="op">**</span><span class="num">2</span><span class="op">)</span><span class="op">**</span><span class="num">1.5</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t294" href="#t294">294</a></span><span class="t">        <span class="op">)</span> <span class="op">/</span> <span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t295" href="#t295">295</a></span><span class="t">            <span class="nam">np</span><span class="op">.</span><span class="nam">sqrt</span><span class="op">(</span><span class="nam">r</span><span class="op">)</span><span class="op">*</span><span class="op">(</span><span class="num">1</span><span class="op">+</span><span class="nam">np</span><span class="op">.</span><span class="nam">sqrt</span><span class="op">(</span><span class="nam">r</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t296" href="#t296">296</a></span><span class="t">        <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t297" href="#t297">297</a></span><span class="t">        <span class="nam">bimodal</span> <span class="op">=</span> <span class="nam">abs</span><span class="op">(</span><span class="nam">mean2</span><span class="op">-</span><span class="nam">mean1</span><span class="op">)</span> <span class="op">></span> <span class="nam">separation_factor</span> <span class="op">*</span> <span class="xx">\</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t298" href="#t298">298</a></span><span class="t">            <span class="op">(</span><span class="nam">np</span><span class="op">.</span><span class="nam">sqrt</span><span class="op">(</span><span class="nam">var1</span><span class="op">)</span> <span class="op">+</span> <span class="nam">np</span><span class="op">.</span><span class="nam">sqrt</span><span class="op">(</span><span class="nam">var2</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t299" href="#t299">299</a></span><span class="t">        <span class="key">return</span> <span class="nam">bimodal</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t300" href="#t300">300</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t27" href="#t27">27</a></span><span class="t"><span class="str">    | Determine binormality/bimodality from a helical parameter series dataset.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t28" href="#t28">28</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t29" href="#t29">29</a></span><span class="t"><span class="str">    Args:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t30" href="#t30">30</a></span><span class="t"><span class="str">        input_csv_file (str): Path to .csv file with helical parameter series. If `input_zip_file` is passed, this should be just the filename of the .csv file inside .zip.  File type: input. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/dna/series_shift_AT.csv>`_. Accepted formats: csv (edam:format_3752).</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t31" href="#t31">31</a></span><span class="t"><span class="str">        input_zip_file (str) (Optional): .zip file containing the `input_csv_file` .csv file. File type: input. Accepted formats: zip (edam:format_3987).</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t32" href="#t32">32</a></span><span class="t"><span class="str">        output_csv_path (str): Path to .csv file where output is saved. File type: output. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/reference/dna/AT_shift_bimod.csv>`_. Accepted formats: csv (edam:format_3752).</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t33" href="#t33">33</a></span><span class="t"><span class="str">        output_jpg_path (str): Path to .jpg file where output is saved. File type: output. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/reference/dna/AT_shift_bimod.jpg>`_. Accepted formats: jpg (edam:format_3579).</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t34" href="#t34">34</a></span><span class="t"><span class="str">        properties (dict):</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t35" href="#t35">35</a></span><span class="t"><span class="str">            * **helpar_name** (*str*) - (Optional) helical parameter name.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t36" href="#t36">36</a></span><span class="t"><span class="str">            * **confidence_level** (*float*) - (5.0) Confidence level for Byes Factor test (in percentage).</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t37" href="#t37">37</a></span><span class="t"><span class="str">            * **max_iter** (*int*) - (400) Number of maximum iterations for EM algorithm.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t38" href="#t38">38</a></span><span class="t"><span class="str">            * **tol** (*float*) - (1e-5) Tolerance value for EM algorithm.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t39" href="#t39">39</a></span><span class="t"><span class="str">            * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t40" href="#t40">40</a></span><span class="t"><span class="str">            * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.1</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t41" href="#t41">41</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t42" href="#t42">42</a></span><span class="t"><span class="str">    Examples:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t43" href="#t43">43</a></span><span class="t"><span class="str">        This is a use example of how to use the building block from Python::</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t44" href="#t44">44</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t45" href="#t45">45</a></span><span class="t"><span class="str">            from biobb_dna.dna.dna_bimodality import dna_bimodality</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t46" href="#t46">46</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t47" href="#t47">47</a></span><span class="t"><span class="str">            prop = {</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t48" href="#t48">48</a></span><span class="t"><span class="str">                'max_iter': 500,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t49" href="#t49">49</a></span><span class="t"><span class="str">            }</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t50" href="#t50">50</a></span><span class="t"><span class="str">            dna_bimodality(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t51" href="#t51">51</a></span><span class="t"><span class="str">                input_csv_file='filename.csv',</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t52" href="#t52">52</a></span><span class="t"><span class="str">                input_zip_file='/path/to/input.zip',</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t53" href="#t53">53</a></span><span class="t"><span class="str">                output_csv_path='/path/to/output.csv',</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t54" href="#t54">54</a></span><span class="t"><span class="str">                output_jpg_path='/path/to/output.jpg',</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t55" href="#t55">55</a></span><span class="t"><span class="str">                properties=prop)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t56" href="#t56">56</a></span><span class="t"><span class="str">    Info:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t57" href="#t57">57</a></span><span class="t"><span class="str">        * wrapped_software:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t58" href="#t58">58</a></span><span class="t"><span class="str">            * name: In house</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t59" href="#t59">59</a></span><span class="t"><span class="str">            * license: Apache-2.0</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t60" href="#t60">60</a></span><span class="t"><span class="str">        * ontology:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t61" href="#t61">61</a></span><span class="t"><span class="str">            * name: EDAM</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t62" href="#t62">62</a></span><span class="t"><span class="str">            * schema: http://edamontology.org/EDAM.owl</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t63" href="#t63">63</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t64" href="#t64">64</a></span><span class="t"><span class="str">    """</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t65" href="#t65">65</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t66" href="#t66">66</a></span><span class="t">    <span class="key">def</span> <span class="nam">__init__</span><span class="op">(</span><span class="nam">self</span><span class="op">,</span> <span class="nam">input_csv_file</span><span class="op">,</span> <span class="nam">output_csv_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t67" href="#t67">67</a></span><span class="t">                 <span class="nam">output_jpg_path</span><span class="op">,</span> <span class="nam">input_zip_file</span><span class="op">=</span><span class="key">None</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t68" href="#t68">68</a></span><span class="t">                 <span class="nam">properties</span><span class="op">=</span><span class="key">None</span><span class="op">,</span> <span class="op">**</span><span class="nam">kwargs</span><span class="op">)</span> <span class="op">-></span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t69" href="#t69">69</a></span><span class="t">        <span class="nam">properties</span> <span class="op">=</span> <span class="nam">properties</span> <span class="key">or</span> <span class="op">{</span><span class="op">}</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t70" href="#t70">70</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t71" href="#t71">71</a></span><span class="t">        <span class="com"># Call parent class constructor</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t72" href="#t72">72</a></span><span class="t">        <span class="nam">super</span><span class="op">(</span><span class="op">)</span><span class="op">.</span><span class="nam">__init__</span><span class="op">(</span><span class="nam">properties</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t73" href="#t73">73</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">locals_var_dict</span> <span class="op">=</span> <span class="nam">locals</span><span class="op">(</span><span class="op">)</span><span class="op">.</span><span class="nam">copy</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t74" href="#t74">74</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t75" href="#t75">75</a></span><span class="t">        <span class="com"># Input/Output files</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t76" href="#t76">76</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span> <span class="op">=</span> <span class="op">{</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t77" href="#t77">77</a></span><span class="t">            <span class="str">'in'</span><span class="op">:</span> <span class="op">{</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t78" href="#t78">78</a></span><span class="t">                <span class="str">'input_csv_file'</span><span class="op">:</span> <span class="nam">input_csv_file</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t79" href="#t79">79</a></span><span class="t">                <span class="str">'input_zip_file'</span><span class="op">:</span> <span class="nam">input_zip_file</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t80" href="#t80">80</a></span><span class="t">            <span class="op">}</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t81" href="#t81">81</a></span><span class="t">            <span class="str">'out'</span><span class="op">:</span> <span class="op">{</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t82" href="#t82">82</a></span><span class="t">                <span class="str">'output_csv_path'</span><span class="op">:</span> <span class="nam">output_csv_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t83" href="#t83">83</a></span><span class="t">                <span class="str">'output_jpg_path'</span><span class="op">:</span> <span class="nam">output_jpg_path</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t84" href="#t84">84</a></span><span class="t">            <span class="op">}</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t85" href="#t85">85</a></span><span class="t">        <span class="op">}</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t86" href="#t86">86</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t87" href="#t87">87</a></span><span class="t">        <span class="com"># Properties specific for BB</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t88" href="#t88">88</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">confidence_level</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t89" href="#t89">89</a></span><span class="t">            <span class="str">"confidence_level"</span><span class="op">,</span> <span class="num">5.0</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t90" href="#t90">90</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">max_iter</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t91" href="#t91">91</a></span><span class="t">            <span class="str">"max_iter"</span><span class="op">,</span> <span class="num">400</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t92" href="#t92">92</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">tol</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t93" href="#t93">93</a></span><span class="t">            <span class="str">"tol"</span><span class="op">,</span> <span class="num">1e-5</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t94" href="#t94">94</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">helpar_name</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"helpar_name"</span><span class="op">,</span> <span class="key">None</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t95" href="#t95">95</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">properties</span> <span class="op">=</span> <span class="nam">properties</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t96" href="#t96">96</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t97" href="#t97">97</a></span><span class="t">        <span class="com"># Check the properties</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t98" href="#t98">98</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_properties</span><span class="op">(</span><span class="nam">properties</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t99" href="#t99">99</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_arguments</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t100" href="#t100">100</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t101" href="#t101">101</a></span><span class="t">    <span class="op">@</span><span class="nam">launchlogger</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t102" href="#t102">102</a></span><span class="t">    <span class="key">def</span> <span class="nam">launch</span><span class="op">(</span><span class="nam">self</span><span class="op">)</span> <span class="op">-></span> <span class="nam">int</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t103" href="#t103">103</a></span><span class="t">        <span class="str">"""Execute the :class:`HelParBimodality &lt;dna.dna_bimodality.HelParBimodality>` object."""</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t104" href="#t104">104</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t105" href="#t105">105</a></span><span class="t">        <span class="com"># Setup Biobb</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t106" href="#t106">106</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">check_restart</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t107" href="#t107">107</a></span><span class="t">            <span class="key">return</span> <span class="num">0</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t108" href="#t108">108</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">stage_files</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t109" href="#t109">109</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t110" href="#t110">110</a></span><span class="t">        <span class="com"># get helical parameter from filename if not specified</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t111" href="#t111">111</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">helpar_name</span> <span class="key">is</span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t112" href="#t112">112</a></span><span class="t">            <span class="key">for</span> <span class="nam">hp</span> <span class="key">in</span> <span class="nam">constants</span><span class="op">.</span><span class="nam">helical_parameters</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t113" href="#t113">113</a></span><span class="t">                <span class="nam">input_zip_path</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'input_zip_file'</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t114" href="#t114">114</a></span><span class="t">                <span class="key">if</span> <span class="nam">input_zip_path</span> <span class="key">is</span> <span class="key">not</span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t115" href="#t115">115</a></span><span class="t">                    <span class="nam">condition_2</span> <span class="op">=</span> <span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t116" href="#t116">116</a></span><span class="t">                        <span class="nam">hp</span><span class="op">.</span><span class="nam">lower</span><span class="op">(</span><span class="op">)</span> <span class="key">in</span> <span class="nam">Path</span><span class="op">(</span><span class="nam">input_zip_path</span><span class="op">)</span><span class="op">.</span><span class="nam">name</span><span class="op">.</span><span class="nam">lower</span><span class="op">(</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t117" href="#t117">117</a></span><span class="t">                <span class="key">else</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t118" href="#t118">118</a></span><span class="t">                    <span class="nam">condition_2</span> <span class="op">=</span> <span class="key">False</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t119" href="#t119">119</a></span><span class="t">                <span class="nam">condition_1</span> <span class="op">=</span> <span class="nam">hp</span><span class="op">.</span><span class="nam">lower</span><span class="op">(</span><span class="op">)</span> <span class="key">in</span> <span class="nam">Path</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t120" href="#t120">120</a></span><span class="t">                    <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'input_csv_file'</span><span class="op">]</span><span class="op">)</span><span class="op">.</span><span class="nam">name</span><span class="op">.</span><span class="nam">lower</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t121" href="#t121">121</a></span><span class="t">                <span class="key">if</span> <span class="op">(</span><span class="nam">condition_1</span> <span class="key">or</span> <span class="nam">condition_2</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t122" href="#t122">122</a></span><span class="t">                    <span class="nam">self</span><span class="op">.</span><span class="nam">helpar_name</span> <span class="op">=</span> <span class="nam">hp</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t123" href="#t123">123</a></span><span class="t">            <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">helpar_name</span> <span class="key">is</span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t124" href="#t124">124</a></span><span class="t">                <span class="key">raise</span> <span class="nam">ValueError</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t125" href="#t125">125</a></span><span class="t">                    <span class="str">"Helical parameter name can't be inferred from file, "</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t126" href="#t126">126</a></span><span class="t">                    <span class="str">"so it must be specified!"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t127" href="#t127">127</a></span><span class="t">        <span class="key">else</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t128" href="#t128">128</a></span><span class="t">            <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">helpar_name</span> <span class="key">not</span> <span class="key">in</span> <span class="nam">constants</span><span class="op">.</span><span class="nam">helical_parameters</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t129" href="#t129">129</a></span><span class="t">                <span class="key">raise</span> <span class="nam">ValueError</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t130" href="#t130">130</a></span><span class="t">                    <span class="str">"Helical parameter name is invalid! "</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t131" href="#t131">131</a></span><span class="t">                    <span class="str">f"Options: {constants.helical_parameters}"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t132" href="#t132">132</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t133" href="#t133">133</a></span><span class="t">        <span class="com"># get  unit from helical parameter name</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t134" href="#t134">134</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">helpar_name</span> <span class="key">in</span> <span class="nam">constants</span><span class="op">.</span><span class="nam">hp_angular</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t135" href="#t135">135</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">hp_unit</span> <span class="op">=</span> <span class="str">"Degrees"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t136" href="#t136">136</a></span><span class="t">        <span class="key">else</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t137" href="#t137">137</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">hp_unit</span> <span class="op">=</span> <span class="str">"Angstroms"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t138" href="#t138">138</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t139" href="#t139">139</a></span><span class="t">        <span class="com"># resolve output</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t140" href="#t140">140</a></span><span class="t">        <span class="nam">output_csv_path</span> <span class="op">=</span> <span class="nam">Path</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t141" href="#t141">141</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'out'</span><span class="op">]</span><span class="op">[</span><span class="str">'output_csv_path'</span><span class="op">]</span><span class="op">)</span><span class="op">.</span><span class="nam">resolve</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t142" href="#t142">142</a></span><span class="t">        <span class="nam">output_jpg_path</span> <span class="op">=</span> <span class="nam">Path</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t143" href="#t143">143</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'out'</span><span class="op">]</span><span class="op">[</span><span class="str">'output_jpg_path'</span><span class="op">]</span><span class="op">)</span><span class="op">.</span><span class="nam">resolve</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t144" href="#t144">144</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t145" href="#t145">145</a></span><span class="t">        <span class="com"># Creating temporary folder</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t146" href="#t146">146</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span> <span class="op">=</span> <span class="nam">fu</span><span class="op">.</span><span class="nam">create_unique_dir</span><span class="op">(</span><span class="nam">prefix</span><span class="op">=</span><span class="str">"bimodality_"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t147" href="#t147">147</a></span><span class="t">        <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="str">'Creating %s temporary folder'</span> <span class="op">%</span> <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t148" href="#t148">148</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t149" href="#t149">149</a></span><span class="t">        <span class="com"># read input</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t150" href="#t150">150</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'input_zip_file'</span><span class="op">]</span> <span class="key">is</span> <span class="key">not</span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t151" href="#t151">151</a></span><span class="t">            <span class="com"># Copy input_file_path1 to temporary folder</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t152" href="#t152">152</a></span><span class="t">            <span class="nam">shutil</span><span class="op">.</span><span class="nam">copy</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'input_zip_file'</span><span class="op">]</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t153" href="#t153">153</a></span><span class="t">            <span class="com"># if zipfile is specified, extract to temporary folder</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t154" href="#t154">154</a></span><span class="t">            <span class="key">with</span> <span class="nam">zipfile</span><span class="op">.</span><span class="nam">ZipFile</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t155" href="#t155">155</a></span><span class="t">                    <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'input_zip_file'</span><span class="op">]</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t156" href="#t156">156</a></span><span class="t">                    <span class="str">'r'</span><span class="op">)</span> <span class="key">as</span> <span class="nam">zip_ref</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t157" href="#t157">157</a></span><span class="t">                <span class="nam">zip_ref</span><span class="op">.</span><span class="nam">extractall</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t158" href="#t158">158</a></span><span class="t">        <span class="key">else</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t159" href="#t159">159</a></span><span class="t">            <span class="com"># copy input files to temporary folder</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t160" href="#t160">160</a></span><span class="t">            <span class="nam">shutil</span><span class="op">.</span><span class="nam">copy</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t161" href="#t161">161</a></span><span class="t">                <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'input_csv_file'</span><span class="op">]</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t162" href="#t162">162</a></span><span class="t">                <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t163" href="#t163">163</a></span><span class="t">        <span class="com"># change directory to temporary folder</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t164" href="#t164">164</a></span><span class="t">        <span class="nam">original_directory</span> <span class="op">=</span> <span class="nam">os</span><span class="op">.</span><span class="nam">getcwd</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t165" href="#t165">165</a></span><span class="t">        <span class="nam">os</span><span class="op">.</span><span class="nam">chdir</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t166" href="#t166">166</a></span><span class="t">        <span class="nam">data</span> <span class="op">=</span> <span class="nam">load_data</span><span class="op">(</span><span class="nam">Path</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'input_csv_file'</span><span class="op">]</span><span class="op">)</span><span class="op">.</span><span class="nam">name</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t167" href="#t167">167</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t168" href="#t168">168</a></span><span class="t">        <span class="nam">means</span><span class="op">,</span> <span class="nam">variances</span><span class="op">,</span> <span class="nam">bics</span><span class="op">,</span> <span class="nam">weights</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">fit_to_model</span><span class="op">(</span><span class="nam">data</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t169" href="#t169">169</a></span><span class="t">        <span class="nam">uninormal</span><span class="op">,</span> <span class="nam">binormal</span><span class="op">,</span> <span class="nam">insuf_ev</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">bayes_factor_criteria</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t170" href="#t170">170</a></span><span class="t">            <span class="nam">bics</span><span class="op">[</span><span class="num">0</span><span class="op">]</span><span class="op">,</span> <span class="nam">bics</span><span class="op">[</span><span class="num">1</span><span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t171" href="#t171">171</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t172" href="#t172">172</a></span><span class="t">        <span class="key">if</span> <span class="nam">binormal</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t173" href="#t173">173</a></span><span class="t">            <span class="nam">maxm</span> <span class="op">=</span> <span class="nam">np</span><span class="op">.</span><span class="nam">argmax</span><span class="op">(</span><span class="nam">means</span><span class="op">[</span><span class="num">1</span><span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t174" href="#t174">174</a></span><span class="t">            <span class="nam">minm</span> <span class="op">=</span> <span class="nam">np</span><span class="op">.</span><span class="nam">argmin</span><span class="op">(</span><span class="nam">means</span><span class="op">[</span><span class="num">1</span><span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t175" href="#t175">175</a></span><span class="t">            <span class="nam">mean1</span> <span class="op">=</span> <span class="nam">means</span><span class="op">[</span><span class="num">1</span><span class="op">]</span><span class="op">[</span><span class="nam">minm</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t176" href="#t176">176</a></span><span class="t">            <span class="nam">var1</span> <span class="op">=</span> <span class="nam">variances</span><span class="op">[</span><span class="num">1</span><span class="op">]</span><span class="op">[</span><span class="nam">minm</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t177" href="#t177">177</a></span><span class="t">            <span class="nam">w1</span> <span class="op">=</span> <span class="nam">weights</span><span class="op">[</span><span class="num">1</span><span class="op">]</span><span class="op">[</span><span class="nam">minm</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t178" href="#t178">178</a></span><span class="t">            <span class="nam">mean2</span> <span class="op">=</span> <span class="nam">means</span><span class="op">[</span><span class="num">1</span><span class="op">]</span><span class="op">[</span><span class="nam">maxm</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t179" href="#t179">179</a></span><span class="t">            <span class="nam">var2</span> <span class="op">=</span> <span class="nam">variances</span><span class="op">[</span><span class="num">1</span><span class="op">]</span><span class="op">[</span><span class="nam">maxm</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t180" href="#t180">180</a></span><span class="t">            <span class="nam">w2</span> <span class="op">=</span> <span class="nam">weights</span><span class="op">[</span><span class="num">1</span><span class="op">]</span><span class="op">[</span><span class="nam">maxm</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t181" href="#t181">181</a></span><span class="t">            <span class="nam">bimodal</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">helguero_theorem</span><span class="op">(</span><span class="nam">mean1</span><span class="op">,</span> <span class="nam">mean2</span><span class="op">,</span> <span class="nam">var1</span><span class="op">,</span> <span class="nam">var2</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t182" href="#t182">182</a></span><span class="t">        <span class="key">else</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t183" href="#t183">183</a></span><span class="t">            <span class="nam">mean1</span> <span class="op">=</span> <span class="nam">means</span><span class="op">[</span><span class="num">0</span><span class="op">]</span><span class="op">[</span><span class="num">0</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t184" href="#t184">184</a></span><span class="t">            <span class="nam">var1</span> <span class="op">=</span> <span class="nam">variances</span><span class="op">[</span><span class="num">0</span><span class="op">]</span><span class="op">[</span><span class="num">0</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t185" href="#t185">185</a></span><span class="t">            <span class="nam">w1</span> <span class="op">=</span> <span class="nam">weights</span><span class="op">[</span><span class="num">0</span><span class="op">]</span><span class="op">[</span><span class="num">0</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t186" href="#t186">186</a></span><span class="t">            <span class="nam">mean2</span><span class="op">,</span> <span class="nam">var2</span><span class="op">,</span> <span class="nam">w2</span> <span class="op">=</span> <span class="nam">np</span><span class="op">.</span><span class="nam">nan</span><span class="op">,</span> <span class="nam">np</span><span class="op">.</span><span class="nam">nan</span><span class="op">,</span> <span class="num">0</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t187" href="#t187">187</a></span><span class="t">            <span class="nam">bimodal</span> <span class="op">=</span> <span class="key">False</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t188" href="#t188">188</a></span><span class="t">        <span class="nam">info</span> <span class="op">=</span> <span class="nam">dict</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t189" href="#t189">189</a></span><span class="t">            <span class="nam">binormal</span><span class="op">=</span><span class="nam">binormal</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t190" href="#t190">190</a></span><span class="t">            <span class="nam">uninormal</span><span class="op">=</span><span class="nam">uninormal</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t191" href="#t191">191</a></span><span class="t">            <span class="nam">insuf_ev</span><span class="op">=</span><span class="nam">insuf_ev</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t192" href="#t192">192</a></span><span class="t">            <span class="nam">bimodal</span><span class="op">=</span><span class="nam">bimodal</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t193" href="#t193">193</a></span><span class="t">            <span class="nam">mean1</span><span class="op">=</span><span class="nam">mean1</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t194" href="#t194">194</a></span><span class="t">            <span class="nam">mean2</span><span class="op">=</span><span class="nam">mean2</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t195" href="#t195">195</a></span><span class="t">            <span class="nam">var1</span><span class="op">=</span><span class="nam">var1</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t196" href="#t196">196</a></span><span class="t">            <span class="nam">var2</span><span class="op">=</span><span class="nam">var2</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t197" href="#t197">197</a></span><span class="t">            <span class="nam">w1</span><span class="op">=</span><span class="nam">w1</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t198" href="#t198">198</a></span><span class="t">            <span class="nam">w2</span><span class="op">=</span><span class="nam">w2</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t199" href="#t199">199</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t200" href="#t200">200</a></span><span class="t">        <span class="com"># save tables</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t201" href="#t201">201</a></span><span class="t">        <span class="nam">pd</span><span class="op">.</span><span class="nam">DataFrame</span><span class="op">(</span><span class="nam">info</span><span class="op">,</span> <span class="nam">index</span><span class="op">=</span><span class="nam">data</span><span class="op">.</span><span class="nam">columns</span><span class="op">)</span><span class="op">.</span><span class="nam">to_csv</span><span class="op">(</span><span class="nam">output_csv_path</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t202" href="#t202">202</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t203" href="#t203">203</a></span><span class="t">        <span class="com"># make and save plot</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t204" href="#t204">204</a></span><span class="t">        <span class="nam">data_size</span> <span class="op">=</span> <span class="nam">len</span><span class="op">(</span><span class="nam">data</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t205" href="#t205">205</a></span><span class="t">        <span class="nam">synth1</span> <span class="op">=</span> <span class="nam">np</span><span class="op">.</span><span class="nam">random</span><span class="op">.</span><span class="nam">normal</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t206" href="#t206">206</a></span><span class="t">            <span class="nam">loc</span><span class="op">=</span><span class="nam">info</span><span class="op">[</span><span class="str">'mean1'</span><span class="op">]</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t207" href="#t207">207</a></span><span class="t">            <span class="nam">scale</span><span class="op">=</span><span class="nam">np</span><span class="op">.</span><span class="nam">sqrt</span><span class="op">(</span><span class="nam">info</span><span class="op">[</span><span class="str">'var1'</span><span class="op">]</span><span class="op">)</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t208" href="#t208">208</a></span><span class="t">            <span class="nam">size</span><span class="op">=</span><span class="nam">int</span><span class="op">(</span><span class="nam">data_size</span> <span class="op">*</span> <span class="nam">info</span><span class="op">[</span><span class="str">'w1'</span><span class="op">]</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t209" href="#t209">209</a></span><span class="t">        <span class="nam">synth2</span> <span class="op">=</span> <span class="nam">np</span><span class="op">.</span><span class="nam">random</span><span class="op">.</span><span class="nam">normal</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t210" href="#t210">210</a></span><span class="t">            <span class="nam">loc</span><span class="op">=</span><span class="nam">info</span><span class="op">[</span><span class="str">'mean2'</span><span class="op">]</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t211" href="#t211">211</a></span><span class="t">            <span class="nam">scale</span><span class="op">=</span><span class="nam">np</span><span class="op">.</span><span class="nam">sqrt</span><span class="op">(</span><span class="nam">info</span><span class="op">[</span><span class="str">'var2'</span><span class="op">]</span><span class="op">)</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t212" href="#t212">212</a></span><span class="t">            <span class="nam">size</span><span class="op">=</span><span class="nam">int</span><span class="op">(</span><span class="nam">data_size</span> <span class="op">*</span> <span class="nam">info</span><span class="op">[</span><span class="str">'w2'</span><span class="op">]</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t213" href="#t213">213</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t214" href="#t214">214</a></span><span class="t">        <span class="nam">plt</span><span class="op">.</span><span class="nam">figure</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t215" href="#t215">215</a></span><span class="t">        <span class="nam">alpha</span> <span class="op">=</span> <span class="num">0.7</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t216" href="#t216">216</a></span><span class="t">        <span class="nam">bins</span> <span class="op">=</span> <span class="num">100</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t217" href="#t217">217</a></span><span class="t">        <span class="key">if</span> <span class="nam">binormal</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t218" href="#t218">218</a></span><span class="t">            <span class="nam">label1</span> <span class="op">=</span> <span class="str">"Low State"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t219" href="#t219">219</a></span><span class="t">        <span class="key">else</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t220" href="#t220">220</a></span><span class="t">            <span class="nam">label1</span> <span class="op">=</span> <span class="str">"Single State"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t221" href="#t221">221</a></span><span class="t">        <span class="nam">out</span> <span class="op">=</span> <span class="nam">plt</span><span class="op">.</span><span class="nam">hist</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t222" href="#t222">222</a></span><span class="t">            <span class="nam">synth1</span><span class="op">,</span> <span class="nam">bins</span><span class="op">=</span><span class="nam">bins</span><span class="op">,</span> <span class="nam">alpha</span><span class="op">=</span><span class="nam">alpha</span><span class="op">,</span> <span class="nam">density</span><span class="op">=</span><span class="key">True</span><span class="op">,</span> <span class="nam">label</span><span class="op">=</span><span class="nam">label1</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t223" href="#t223">223</a></span><span class="t">        <span class="nam">ylim</span> <span class="op">=</span> <span class="nam">max</span><span class="op">(</span><span class="nam">out</span><span class="op">[</span><span class="num">0</span><span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t224" href="#t224">224</a></span><span class="t">        <span class="nam">plt</span><span class="op">.</span><span class="nam">vlines</span><span class="op">(</span><span class="nam">info</span><span class="op">[</span><span class="str">'mean1'</span><span class="op">]</span><span class="op">,</span> <span class="num">0</span><span class="op">,</span> <span class="nam">ylim</span><span class="op">,</span> <span class="nam">colors</span><span class="op">=</span><span class="str">"r"</span><span class="op">,</span> <span class="nam">linestyles</span><span class="op">=</span><span class="str">"dashed"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t225" href="#t225">225</a></span><span class="t">        <span class="key">if</span> <span class="nam">binormal</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t226" href="#t226">226</a></span><span class="t">            <span class="nam">out</span> <span class="op">=</span> <span class="nam">plt</span><span class="op">.</span><span class="nam">hist</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t227" href="#t227">227</a></span><span class="t">                <span class="nam">synth2</span><span class="op">,</span> <span class="nam">bins</span><span class="op">=</span><span class="nam">bins</span><span class="op">,</span> <span class="nam">alpha</span><span class="op">=</span><span class="nam">alpha</span><span class="op">,</span> <span class="nam">density</span><span class="op">=</span><span class="key">True</span><span class="op">,</span> <span class="nam">label</span><span class="op">=</span><span class="str">"high state"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t228" href="#t228">228</a></span><span class="t">            <span class="nam">ylim</span> <span class="op">=</span> <span class="nam">max</span><span class="op">(</span><span class="nam">out</span><span class="op">[</span><span class="num">0</span><span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t229" href="#t229">229</a></span><span class="t">            <span class="nam">plt</span><span class="op">.</span><span class="nam">vlines</span><span class="op">(</span><span class="nam">info</span><span class="op">[</span><span class="str">'mean2'</span><span class="op">]</span><span class="op">,</span> <span class="num">0</span><span class="op">,</span> <span class="nam">ylim</span><span class="op">,</span> <span class="nam">colors</span><span class="op">=</span><span class="str">"r"</span><span class="op">,</span> <span class="nam">linestyles</span><span class="op">=</span><span class="str">"dashed"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t230" href="#t230">230</a></span><span class="t">        <span class="nam">plt</span><span class="op">.</span><span class="nam">legend</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t231" href="#t231">231</a></span><span class="t">        <span class="nam">plt</span><span class="op">.</span><span class="nam">ylabel</span><span class="op">(</span><span class="str">"Density"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t232" href="#t232">232</a></span><span class="t">        <span class="nam">plt</span><span class="op">.</span><span class="nam">xlabel</span><span class="op">(</span><span class="str">f"{self.helpar_name.capitalize()} ({self.hp_unit})"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t233" href="#t233">233</a></span><span class="t">        <span class="nam">plt</span><span class="op">.</span><span class="nam">title</span><span class="op">(</span><span class="str">f"Distribution of {self.helpar_name} states"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t234" href="#t234">234</a></span><span class="t">        <span class="nam">plt</span><span class="op">.</span><span class="nam">savefig</span><span class="op">(</span><span class="nam">output_jpg_path</span><span class="op">,</span> <span class="nam">format</span><span class="op">=</span><span class="str">"jpg"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t235" href="#t235">235</a></span><span class="t">        <span class="nam">plt</span><span class="op">.</span><span class="nam">close</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t236" href="#t236">236</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t237" href="#t237">237</a></span><span class="t">        <span class="com"># change back to original directory</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t238" href="#t238">238</a></span><span class="t">        <span class="nam">os</span><span class="op">.</span><span class="nam">chdir</span><span class="op">(</span><span class="nam">original_directory</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t239" href="#t239">239</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t240" href="#t240">240</a></span><span class="t">        <span class="com"># Remove temporary file(s)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t241" href="#t241">241</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_files</span><span class="op">.</span><span class="nam">extend</span><span class="op">(</span><span class="op">[</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t242" href="#t242">242</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"unique_dir"</span><span class="op">)</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t243" href="#t243">243</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t244" href="#t244">244</a></span><span class="t">        <span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t245" href="#t245">245</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">remove_tmp_files</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t246" href="#t246">246</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t247" href="#t247">247</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_arguments</span><span class="op">(</span><span class="nam">output_files_created</span><span class="op">=</span><span class="key">True</span><span class="op">,</span> <span class="nam">raise_exception</span><span class="op">=</span><span class="key">False</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t248" href="#t248">248</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t249" href="#t249">249</a></span><span class="t">        <span class="key">return</span> <span class="num">0</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t250" href="#t250">250</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t251" href="#t251">251</a></span><span class="t">    <span class="key">def</span> <span class="nam">fit_to_model</span><span class="op">(</span><span class="nam">self</span><span class="op">,</span> <span class="nam">data</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t252" href="#t252">252</a></span><span class="t">        <span class="str">"""</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t253" href="#t253">253</a></span><span class="t"><span class="str">        Fit data to Gaussian Mixture models.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t254" href="#t254">254</a></span><span class="t"><span class="str">        Return dictionary with distribution data.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t255" href="#t255">255</a></span><span class="t"><span class="str">        """</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t256" href="#t256">256</a></span><span class="t">        <span class="nam">means</span> <span class="op">=</span> <span class="op">[</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t257" href="#t257">257</a></span><span class="t">        <span class="nam">variances</span> <span class="op">=</span> <span class="op">[</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t258" href="#t258">258</a></span><span class="t">        <span class="nam">bics</span> <span class="op">=</span> <span class="op">[</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t259" href="#t259">259</a></span><span class="t">        <span class="nam">weights</span> <span class="op">=</span> <span class="op">[</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t260" href="#t260">260</a></span><span class="t">        <span class="key">for</span> <span class="nam">n_components</span> <span class="key">in</span> <span class="op">(</span><span class="num">1</span><span class="op">,</span> <span class="num">2</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t261" href="#t261">261</a></span><span class="t">            <span class="nam">gmm</span> <span class="op">=</span> <span class="nam">GaussianMixture</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t262" href="#t262">262</a></span><span class="t">                <span class="nam">n_components</span><span class="op">=</span><span class="nam">n_components</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t263" href="#t263">263</a></span><span class="t">                <span class="nam">max_iter</span><span class="op">=</span><span class="nam">self</span><span class="op">.</span><span class="nam">max_iter</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t264" href="#t264">264</a></span><span class="t">                <span class="nam">tol</span><span class="op">=</span><span class="nam">self</span><span class="op">.</span><span class="nam">tol</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t265" href="#t265">265</a></span><span class="t">            <span class="nam">gmm</span> <span class="op">=</span> <span class="nam">gmm</span><span class="op">.</span><span class="nam">fit</span><span class="op">(</span><span class="nam">data</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t266" href="#t266">266</a></span><span class="t">            <span class="nam">m</span> <span class="op">=</span> <span class="nam">gmm</span><span class="op">.</span><span class="nam">means_</span><span class="op">.</span><span class="nam">flatten</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t267" href="#t267">267</a></span><span class="t">            <span class="nam">v</span> <span class="op">=</span> <span class="nam">gmm</span><span class="op">.</span><span class="nam">covariances_</span><span class="op">.</span><span class="nam">flatten</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t268" href="#t268">268</a></span><span class="t">            <span class="nam">b</span> <span class="op">=</span> <span class="nam">gmm</span><span class="op">.</span><span class="nam">bic</span><span class="op">(</span><span class="nam">data</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t269" href="#t269">269</a></span><span class="t">            <span class="nam">w</span> <span class="op">=</span> <span class="nam">gmm</span><span class="op">.</span><span class="nam">weights_</span><span class="op">.</span><span class="nam">flatten</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t270" href="#t270">270</a></span><span class="t">            <span class="nam">means</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="nam">m</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t271" href="#t271">271</a></span><span class="t">            <span class="nam">variances</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="nam">v</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t272" href="#t272">272</a></span><span class="t">            <span class="nam">bics</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="nam">b</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t273" href="#t273">273</a></span><span class="t">            <span class="nam">weights</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="nam">w</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t274" href="#t274">274</a></span><span class="t">        <span class="key">return</span> <span class="nam">means</span><span class="op">,</span> <span class="nam">variances</span><span class="op">,</span> <span class="nam">bics</span><span class="op">,</span> <span class="nam">weights</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t275" href="#t275">275</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t276" href="#t276">276</a></span><span class="t">    <span class="key">def</span> <span class="nam">bayes_factor_criteria</span><span class="op">(</span><span class="nam">self</span><span class="op">,</span> <span class="nam">bic1</span><span class="op">,</span> <span class="nam">bic2</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t277" href="#t277">277</a></span><span class="t">        <span class="nam">diff_bic</span> <span class="op">=</span> <span class="nam">bic2</span> <span class="op">-</span> <span class="nam">bic1</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t278" href="#t278">278</a></span><span class="t">        <span class="com"># probability of a two-component model</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t279" href="#t279">279</a></span><span class="t">        <span class="nam">p</span> <span class="op">=</span> <span class="num">1</span> <span class="op">/</span> <span class="op">(</span><span class="num">1</span> <span class="op">+</span> <span class="nam">np</span><span class="op">.</span><span class="nam">exp</span><span class="op">(</span><span class="num">0.5</span><span class="op">*</span><span class="nam">diff_bic</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t280" href="#t280">280</a></span><span class="t">        <span class="key">if</span> <span class="nam">p</span> <span class="op">==</span> <span class="nam">np</span><span class="op">.</span><span class="nam">nan</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t281" href="#t281">281</a></span><span class="t">            <span class="key">if</span> <span class="nam">bic1</span> <span class="op">==</span> <span class="nam">np</span><span class="op">.</span><span class="nam">nan</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t282" href="#t282">282</a></span><span class="t">                <span class="nam">p</span> <span class="op">=</span> <span class="num">1</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t283" href="#t283">283</a></span><span class="t">            <span class="key">elif</span> <span class="nam">bic2</span> <span class="op">==</span> <span class="nam">np</span><span class="op">.</span><span class="nam">nan</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t284" href="#t284">284</a></span><span class="t">                <span class="nam">p</span> <span class="op">=</span> <span class="num">0</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t285" href="#t285">285</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t286" href="#t286">286</a></span><span class="t">        <span class="nam">uninormal</span> <span class="op">=</span> <span class="nam">p</span> <span class="op">&lt;</span> <span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">confidence_level</span> <span class="op">/</span> <span class="num">100</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t287" href="#t287">287</a></span><span class="t">        <span class="nam">binormal</span> <span class="op">=</span> <span class="nam">p</span> <span class="op">></span> <span class="op">(</span><span class="num">1</span> <span class="op">-</span> <span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">confidence_level</span> <span class="op">/</span> <span class="num">100</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t288" href="#t288">288</a></span><span class="t">        <span class="nam">insuf_ev</span> <span class="op">=</span> <span class="key">True</span> <span class="key">if</span> <span class="op">(</span><span class="key">not</span> <span class="nam">uninormal</span> <span class="key">and</span> <span class="key">not</span> <span class="nam">binormal</span><span class="op">)</span> <span class="key">else</span> <span class="key">False</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t289" href="#t289">289</a></span><span class="t">        <span class="key">return</span> <span class="nam">uninormal</span><span class="op">,</span> <span class="nam">binormal</span><span class="op">,</span> <span class="nam">insuf_ev</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t290" href="#t290">290</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t291" href="#t291">291</a></span><span class="t">    <span class="key">def</span> <span class="nam">helguero_theorem</span><span class="op">(</span><span class="nam">self</span><span class="op">,</span> <span class="nam">mean1</span><span class="op">,</span> <span class="nam">mean2</span><span class="op">,</span> <span class="nam">var1</span><span class="op">,</span> <span class="nam">var2</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t292" href="#t292">292</a></span><span class="t">        <span class="nam">r</span> <span class="op">=</span> <span class="nam">var1</span> <span class="op">/</span> <span class="nam">var2</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t293" href="#t293">293</a></span><span class="t">        <span class="nam">separation_factor</span> <span class="op">=</span> <span class="nam">np</span><span class="op">.</span><span class="nam">sqrt</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t294" href="#t294">294</a></span><span class="t">            <span class="op">-</span><span class="num">2</span> <span class="op">+</span> <span class="num">3</span><span class="op">*</span><span class="nam">r</span> <span class="op">+</span> <span class="num">3</span><span class="op">*</span><span class="nam">r</span><span class="op">**</span><span class="num">2</span> <span class="op">-</span> <span class="num">2</span><span class="op">*</span><span class="nam">r</span><span class="op">**</span><span class="num">3</span> <span class="op">+</span> <span class="num">2</span><span class="op">*</span><span class="op">(</span><span class="num">1</span> <span class="op">-</span> <span class="nam">r</span> <span class="op">+</span> <span class="nam">r</span><span class="op">**</span><span class="num">2</span><span class="op">)</span><span class="op">**</span><span class="num">1.5</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t295" href="#t295">295</a></span><span class="t">        <span class="op">)</span> <span class="op">/</span> <span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t296" href="#t296">296</a></span><span class="t">            <span class="nam">np</span><span class="op">.</span><span class="nam">sqrt</span><span class="op">(</span><span class="nam">r</span><span class="op">)</span><span class="op">*</span><span class="op">(</span><span class="num">1</span><span class="op">+</span><span class="nam">np</span><span class="op">.</span><span class="nam">sqrt</span><span class="op">(</span><span class="nam">r</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t297" href="#t297">297</a></span><span class="t">        <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t298" href="#t298">298</a></span><span class="t">        <span class="nam">bimodal</span> <span class="op">=</span> <span class="nam">abs</span><span class="op">(</span><span class="nam">mean2</span><span class="op">-</span><span class="nam">mean1</span><span class="op">)</span> <span class="op">></span> <span class="nam">separation_factor</span> <span class="op">*</span> <span class="xx">\</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t299" href="#t299">299</a></span><span class="t">            <span class="op">(</span><span class="nam">np</span><span class="op">.</span><span class="nam">sqrt</span><span class="op">(</span><span class="nam">var1</span><span class="op">)</span> <span class="op">+</span> <span class="nam">np</span><span class="op">.</span><span class="nam">sqrt</span><span class="op">(</span><span class="nam">var2</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t300" href="#t300">300</a></span><span class="t">        <span class="key">return</span> <span class="nam">bimodal</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t301" href="#t301">301</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t302" href="#t302">302</a></span><span class="t"><span class="key">def</span> <span class="nam">dna_bimodality</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t303" href="#t303">303</a></span><span class="t">        <span class="nam">input_csv_file</span><span class="op">,</span> <span class="nam">output_csv_path</span><span class="op">,</span> <span class="nam">output_jpg_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t304" href="#t304">304</a></span><span class="t">        <span class="nam">input_zip_file</span><span class="op">:</span> <span class="nam">str</span> <span class="op">=</span> <span class="key">None</span><span class="op">,</span> <span class="nam">properties</span><span class="op">:</span> <span class="nam">dict</span> <span class="op">=</span> <span class="key">None</span><span class="op">,</span> <span class="op">**</span><span class="nam">kwargs</span><span class="op">)</span> <span class="op">-></span> <span class="nam">int</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t305" href="#t305">305</a></span><span class="t">    <span class="str">"""Create :class:`HelParBimodality &lt;dna.dna_bimodality.HelParBimodality>` class and</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t306" href="#t306">306</a></span><span class="t"><span class="str">    execute the :meth:`launch() &lt;dna.dna_bimodality.HelParBimodality.launch>` method."""</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t307" href="#t307">307</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t308" href="#t308">308</a></span><span class="t">    <span class="key">return</span> <span class="nam">HelParBimodality</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t309" href="#t309">309</a></span><span class="t">        <span class="nam">input_csv_file</span><span class="op">=</span><span class="nam">input_csv_file</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t310" href="#t310">310</a></span><span class="t">        <span class="nam">input_zip_file</span><span class="op">=</span><span class="nam">input_zip_file</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t311" href="#t311">311</a></span><span class="t">        <span class="nam">output_csv_path</span><span class="op">=</span><span class="nam">output_csv_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t312" href="#t312">312</a></span><span class="t">        <span class="nam">output_jpg_path</span><span class="op">=</span><span class="nam">output_jpg_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t313" href="#t313">313</a></span><span class="t">        <span class="nam">properties</span><span class="op">=</span><span class="nam">properties</span><span class="op">,</span> <span class="op">**</span><span class="nam">kwargs</span><span class="op">)</span><span class="op">.</span><span class="nam">launch</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t314" href="#t314">314</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t302" href="#t302">302</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t303" href="#t303">303</a></span><span class="t"><span class="key">def</span> <span class="nam">dna_bimodality</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t304" href="#t304">304</a></span><span class="t">        <span class="nam">input_csv_file</span><span class="op">,</span> <span class="nam">output_csv_path</span><span class="op">,</span> <span class="nam">output_jpg_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t305" href="#t305">305</a></span><span class="t">        <span class="nam">input_zip_file</span><span class="op">:</span> <span class="nam">str</span> <span class="op">=</span> <span class="key">None</span><span class="op">,</span> <span class="nam">properties</span><span class="op">:</span> <span class="nam">dict</span> <span class="op">=</span> <span class="key">None</span><span class="op">,</span> <span class="op">**</span><span class="nam">kwargs</span><span class="op">)</span> <span class="op">-></span> <span class="nam">int</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t306" href="#t306">306</a></span><span class="t">    <span class="str">"""Create :class:`HelParBimodality &lt;dna.dna_bimodality.HelParBimodality>` class and</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t307" href="#t307">307</a></span><span class="t"><span class="str">    execute the :meth:`launch() &lt;dna.dna_bimodality.HelParBimodality.launch>` method."""</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t308" href="#t308">308</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t309" href="#t309">309</a></span><span class="t">    <span class="key">return</span> <span class="nam">HelParBimodality</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t310" href="#t310">310</a></span><span class="t">        <span class="nam">input_csv_file</span><span class="op">=</span><span class="nam">input_csv_file</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t311" href="#t311">311</a></span><span class="t">        <span class="nam">input_zip_file</span><span class="op">=</span><span class="nam">input_zip_file</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t312" href="#t312">312</a></span><span class="t">        <span class="nam">output_csv_path</span><span class="op">=</span><span class="nam">output_csv_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t313" href="#t313">313</a></span><span class="t">        <span class="nam">output_jpg_path</span><span class="op">=</span><span class="nam">output_jpg_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t314" href="#t314">314</a></span><span class="t">        <span class="nam">properties</span><span class="op">=</span><span class="nam">properties</span><span class="op">,</span> <span class="op">**</span><span class="nam">kwargs</span><span class="op">)</span><span class="op">.</span><span class="nam">launch</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t315" href="#t315">315</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t316" href="#t316">316</a></span><span class="t"><span class="key">def</span> <span class="nam">main</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t317" href="#t317">317</a></span><span class="t">    <span class="str">"""Command line execution of this building block. Please check the command line documentation."""</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t318" href="#t318">318</a></span><span class="t">    <span class="nam">parser</span> <span class="op">=</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">ArgumentParser</span><span class="op">(</span><span class="nam">description</span><span class="op">=</span><span class="str">'Determine binormality/bimodality from a helical parameter dataset.'</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t319" href="#t319">319</a></span><span class="t">                                     <span class="nam">formatter_class</span><span class="op">=</span><span class="key">lambda</span> <span class="nam">prog</span><span class="op">:</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">RawTextHelpFormatter</span><span class="op">(</span><span class="nam">prog</span><span class="op">,</span> <span class="nam">width</span><span class="op">=</span><span class="num">99999</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t320" href="#t320">320</a></span><span class="t">    <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--config'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">False</span><span class="op">,</span> <span class="nam">help</span><span class="op">=</span><span class="str">'Configuration file'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t321" href="#t321">321</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t322" href="#t322">322</a></span><span class="t">    <span class="nam">required_args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument_group</span><span class="op">(</span><span class="str">'required arguments'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t323" href="#t323">323</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--input_csv_file'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t324" href="#t324">324</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Path to csv file with data. Accepted formats: csv.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t325" href="#t325">325</a></span><span class="t">    <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--input_zip_file'</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t326" href="#t326">326</a></span><span class="t">                        <span class="nam">help</span><span class="op">=</span><span class="str">'Path to zip file containing csv input files. Accepted formats: zip.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t327" href="#t327">327</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--output_csv_path'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t328" href="#t328">328</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Filename and/or path of output csv file.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t329" href="#t329">329</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--output_jpg_path'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t330" href="#t330">330</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Filename and/or path of output jpg file.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t331" href="#t331">331</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t332" href="#t332">332</a></span><span class="t">    <span class="nam">args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">parse_args</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t333" href="#t333">333</a></span><span class="t">    <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="op">=</span> <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="key">or</span> <span class="str">"{}"</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t334" href="#t334">334</a></span><span class="t">    <span class="nam">properties</span> <span class="op">=</span> <span class="nam">settings</span><span class="op">.</span><span class="nam">ConfReader</span><span class="op">(</span><span class="nam">config</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">config</span><span class="op">)</span><span class="op">.</span><span class="nam">get_prop_dic</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t335" href="#t335">335</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t336" href="#t336">336</a></span><span class="t">    <span class="nam">dna_bimodality</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t337" href="#t337">337</a></span><span class="t">        <span class="nam">input_csv_file</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_csv_file</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t338" href="#t338">338</a></span><span class="t">        <span class="nam">input_zip_file</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_zip_file</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t339" href="#t339">339</a></span><span class="t">        <span class="nam">output_csv_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">output_csv_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t340" href="#t340">340</a></span><span class="t">        <span class="nam">output_jpg_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">output_jpg_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t341" href="#t341">341</a></span><span class="t">        <span class="nam">properties</span><span class="op">=</span><span class="nam">properties</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t342" href="#t342">342</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t316" href="#t316">316</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t317" href="#t317">317</a></span><span class="t"><span class="key">def</span> <span class="nam">main</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t318" href="#t318">318</a></span><span class="t">    <span class="str">"""Command line execution of this building block. Please check the command line documentation."""</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t319" href="#t319">319</a></span><span class="t">    <span class="nam">parser</span> <span class="op">=</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">ArgumentParser</span><span class="op">(</span><span class="nam">description</span><span class="op">=</span><span class="str">'Determine binormality/bimodality from a helical parameter dataset.'</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t320" href="#t320">320</a></span><span class="t">                                     <span class="nam">formatter_class</span><span class="op">=</span><span class="key">lambda</span> <span class="nam">prog</span><span class="op">:</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">RawTextHelpFormatter</span><span class="op">(</span><span class="nam">prog</span><span class="op">,</span> <span class="nam">width</span><span class="op">=</span><span class="num">99999</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t321" href="#t321">321</a></span><span class="t">    <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--config'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">False</span><span class="op">,</span> <span class="nam">help</span><span class="op">=</span><span class="str">'Configuration file'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t322" href="#t322">322</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t323" href="#t323">323</a></span><span class="t">    <span class="nam">required_args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument_group</span><span class="op">(</span><span class="str">'required arguments'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t324" href="#t324">324</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--input_csv_file'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t325" href="#t325">325</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Path to csv file with data. Accepted formats: csv.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t326" href="#t326">326</a></span><span class="t">    <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--input_zip_file'</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t327" href="#t327">327</a></span><span class="t">                        <span class="nam">help</span><span class="op">=</span><span class="str">'Path to zip file containing csv input files. Accepted formats: zip.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t328" href="#t328">328</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--output_csv_path'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t329" href="#t329">329</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Filename and/or path of output csv file.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t330" href="#t330">330</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--output_jpg_path'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t331" href="#t331">331</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Filename and/or path of output jpg file.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t332" href="#t332">332</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t333" href="#t333">333</a></span><span class="t">    <span class="nam">args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">parse_args</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t334" href="#t334">334</a></span><span class="t">    <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="op">=</span> <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="key">or</span> <span class="str">"{}"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t335" href="#t335">335</a></span><span class="t">    <span class="nam">properties</span> <span class="op">=</span> <span class="nam">settings</span><span class="op">.</span><span class="nam">ConfReader</span><span class="op">(</span><span class="nam">config</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">config</span><span class="op">)</span><span class="op">.</span><span class="nam">get_prop_dic</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t336" href="#t336">336</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t337" href="#t337">337</a></span><span class="t">    <span class="nam">dna_bimodality</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t338" href="#t338">338</a></span><span class="t">        <span class="nam">input_csv_file</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_csv_file</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t339" href="#t339">339</a></span><span class="t">        <span class="nam">input_zip_file</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_zip_file</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t340" href="#t340">340</a></span><span class="t">        <span class="nam">output_csv_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">output_csv_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t341" href="#t341">341</a></span><span class="t">        <span class="nam">output_jpg_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">output_jpg_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t342" href="#t342">342</a></span><span class="t">        <span class="nam">properties</span><span class="op">=</span><span class="nam">properties</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t343" href="#t343">343</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t344" href="#t344">344</a></span><span class="t"><span class="key">if</span> <span class="nam">__name__</span> <span class="op">==</span> <span class="str">'__main__'</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t345" href="#t345">345</a></span><span class="t">    <span class="nam">main</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t344" href="#t344">344</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t345" href="#t345">345</a></span><span class="t"><span class="key">if</span> <span class="nam">__name__</span> <span class="op">==</span> <span class="str">'__main__'</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t346" href="#t346">346</a></span><span class="t">    <span class="nam">main</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
 </main>
 <footer>
     <div class="content">
@@ -434,7 +435,7 @@ <h2>
             <a class="nav" href="z_3afbcd666ed82c91_dna_timeseries_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.5.1">coverage.py v7.5.1</a>,
-            created at 2024-05-07 09:06 +0000
+            created at 2024-05-24 09:29 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_3afbcd666ed82c91_dna_timeseries_py.html b/coverage/z_3afbcd666ed82c91_dna_timeseries_py.html
index 41297bb8..eb15e5ab 100644
--- a/coverage/z_3afbcd666ed82c91_dna_timeseries_py.html
+++ b/coverage/z_3afbcd666ed82c91_dna_timeseries_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_8a2a7f872cf1434f___init___py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.5.1">coverage.py v7.5.1</a>,
-            created at 2024-05-07 09:06 +0000
+            created at 2024-05-24 09:29 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -102,257 +102,258 @@ <h2>
     <p class="pln"><span class="n"><a id="t20" href="#t20">20</a></span><span class="t">    <span class="str">"""</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t21" href="#t21">21</a></span><span class="t"><span class="str">    | biobb_dna HelParTimeSeries</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t22" href="#t22">22</a></span><span class="t"><span class="str">    | Created time series and histogram plots for each base pair from a helical parameter series file.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t23" href="#t23">23</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t24" href="#t24">24</a></span><span class="t"><span class="str">    Args:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t25" href="#t25">25</a></span><span class="t"><span class="str">        input_ser_path (str): Path to .ser file for helical parameter. File is expected to be a table, with the first column being an index and the rest the helical parameter values for each base/basepair. File type: input. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/dna/canal_output_shift.ser>`_. Accepted formats: ser (edam:format_2330).</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t26" href="#t26">26</a></span><span class="t"><span class="str">        output_zip_path (str): Path to output .zip files where data is saved. File type: output. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/reference/dna/timeseries_output.zip>`_. Accepted formats: zip (edam:format_3987).</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t27" href="#t27">27</a></span><span class="t"><span class="str">        properties (dict):</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t28" href="#t28">28</a></span><span class="t"><span class="str">            * **sequence** (*str*) - (None) Nucleic acid sequence corresponding to the input .ser file. Length of sequence is expected to be the same as the total number of columns in the .ser file, minus the index column (even if later on a subset of columns is selected with the *usecols* option).</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t29" href="#t29">29</a></span><span class="t"><span class="str">            * **bins** (*int*) - (None) Bins for histogram. Parameter has same options as matplotlib.pyplot.hist.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t30" href="#t30">30</a></span><span class="t"><span class="str">            * **helpar_name** (*str*) - (Optional) helical parameter name.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t31" href="#t31">31</a></span><span class="t"><span class="str">            * **stride** (*int*) - (1000) granularity of the number of snapshots for plotting time series.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t32" href="#t32">32</a></span><span class="t"><span class="str">            * **seqpos** (*list*) - (None) list of sequence positions (columns indices starting by 0) to analyze.  If not specified it will analyse the complete sequence.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t33" href="#t33">33</a></span><span class="t"><span class="str">            * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t34" href="#t34">34</a></span><span class="t"><span class="str">            * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t35" href="#t35">35</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t36" href="#t36">36</a></span><span class="t"><span class="str">    Examples:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t37" href="#t37">37</a></span><span class="t"><span class="str">        This is a use example of how to use the building block from Python::</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t38" href="#t38">38</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t39" href="#t39">39</a></span><span class="t"><span class="str">            from biobb_dna.dna.dna_timeseries import dna_timeseries</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t40" href="#t40">40</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t41" href="#t41">41</a></span><span class="t"><span class="str">            prop = {</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t42" href="#t42">42</a></span><span class="t"><span class="str">                'helpar_name': 'twist',</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t43" href="#t43">43</a></span><span class="t"><span class="str">                'seqpos': [1,2,3,4,5],</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t44" href="#t44">44</a></span><span class="t"><span class="str">                'sequence': 'GCAACGTGCTATGGAAGC',</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t45" href="#t45">45</a></span><span class="t"><span class="str">            }</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t46" href="#t46">46</a></span><span class="t"><span class="str">            dna_timeseries(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t47" href="#t47">47</a></span><span class="t"><span class="str">                input_ser_path='/path/to/twist.ser',</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t48" href="#t48">48</a></span><span class="t"><span class="str">                output_zip_path='/path/to/output/file.zip'</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t49" href="#t49">49</a></span><span class="t"><span class="str">                properties=prop)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t50" href="#t50">50</a></span><span class="t"><span class="str">    Info:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t51" href="#t51">51</a></span><span class="t"><span class="str">        * wrapped_software:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t52" href="#t52">52</a></span><span class="t"><span class="str">            * name: In house</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t53" href="#t53">53</a></span><span class="t"><span class="str">            * license: Apache-2.0</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t54" href="#t54">54</a></span><span class="t"><span class="str">        * ontology:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t55" href="#t55">55</a></span><span class="t"><span class="str">            * name: EDAM</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t56" href="#t56">56</a></span><span class="t"><span class="str">            * schema: http://edamontology.org/EDAM.owl</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t57" href="#t57">57</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t58" href="#t58">58</a></span><span class="t"><span class="str">    """</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t59" href="#t59">59</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t60" href="#t60">60</a></span><span class="t">    <span class="key">def</span> <span class="nam">__init__</span><span class="op">(</span><span class="nam">self</span><span class="op">,</span> <span class="nam">input_ser_path</span><span class="op">,</span> <span class="nam">output_zip_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t61" href="#t61">61</a></span><span class="t">                 <span class="nam">properties</span><span class="op">=</span><span class="key">None</span><span class="op">,</span> <span class="op">**</span><span class="nam">kwargs</span><span class="op">)</span> <span class="op">-></span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t62" href="#t62">62</a></span><span class="t">        <span class="nam">properties</span> <span class="op">=</span> <span class="nam">properties</span> <span class="key">or</span> <span class="op">{</span><span class="op">}</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t63" href="#t63">63</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t64" href="#t64">64</a></span><span class="t">        <span class="com"># Call parent class constructor</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t65" href="#t65">65</a></span><span class="t">        <span class="nam">super</span><span class="op">(</span><span class="op">)</span><span class="op">.</span><span class="nam">__init__</span><span class="op">(</span><span class="nam">properties</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t66" href="#t66">66</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">locals_var_dict</span> <span class="op">=</span> <span class="nam">locals</span><span class="op">(</span><span class="op">)</span><span class="op">.</span><span class="nam">copy</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t67" href="#t67">67</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t68" href="#t68">68</a></span><span class="t">        <span class="com"># Input/Output files</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t69" href="#t69">69</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span> <span class="op">=</span> <span class="op">{</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t70" href="#t70">70</a></span><span class="t">            <span class="str">'in'</span><span class="op">:</span> <span class="op">{</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t71" href="#t71">71</a></span><span class="t">                <span class="str">'input_ser_path'</span><span class="op">:</span> <span class="nam">input_ser_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t72" href="#t72">72</a></span><span class="t">            <span class="op">}</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t73" href="#t73">73</a></span><span class="t">            <span class="str">'out'</span><span class="op">:</span> <span class="op">{</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t74" href="#t74">74</a></span><span class="t">                <span class="str">'output_zip_path'</span><span class="op">:</span> <span class="nam">output_zip_path</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t75" href="#t75">75</a></span><span class="t">            <span class="op">}</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t76" href="#t76">76</a></span><span class="t">        <span class="op">}</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t77" href="#t77">77</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t78" href="#t78">78</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">properties</span> <span class="op">=</span> <span class="nam">properties</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t79" href="#t79">79</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"sequence"</span><span class="op">,</span> <span class="key">None</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t80" href="#t80">80</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">bins</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"bins"</span><span class="op">,</span> <span class="str">"auto"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t81" href="#t81">81</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">stride</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t82" href="#t82">82</a></span><span class="t">            <span class="str">"stride"</span><span class="op">,</span> <span class="num">10</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t83" href="#t83">83</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t84" href="#t84">84</a></span><span class="t">            <span class="str">"seqpos"</span><span class="op">,</span> <span class="key">None</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t85" href="#t85">85</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">helpar_name</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t86" href="#t86">86</a></span><span class="t">            <span class="str">"helpar_name"</span><span class="op">,</span> <span class="key">None</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t87" href="#t87">87</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t88" href="#t88">88</a></span><span class="t">        <span class="com"># get helical parameter from filename if not specified</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t89" href="#t89">89</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">helpar_name</span> <span class="key">is</span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t90" href="#t90">90</a></span><span class="t">            <span class="key">for</span> <span class="nam">hp</span> <span class="key">in</span> <span class="nam">constants</span><span class="op">.</span><span class="nam">helical_parameters</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t91" href="#t91">91</a></span><span class="t">                <span class="key">if</span> <span class="nam">hp</span><span class="op">.</span><span class="nam">lower</span><span class="op">(</span><span class="op">)</span> <span class="key">in</span> <span class="nam">Path</span><span class="op">(</span><span class="nam">input_ser_path</span><span class="op">)</span><span class="op">.</span><span class="nam">name</span><span class="op">.</span><span class="nam">lower</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t92" href="#t92">92</a></span><span class="t">                    <span class="nam">self</span><span class="op">.</span><span class="nam">helpar_name</span> <span class="op">=</span> <span class="nam">hp</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t93" href="#t93">93</a></span><span class="t">            <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">helpar_name</span> <span class="key">is</span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t94" href="#t94">94</a></span><span class="t">                <span class="key">raise</span> <span class="nam">ValueError</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t95" href="#t95">95</a></span><span class="t">                    <span class="str">"Helical parameter name can't be inferred from file, "</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t96" href="#t96">96</a></span><span class="t">                    <span class="str">"so it must be specified!"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t97" href="#t97">97</a></span><span class="t">        <span class="key">else</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t98" href="#t98">98</a></span><span class="t">            <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">helpar_name</span> <span class="key">not</span> <span class="key">in</span> <span class="nam">constants</span><span class="op">.</span><span class="nam">helical_parameters</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t99" href="#t99">99</a></span><span class="t">                <span class="key">raise</span> <span class="nam">ValueError</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t100" href="#t100">100</a></span><span class="t">                    <span class="str">"Helical parameter name is invalid! "</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t101" href="#t101">101</a></span><span class="t">                    <span class="str">f"Options: {constants.helical_parameters}"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t102" href="#t102">102</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t103" href="#t103">103</a></span><span class="t">        <span class="com"># get base length and unit from helical parameter name</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t104" href="#t104">104</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">helpar_name</span><span class="op">.</span><span class="nam">lower</span><span class="op">(</span><span class="op">)</span> <span class="key">in</span> <span class="nam">constants</span><span class="op">.</span><span class="nam">hp_singlebases</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t105" href="#t105">105</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">baselen</span> <span class="op">=</span> <span class="num">0</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t106" href="#t106">106</a></span><span class="t">        <span class="key">else</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t107" href="#t107">107</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">baselen</span> <span class="op">=</span> <span class="num">1</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t108" href="#t108">108</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">helpar_name</span> <span class="key">in</span> <span class="nam">constants</span><span class="op">.</span><span class="nam">hp_angular</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t109" href="#t109">109</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">hp_unit</span> <span class="op">=</span> <span class="str">"Degrees"</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t110" href="#t110">110</a></span><span class="t">        <span class="key">else</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t111" href="#t111">111</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">hp_unit</span> <span class="op">=</span> <span class="str">"Angstroms"</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t112" href="#t112">112</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t113" href="#t113">113</a></span><span class="t">        <span class="com"># Check the properties</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t114" href="#t114">114</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_properties</span><span class="op">(</span><span class="nam">properties</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t115" href="#t115">115</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_arguments</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t116" href="#t116">116</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t117" href="#t117">117</a></span><span class="t">    <span class="op">@</span><span class="nam">launchlogger</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t118" href="#t118">118</a></span><span class="t">    <span class="key">def</span> <span class="nam">launch</span><span class="op">(</span><span class="nam">self</span><span class="op">)</span> <span class="op">-></span> <span class="nam">int</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t119" href="#t119">119</a></span><span class="t">        <span class="str">"""Execute the :class:`HelParTimeSeries &lt;dna.dna_timeseries.HelParTimeSeries>` object."""</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t120" href="#t120">120</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t121" href="#t121">121</a></span><span class="t">        <span class="com"># Setup Biobb</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t122" href="#t122">122</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">check_restart</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t123" href="#t123">123</a></span><span class="t">            <span class="key">return</span> <span class="num">0</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t124" href="#t124">124</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">stage_files</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t125" href="#t125">125</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t126" href="#t126">126</a></span><span class="t">        <span class="com"># check sequence</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t127" href="#t127">127</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span> <span class="key">is</span> <span class="key">None</span> <span class="key">or</span> <span class="nam">len</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span><span class="op">)</span> <span class="op">&lt;</span> <span class="num">2</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t128" href="#t128">128</a></span><span class="t">            <span class="key">raise</span> <span class="nam">ValueError</span><span class="op">(</span><span class="str">"sequence is null or too short!"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t129" href="#t129">129</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t130" href="#t130">130</a></span><span class="t">        <span class="com"># check seqpos</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t131" href="#t131">131</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span> <span class="key">is</span> <span class="key">not</span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t132" href="#t132">132</a></span><span class="t">            <span class="key">if</span> <span class="op">(</span><span class="nam">max</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">)</span> <span class="op">></span> <span class="nam">len</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span><span class="op">)</span> <span class="op">-</span> <span class="num">2</span><span class="op">)</span> <span class="key">or</span> <span class="op">(</span><span class="nam">min</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">)</span> <span class="op">&lt;</span> <span class="num">1</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t133" href="#t133">133</a></span><span class="t">                <span class="key">raise</span> <span class="nam">ValueError</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t134" href="#t134">134</a></span><span class="t">                    <span class="str">f"seqpos values must be between 1 and {len(self.sequence) - 2}"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t135" href="#t135">135</a></span><span class="t">            <span class="key">if</span> <span class="key">not</span> <span class="op">(</span><span class="nam">isinstance</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">,</span> <span class="nam">list</span><span class="op">)</span> <span class="key">and</span> <span class="nam">len</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">)</span> <span class="op">></span> <span class="num">1</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t136" href="#t136">136</a></span><span class="t">                <span class="key">raise</span> <span class="nam">ValueError</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t137" href="#t137">137</a></span><span class="t">                    <span class="str">"seqpos must be a list of at least two integers"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t138" href="#t138">138</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t139" href="#t139">139</a></span><span class="t">        <span class="com"># Creating temporary folder</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t140" href="#t140">140</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span> <span class="op">=</span> <span class="nam">fu</span><span class="op">.</span><span class="nam">create_unique_dir</span><span class="op">(</span><span class="nam">prefix</span><span class="op">=</span><span class="str">"timeseries_"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t141" href="#t141">141</a></span><span class="t">        <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="str">'Creating %s temporary folder'</span> <span class="op">%</span> <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t142" href="#t142">142</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t143" href="#t143">143</a></span><span class="t">        <span class="com"># Copy input_ser_path to temporary folder</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t144" href="#t144">144</a></span><span class="t">        <span class="nam">shutil</span><span class="op">.</span><span class="nam">copy</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'input_ser_path'</span><span class="op">]</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t145" href="#t145">145</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t146" href="#t146">146</a></span><span class="t">        <span class="com"># read input .ser file</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t147" href="#t147">147</a></span><span class="t">        <span class="nam">ser_data</span> <span class="op">=</span> <span class="nam">read_series</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t148" href="#t148">148</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'input_ser_path'</span><span class="op">]</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t149" href="#t149">149</a></span><span class="t">            <span class="nam">usecols</span><span class="op">=</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t150" href="#t150">150</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span> <span class="key">is</span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t151" href="#t151">151</a></span><span class="t">            <span class="nam">ser_data</span> <span class="op">=</span> <span class="nam">ser_data</span><span class="op">[</span><span class="nam">ser_data</span><span class="op">.</span><span class="nam">columns</span><span class="op">[</span><span class="num">1</span><span class="op">:</span><span class="op">-</span><span class="num">1</span><span class="op">]</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t152" href="#t152">152</a></span><span class="t">            <span class="com"># discard first and last base(pairs) from sequence</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t153" href="#t153">153</a></span><span class="t">            <span class="nam">sequence</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span><span class="op">[</span><span class="num">1</span><span class="op">:</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t154" href="#t154">154</a></span><span class="t">            <span class="nam">subunits</span> <span class="op">=</span> <span class="op">[</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t155" href="#t155">155</a></span><span class="t">                <span class="str">f"{i+1}_{sequence[i:i+1+self.baselen]}"</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t156" href="#t156">156</a></span><span class="t">                <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">range</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">ser_data</span><span class="op">.</span><span class="nam">columns</span><span class="op">)</span><span class="op">)</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t157" href="#t157">157</a></span><span class="t">        <span class="key">else</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t158" href="#t158">158</a></span><span class="t">            <span class="nam">sequence</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t159" href="#t159">159</a></span><span class="t">            <span class="nam">subunits</span> <span class="op">=</span> <span class="op">[</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t160" href="#t160">160</a></span><span class="t">                <span class="str">f"{i+1}_{sequence[i:i+1+self.baselen]}"</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t161" href="#t161">161</a></span><span class="t">                <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t162" href="#t162">162</a></span><span class="t">        <span class="nam">ser_data</span><span class="op">.</span><span class="nam">columns</span> <span class="op">=</span> <span class="nam">subunits</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t163" href="#t163">163</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t164" href="#t164">164</a></span><span class="t">        <span class="com"># write output files for all selected bases (one per column)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t165" href="#t165">165</a></span><span class="t">        <span class="nam">zf</span> <span class="op">=</span> <span class="nam">zipfile</span><span class="op">.</span><span class="nam">ZipFile</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t166" href="#t166">166</a></span><span class="t">            <span class="nam">Path</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">"out"</span><span class="op">]</span><span class="op">[</span><span class="str">"output_zip_path"</span><span class="op">]</span><span class="op">)</span><span class="op">,</span> <span class="str">"w"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t167" href="#t167">167</a></span><span class="t">        <span class="key">for</span> <span class="nam">col</span> <span class="key">in</span> <span class="nam">ser_data</span><span class="op">.</span><span class="nam">columns</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t168" href="#t168">168</a></span><span class="t">            <span class="com"># unstack columns to prevent errors from repeated base pairs</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t169" href="#t169">169</a></span><span class="t">            <span class="nam">column_data</span> <span class="op">=</span> <span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t170" href="#t170">170</a></span><span class="t">                <span class="nam">ser_data</span><span class="op">[</span><span class="op">[</span><span class="nam">col</span><span class="op">]</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t171" href="#t171">171</a></span><span class="t">                <span class="op">.</span><span class="nam">unstack</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t172" href="#t172">172</a></span><span class="t">                <span class="op">.</span><span class="nam">dropna</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t173" href="#t173">173</a></span><span class="t">                <span class="op">.</span><span class="nam">reset_index</span><span class="op">(</span><span class="nam">drop</span><span class="op">=</span><span class="key">True</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t174" href="#t174">174</a></span><span class="t">            <span class="nam">column_data</span><span class="op">.</span><span class="nam">name</span> <span class="op">=</span> <span class="nam">col</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t175" href="#t175">175</a></span><span class="t">            <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="str">f"Computing base number {col}..."</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t176" href="#t176">176</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t177" href="#t177">177</a></span><span class="t">            <span class="com"># column series</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t178" href="#t178">178</a></span><span class="t">            <span class="nam">series_colfn</span> <span class="op">=</span> <span class="str">f"series_{self.helpar_name}_{col}"</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t179" href="#t179">179</a></span><span class="t">            <span class="nam">column_data</span><span class="op">.</span><span class="nam">to_csv</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t180" href="#t180">180</a></span><span class="t">                <span class="nam">Path</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span><span class="op">)</span> <span class="op">/</span> <span class="str">f"{series_colfn}.csv"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t181" href="#t181">181</a></span><span class="t">            <span class="com"># save table</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t182" href="#t182">182</a></span><span class="t">            <span class="nam">zf</span><span class="op">.</span><span class="nam">write</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t183" href="#t183">183</a></span><span class="t">                <span class="nam">Path</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span><span class="op">)</span> <span class="op">/</span> <span class="str">f"{series_colfn}.csv"</span><span class="op">,</span> <span class="nam">arcname</span><span class="op">=</span><span class="str">f"{series_colfn}.csv"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t184" href="#t184">184</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t185" href="#t185">185</a></span><span class="t">            <span class="nam">fig</span><span class="op">,</span> <span class="nam">axs</span> <span class="op">=</span> <span class="nam">plt</span><span class="op">.</span><span class="nam">subplots</span><span class="op">(</span><span class="num">1</span><span class="op">,</span> <span class="num">1</span><span class="op">,</span> <span class="nam">dpi</span><span class="op">=</span><span class="num">300</span><span class="op">,</span> <span class="nam">tight_layout</span><span class="op">=</span><span class="key">True</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t186" href="#t186">186</a></span><span class="t">            <span class="nam">reduced_data</span> <span class="op">=</span> <span class="nam">column_data</span><span class="op">.</span><span class="nam">iloc</span><span class="op">[</span><span class="op">:</span><span class="op">:</span><span class="nam">self</span><span class="op">.</span><span class="nam">stride</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t187" href="#t187">187</a></span><span class="t">            <span class="nam">axs</span><span class="op">.</span><span class="nam">plot</span><span class="op">(</span><span class="nam">reduced_data</span><span class="op">.</span><span class="nam">index</span><span class="op">,</span> <span class="nam">reduced_data</span><span class="op">.</span><span class="nam">to_numpy</span><span class="op">(</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t188" href="#t188">188</a></span><span class="t">            <span class="nam">axs</span><span class="op">.</span><span class="nam">set_xlabel</span><span class="op">(</span><span class="str">"Time (Snapshots)"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t189" href="#t189">189</a></span><span class="t">            <span class="nam">axs</span><span class="op">.</span><span class="nam">set_ylabel</span><span class="op">(</span><span class="str">f"{self.helpar_name.capitalize()} ({self.hp_unit})"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t190" href="#t190">190</a></span><span class="t">            <span class="nam">axs</span><span class="op">.</span><span class="nam">set_title</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t191" href="#t191">191</a></span><span class="t">                <span class="str">f"Helical Parameter vs Time: {self.helpar_name.capitalize()} "</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t192" href="#t192">192</a></span><span class="t">                <span class="str">"(base pair "</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t193" href="#t193">193</a></span><span class="t">                <span class="str">f"{'step' if self.baselen==1 else ''} {col})"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t194" href="#t194">194</a></span><span class="t">            <span class="nam">fig</span><span class="op">.</span><span class="nam">savefig</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t195" href="#t195">195</a></span><span class="t">                <span class="nam">Path</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span><span class="op">)</span> <span class="op">/</span> <span class="str">f"{series_colfn}.jpg"</span><span class="op">,</span> <span class="nam">format</span><span class="op">=</span><span class="str">"jpg"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t196" href="#t196">196</a></span><span class="t">            <span class="com"># save plot</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t197" href="#t197">197</a></span><span class="t">            <span class="nam">zf</span><span class="op">.</span><span class="nam">write</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t198" href="#t198">198</a></span><span class="t">                <span class="nam">Path</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span><span class="op">)</span> <span class="op">/</span> <span class="str">f"{series_colfn}.jpg"</span><span class="op">,</span> <span class="nam">arcname</span><span class="op">=</span><span class="str">f"{series_colfn}.jpg"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t199" href="#t199">199</a></span><span class="t">            <span class="nam">plt</span><span class="op">.</span><span class="nam">close</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t200" href="#t200">200</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t201" href="#t201">201</a></span><span class="t">            <span class="com"># columns histogram</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t202" href="#t202">202</a></span><span class="t">            <span class="nam">hist_colfn</span> <span class="op">=</span> <span class="str">f"hist_{self.helpar_name}_{col}"</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t203" href="#t203">203</a></span><span class="t">            <span class="nam">fig</span><span class="op">,</span> <span class="nam">axs</span> <span class="op">=</span> <span class="nam">plt</span><span class="op">.</span><span class="nam">subplots</span><span class="op">(</span><span class="num">1</span><span class="op">,</span> <span class="num">1</span><span class="op">,</span> <span class="nam">dpi</span><span class="op">=</span><span class="num">300</span><span class="op">,</span> <span class="nam">tight_layout</span><span class="op">=</span><span class="key">True</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t204" href="#t204">204</a></span><span class="t">            <span class="nam">ybins</span><span class="op">,</span> <span class="nam">x</span><span class="op">,</span> <span class="nam">_</span> <span class="op">=</span> <span class="nam">axs</span><span class="op">.</span><span class="nam">hist</span><span class="op">(</span><span class="nam">column_data</span><span class="op">,</span> <span class="nam">bins</span><span class="op">=</span><span class="nam">self</span><span class="op">.</span><span class="nam">bins</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t205" href="#t205">205</a></span><span class="t">            <span class="nam">pd</span><span class="op">.</span><span class="nam">DataFrame</span><span class="op">(</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">helpar_name</span><span class="op">:</span> <span class="nam">x</span><span class="op">[</span><span class="op">:</span><span class="op">-</span><span class="num">1</span><span class="op">]</span><span class="op">,</span> <span class="str">"density"</span><span class="op">:</span> <span class="nam">ybins</span><span class="op">}</span><span class="op">)</span><span class="op">.</span><span class="nam">to_csv</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t206" href="#t206">206</a></span><span class="t">                <span class="nam">Path</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span><span class="op">)</span> <span class="op">/</span> <span class="str">f"{hist_colfn}.csv"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t207" href="#t207">207</a></span><span class="t">                <span class="nam">index</span><span class="op">=</span><span class="key">False</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t208" href="#t208">208</a></span><span class="t">            <span class="com"># save table</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t209" href="#t209">209</a></span><span class="t">            <span class="nam">zf</span><span class="op">.</span><span class="nam">write</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t210" href="#t210">210</a></span><span class="t">                <span class="nam">Path</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span><span class="op">)</span> <span class="op">/</span> <span class="str">f"{hist_colfn}.csv"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t211" href="#t211">211</a></span><span class="t">                <span class="nam">arcname</span><span class="op">=</span><span class="str">f"{hist_colfn}.csv"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t212" href="#t212">212</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t213" href="#t213">213</a></span><span class="t">            <span class="nam">axs</span><span class="op">.</span><span class="nam">set_ylabel</span><span class="op">(</span><span class="str">"Density"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t214" href="#t214">214</a></span><span class="t">            <span class="nam">axs</span><span class="op">.</span><span class="nam">set_xlabel</span><span class="op">(</span><span class="str">f"{self.helpar_name.capitalize()} ({self.hp_unit})"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t215" href="#t215">215</a></span><span class="t">            <span class="nam">fig</span><span class="op">.</span><span class="nam">savefig</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t216" href="#t216">216</a></span><span class="t">                <span class="nam">Path</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span><span class="op">)</span> <span class="op">/</span> <span class="str">f"{hist_colfn}.jpg"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t217" href="#t217">217</a></span><span class="t">                <span class="nam">format</span><span class="op">=</span><span class="str">"jpg"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t218" href="#t218">218</a></span><span class="t">            <span class="com"># save plot</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t219" href="#t219">219</a></span><span class="t">            <span class="nam">zf</span><span class="op">.</span><span class="nam">write</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t220" href="#t220">220</a></span><span class="t">                <span class="nam">Path</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span><span class="op">)</span> <span class="op">/</span> <span class="str">f"{hist_colfn}.jpg"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t221" href="#t221">221</a></span><span class="t">                <span class="nam">arcname</span><span class="op">=</span><span class="str">f"{hist_colfn}.jpg"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t222" href="#t222">222</a></span><span class="t">            <span class="nam">plt</span><span class="op">.</span><span class="nam">close</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t223" href="#t223">223</a></span><span class="t">        <span class="nam">zf</span><span class="op">.</span><span class="nam">close</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t224" href="#t224">224</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t225" href="#t225">225</a></span><span class="t">        <span class="com"># Remove temporary file(s)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t226" href="#t226">226</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_files</span><span class="op">.</span><span class="nam">extend</span><span class="op">(</span><span class="op">[</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t227" href="#t227">227</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"unique_dir"</span><span class="op">)</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t228" href="#t228">228</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t229" href="#t229">229</a></span><span class="t">        <span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t230" href="#t230">230</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">remove_tmp_files</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t231" href="#t231">231</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t232" href="#t232">232</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_arguments</span><span class="op">(</span><span class="nam">output_files_created</span><span class="op">=</span><span class="key">True</span><span class="op">,</span> <span class="nam">raise_exception</span><span class="op">=</span><span class="key">False</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t233" href="#t233">233</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t234" href="#t234">234</a></span><span class="t">        <span class="key">return</span> <span class="num">0</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t235" href="#t235">235</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t23" href="#t23">23</a></span><span class="t"><span class="str">    | The helical parameter series file is expected to be a table, with the first column being an index and the rest the helical parameter values for each base/basepair.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t24" href="#t24">24</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t25" href="#t25">25</a></span><span class="t"><span class="str">    Args:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t26" href="#t26">26</a></span><span class="t"><span class="str">        input_ser_path (str): Path to .ser file for helical parameter. File is expected to be a table, with the first column being an index and the rest the helical parameter values for each base/basepair. File type: input. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/dna/canal_output_shift.ser>`_. Accepted formats: ser (edam:format_2330).</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t27" href="#t27">27</a></span><span class="t"><span class="str">        output_zip_path (str): Path to output .zip files where data is saved. File type: output. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/reference/dna/timeseries_output.zip>`_. Accepted formats: zip (edam:format_3987).</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t28" href="#t28">28</a></span><span class="t"><span class="str">        properties (dict):</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t29" href="#t29">29</a></span><span class="t"><span class="str">            * **sequence** (*str*) - (None) Nucleic acid sequence corresponding to the input .ser file. Length of sequence is expected to be the same as the total number of columns in the .ser file, minus the index column (even if later on a subset of columns is selected with the *usecols* option).</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t30" href="#t30">30</a></span><span class="t"><span class="str">            * **bins** (*int*) - (None) Bins for histogram. Parameter has same options as matplotlib.pyplot.hist.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t31" href="#t31">31</a></span><span class="t"><span class="str">            * **helpar_name** (*str*) - (Optional) helical parameter name.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t32" href="#t32">32</a></span><span class="t"><span class="str">            * **stride** (*int*) - (1000) granularity of the number of snapshots for plotting time series.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t33" href="#t33">33</a></span><span class="t"><span class="str">            * **seqpos** (*list*) - (None) list of sequence positions (columns indices starting by 0) to analyze.  If not specified it will analyse the complete sequence.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t34" href="#t34">34</a></span><span class="t"><span class="str">            * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t35" href="#t35">35</a></span><span class="t"><span class="str">            * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t36" href="#t36">36</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t37" href="#t37">37</a></span><span class="t"><span class="str">    Examples:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t38" href="#t38">38</a></span><span class="t"><span class="str">        This is a use example of how to use the building block from Python::</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t39" href="#t39">39</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t40" href="#t40">40</a></span><span class="t"><span class="str">            from biobb_dna.dna.dna_timeseries import dna_timeseries</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t41" href="#t41">41</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t42" href="#t42">42</a></span><span class="t"><span class="str">            prop = {</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t43" href="#t43">43</a></span><span class="t"><span class="str">                'helpar_name': 'twist',</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t44" href="#t44">44</a></span><span class="t"><span class="str">                'seqpos': [1,2,3,4,5],</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t45" href="#t45">45</a></span><span class="t"><span class="str">                'sequence': 'GCAACGTGCTATGGAAGC',</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t46" href="#t46">46</a></span><span class="t"><span class="str">            }</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t47" href="#t47">47</a></span><span class="t"><span class="str">            dna_timeseries(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t48" href="#t48">48</a></span><span class="t"><span class="str">                input_ser_path='/path/to/twist.ser',</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t49" href="#t49">49</a></span><span class="t"><span class="str">                output_zip_path='/path/to/output/file.zip'</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t50" href="#t50">50</a></span><span class="t"><span class="str">                properties=prop)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t51" href="#t51">51</a></span><span class="t"><span class="str">    Info:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t52" href="#t52">52</a></span><span class="t"><span class="str">        * wrapped_software:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t53" href="#t53">53</a></span><span class="t"><span class="str">            * name: In house</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t54" href="#t54">54</a></span><span class="t"><span class="str">            * license: Apache-2.0</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t55" href="#t55">55</a></span><span class="t"><span class="str">        * ontology:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t56" href="#t56">56</a></span><span class="t"><span class="str">            * name: EDAM</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t57" href="#t57">57</a></span><span class="t"><span class="str">            * schema: http://edamontology.org/EDAM.owl</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t58" href="#t58">58</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t59" href="#t59">59</a></span><span class="t"><span class="str">    """</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t60" href="#t60">60</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t61" href="#t61">61</a></span><span class="t">    <span class="key">def</span> <span class="nam">__init__</span><span class="op">(</span><span class="nam">self</span><span class="op">,</span> <span class="nam">input_ser_path</span><span class="op">,</span> <span class="nam">output_zip_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t62" href="#t62">62</a></span><span class="t">                 <span class="nam">properties</span><span class="op">=</span><span class="key">None</span><span class="op">,</span> <span class="op">**</span><span class="nam">kwargs</span><span class="op">)</span> <span class="op">-></span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t63" href="#t63">63</a></span><span class="t">        <span class="nam">properties</span> <span class="op">=</span> <span class="nam">properties</span> <span class="key">or</span> <span class="op">{</span><span class="op">}</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t64" href="#t64">64</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t65" href="#t65">65</a></span><span class="t">        <span class="com"># Call parent class constructor</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t66" href="#t66">66</a></span><span class="t">        <span class="nam">super</span><span class="op">(</span><span class="op">)</span><span class="op">.</span><span class="nam">__init__</span><span class="op">(</span><span class="nam">properties</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t67" href="#t67">67</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">locals_var_dict</span> <span class="op">=</span> <span class="nam">locals</span><span class="op">(</span><span class="op">)</span><span class="op">.</span><span class="nam">copy</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t68" href="#t68">68</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t69" href="#t69">69</a></span><span class="t">        <span class="com"># Input/Output files</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t70" href="#t70">70</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span> <span class="op">=</span> <span class="op">{</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t71" href="#t71">71</a></span><span class="t">            <span class="str">'in'</span><span class="op">:</span> <span class="op">{</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t72" href="#t72">72</a></span><span class="t">                <span class="str">'input_ser_path'</span><span class="op">:</span> <span class="nam">input_ser_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t73" href="#t73">73</a></span><span class="t">            <span class="op">}</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t74" href="#t74">74</a></span><span class="t">            <span class="str">'out'</span><span class="op">:</span> <span class="op">{</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t75" href="#t75">75</a></span><span class="t">                <span class="str">'output_zip_path'</span><span class="op">:</span> <span class="nam">output_zip_path</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t76" href="#t76">76</a></span><span class="t">            <span class="op">}</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t77" href="#t77">77</a></span><span class="t">        <span class="op">}</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t78" href="#t78">78</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t79" href="#t79">79</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">properties</span> <span class="op">=</span> <span class="nam">properties</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t80" href="#t80">80</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"sequence"</span><span class="op">,</span> <span class="key">None</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t81" href="#t81">81</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">bins</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"bins"</span><span class="op">,</span> <span class="str">"auto"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t82" href="#t82">82</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">stride</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t83" href="#t83">83</a></span><span class="t">            <span class="str">"stride"</span><span class="op">,</span> <span class="num">10</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t84" href="#t84">84</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t85" href="#t85">85</a></span><span class="t">            <span class="str">"seqpos"</span><span class="op">,</span> <span class="key">None</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t86" href="#t86">86</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">helpar_name</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t87" href="#t87">87</a></span><span class="t">            <span class="str">"helpar_name"</span><span class="op">,</span> <span class="key">None</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t88" href="#t88">88</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t89" href="#t89">89</a></span><span class="t">        <span class="com"># get helical parameter from filename if not specified</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t90" href="#t90">90</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">helpar_name</span> <span class="key">is</span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t91" href="#t91">91</a></span><span class="t">            <span class="key">for</span> <span class="nam">hp</span> <span class="key">in</span> <span class="nam">constants</span><span class="op">.</span><span class="nam">helical_parameters</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t92" href="#t92">92</a></span><span class="t">                <span class="key">if</span> <span class="nam">hp</span><span class="op">.</span><span class="nam">lower</span><span class="op">(</span><span class="op">)</span> <span class="key">in</span> <span class="nam">Path</span><span class="op">(</span><span class="nam">input_ser_path</span><span class="op">)</span><span class="op">.</span><span class="nam">name</span><span class="op">.</span><span class="nam">lower</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t93" href="#t93">93</a></span><span class="t">                    <span class="nam">self</span><span class="op">.</span><span class="nam">helpar_name</span> <span class="op">=</span> <span class="nam">hp</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t94" href="#t94">94</a></span><span class="t">            <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">helpar_name</span> <span class="key">is</span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t95" href="#t95">95</a></span><span class="t">                <span class="key">raise</span> <span class="nam">ValueError</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t96" href="#t96">96</a></span><span class="t">                    <span class="str">"Helical parameter name can't be inferred from file, "</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t97" href="#t97">97</a></span><span class="t">                    <span class="str">"so it must be specified!"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t98" href="#t98">98</a></span><span class="t">        <span class="key">else</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t99" href="#t99">99</a></span><span class="t">            <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">helpar_name</span> <span class="key">not</span> <span class="key">in</span> <span class="nam">constants</span><span class="op">.</span><span class="nam">helical_parameters</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t100" href="#t100">100</a></span><span class="t">                <span class="key">raise</span> <span class="nam">ValueError</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t101" href="#t101">101</a></span><span class="t">                    <span class="str">"Helical parameter name is invalid! "</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t102" href="#t102">102</a></span><span class="t">                    <span class="str">f"Options: {constants.helical_parameters}"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t103" href="#t103">103</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t104" href="#t104">104</a></span><span class="t">        <span class="com"># get base length and unit from helical parameter name</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t105" href="#t105">105</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">helpar_name</span><span class="op">.</span><span class="nam">lower</span><span class="op">(</span><span class="op">)</span> <span class="key">in</span> <span class="nam">constants</span><span class="op">.</span><span class="nam">hp_singlebases</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t106" href="#t106">106</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">baselen</span> <span class="op">=</span> <span class="num">0</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t107" href="#t107">107</a></span><span class="t">        <span class="key">else</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t108" href="#t108">108</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">baselen</span> <span class="op">=</span> <span class="num">1</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t109" href="#t109">109</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">helpar_name</span> <span class="key">in</span> <span class="nam">constants</span><span class="op">.</span><span class="nam">hp_angular</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t110" href="#t110">110</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">hp_unit</span> <span class="op">=</span> <span class="str">"Degrees"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t111" href="#t111">111</a></span><span class="t">        <span class="key">else</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t112" href="#t112">112</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">hp_unit</span> <span class="op">=</span> <span class="str">"Angstroms"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t113" href="#t113">113</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t114" href="#t114">114</a></span><span class="t">        <span class="com"># Check the properties</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t115" href="#t115">115</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_properties</span><span class="op">(</span><span class="nam">properties</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t116" href="#t116">116</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_arguments</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t117" href="#t117">117</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t118" href="#t118">118</a></span><span class="t">    <span class="op">@</span><span class="nam">launchlogger</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t119" href="#t119">119</a></span><span class="t">    <span class="key">def</span> <span class="nam">launch</span><span class="op">(</span><span class="nam">self</span><span class="op">)</span> <span class="op">-></span> <span class="nam">int</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t120" href="#t120">120</a></span><span class="t">        <span class="str">"""Execute the :class:`HelParTimeSeries &lt;dna.dna_timeseries.HelParTimeSeries>` object."""</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t121" href="#t121">121</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t122" href="#t122">122</a></span><span class="t">        <span class="com"># Setup Biobb</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t123" href="#t123">123</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">check_restart</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t124" href="#t124">124</a></span><span class="t">            <span class="key">return</span> <span class="num">0</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t125" href="#t125">125</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">stage_files</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t126" href="#t126">126</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t127" href="#t127">127</a></span><span class="t">        <span class="com"># check sequence</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t128" href="#t128">128</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span> <span class="key">is</span> <span class="key">None</span> <span class="key">or</span> <span class="nam">len</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span><span class="op">)</span> <span class="op">&lt;</span> <span class="num">2</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t129" href="#t129">129</a></span><span class="t">            <span class="key">raise</span> <span class="nam">ValueError</span><span class="op">(</span><span class="str">"sequence is null or too short!"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t130" href="#t130">130</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t131" href="#t131">131</a></span><span class="t">        <span class="com"># check seqpos</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t132" href="#t132">132</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span> <span class="key">is</span> <span class="key">not</span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t133" href="#t133">133</a></span><span class="t">            <span class="key">if</span> <span class="op">(</span><span class="nam">max</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">)</span> <span class="op">></span> <span class="nam">len</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span><span class="op">)</span> <span class="op">-</span> <span class="num">2</span><span class="op">)</span> <span class="key">or</span> <span class="op">(</span><span class="nam">min</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">)</span> <span class="op">&lt;</span> <span class="num">1</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t134" href="#t134">134</a></span><span class="t">                <span class="key">raise</span> <span class="nam">ValueError</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t135" href="#t135">135</a></span><span class="t">                    <span class="str">f"seqpos values must be between 1 and {len(self.sequence) - 2}"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t136" href="#t136">136</a></span><span class="t">            <span class="key">if</span> <span class="key">not</span> <span class="op">(</span><span class="nam">isinstance</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">,</span> <span class="nam">list</span><span class="op">)</span> <span class="key">and</span> <span class="nam">len</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">)</span> <span class="op">></span> <span class="num">1</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t137" href="#t137">137</a></span><span class="t">                <span class="key">raise</span> <span class="nam">ValueError</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t138" href="#t138">138</a></span><span class="t">                    <span class="str">"seqpos must be a list of at least two integers"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t139" href="#t139">139</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t140" href="#t140">140</a></span><span class="t">        <span class="com"># Creating temporary folder</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t141" href="#t141">141</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span> <span class="op">=</span> <span class="nam">fu</span><span class="op">.</span><span class="nam">create_unique_dir</span><span class="op">(</span><span class="nam">prefix</span><span class="op">=</span><span class="str">"timeseries_"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t142" href="#t142">142</a></span><span class="t">        <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="str">'Creating %s temporary folder'</span> <span class="op">%</span> <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t143" href="#t143">143</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t144" href="#t144">144</a></span><span class="t">        <span class="com"># Copy input_ser_path to temporary folder</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t145" href="#t145">145</a></span><span class="t">        <span class="nam">shutil</span><span class="op">.</span><span class="nam">copy</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'input_ser_path'</span><span class="op">]</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t146" href="#t146">146</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t147" href="#t147">147</a></span><span class="t">        <span class="com"># read input .ser file</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t148" href="#t148">148</a></span><span class="t">        <span class="nam">ser_data</span> <span class="op">=</span> <span class="nam">read_series</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t149" href="#t149">149</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'input_ser_path'</span><span class="op">]</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t150" href="#t150">150</a></span><span class="t">            <span class="nam">usecols</span><span class="op">=</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t151" href="#t151">151</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span> <span class="key">is</span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t152" href="#t152">152</a></span><span class="t">            <span class="nam">ser_data</span> <span class="op">=</span> <span class="nam">ser_data</span><span class="op">[</span><span class="nam">ser_data</span><span class="op">.</span><span class="nam">columns</span><span class="op">[</span><span class="num">1</span><span class="op">:</span><span class="op">-</span><span class="num">1</span><span class="op">]</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t153" href="#t153">153</a></span><span class="t">            <span class="com"># discard first and last base(pairs) from sequence</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t154" href="#t154">154</a></span><span class="t">            <span class="nam">sequence</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span><span class="op">[</span><span class="num">1</span><span class="op">:</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t155" href="#t155">155</a></span><span class="t">            <span class="nam">subunits</span> <span class="op">=</span> <span class="op">[</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t156" href="#t156">156</a></span><span class="t">                <span class="str">f"{i+1}_{sequence[i:i+1+self.baselen]}"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t157" href="#t157">157</a></span><span class="t">                <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">range</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">ser_data</span><span class="op">.</span><span class="nam">columns</span><span class="op">)</span><span class="op">)</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t158" href="#t158">158</a></span><span class="t">        <span class="key">else</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t159" href="#t159">159</a></span><span class="t">            <span class="nam">sequence</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t160" href="#t160">160</a></span><span class="t">            <span class="nam">subunits</span> <span class="op">=</span> <span class="op">[</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t161" href="#t161">161</a></span><span class="t">                <span class="str">f"{i+1}_{sequence[i:i+1+self.baselen]}"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t162" href="#t162">162</a></span><span class="t">                <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t163" href="#t163">163</a></span><span class="t">        <span class="nam">ser_data</span><span class="op">.</span><span class="nam">columns</span> <span class="op">=</span> <span class="nam">subunits</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t164" href="#t164">164</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t165" href="#t165">165</a></span><span class="t">        <span class="com"># write output files for all selected bases (one per column)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t166" href="#t166">166</a></span><span class="t">        <span class="nam">zf</span> <span class="op">=</span> <span class="nam">zipfile</span><span class="op">.</span><span class="nam">ZipFile</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t167" href="#t167">167</a></span><span class="t">            <span class="nam">Path</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">"out"</span><span class="op">]</span><span class="op">[</span><span class="str">"output_zip_path"</span><span class="op">]</span><span class="op">)</span><span class="op">,</span> <span class="str">"w"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t168" href="#t168">168</a></span><span class="t">        <span class="key">for</span> <span class="nam">col</span> <span class="key">in</span> <span class="nam">ser_data</span><span class="op">.</span><span class="nam">columns</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t169" href="#t169">169</a></span><span class="t">            <span class="com"># unstack columns to prevent errors from repeated base pairs</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t170" href="#t170">170</a></span><span class="t">            <span class="nam">column_data</span> <span class="op">=</span> <span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t171" href="#t171">171</a></span><span class="t">                <span class="nam">ser_data</span><span class="op">[</span><span class="op">[</span><span class="nam">col</span><span class="op">]</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t172" href="#t172">172</a></span><span class="t">                <span class="op">.</span><span class="nam">unstack</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t173" href="#t173">173</a></span><span class="t">                <span class="op">.</span><span class="nam">dropna</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t174" href="#t174">174</a></span><span class="t">                <span class="op">.</span><span class="nam">reset_index</span><span class="op">(</span><span class="nam">drop</span><span class="op">=</span><span class="key">True</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t175" href="#t175">175</a></span><span class="t">            <span class="nam">column_data</span><span class="op">.</span><span class="nam">name</span> <span class="op">=</span> <span class="nam">col</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t176" href="#t176">176</a></span><span class="t">            <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="str">f"Computing base number {col}..."</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t177" href="#t177">177</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t178" href="#t178">178</a></span><span class="t">            <span class="com"># column series</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t179" href="#t179">179</a></span><span class="t">            <span class="nam">series_colfn</span> <span class="op">=</span> <span class="str">f"series_{self.helpar_name}_{col}"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t180" href="#t180">180</a></span><span class="t">            <span class="nam">column_data</span><span class="op">.</span><span class="nam">to_csv</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t181" href="#t181">181</a></span><span class="t">                <span class="nam">Path</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span><span class="op">)</span> <span class="op">/</span> <span class="str">f"{series_colfn}.csv"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t182" href="#t182">182</a></span><span class="t">            <span class="com"># save table</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t183" href="#t183">183</a></span><span class="t">            <span class="nam">zf</span><span class="op">.</span><span class="nam">write</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t184" href="#t184">184</a></span><span class="t">                <span class="nam">Path</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span><span class="op">)</span> <span class="op">/</span> <span class="str">f"{series_colfn}.csv"</span><span class="op">,</span> <span class="nam">arcname</span><span class="op">=</span><span class="str">f"{series_colfn}.csv"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t185" href="#t185">185</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t186" href="#t186">186</a></span><span class="t">            <span class="nam">fig</span><span class="op">,</span> <span class="nam">axs</span> <span class="op">=</span> <span class="nam">plt</span><span class="op">.</span><span class="nam">subplots</span><span class="op">(</span><span class="num">1</span><span class="op">,</span> <span class="num">1</span><span class="op">,</span> <span class="nam">dpi</span><span class="op">=</span><span class="num">300</span><span class="op">,</span> <span class="nam">tight_layout</span><span class="op">=</span><span class="key">True</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t187" href="#t187">187</a></span><span class="t">            <span class="nam">reduced_data</span> <span class="op">=</span> <span class="nam">column_data</span><span class="op">.</span><span class="nam">iloc</span><span class="op">[</span><span class="op">:</span><span class="op">:</span><span class="nam">self</span><span class="op">.</span><span class="nam">stride</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t188" href="#t188">188</a></span><span class="t">            <span class="nam">axs</span><span class="op">.</span><span class="nam">plot</span><span class="op">(</span><span class="nam">reduced_data</span><span class="op">.</span><span class="nam">index</span><span class="op">,</span> <span class="nam">reduced_data</span><span class="op">.</span><span class="nam">to_numpy</span><span class="op">(</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t189" href="#t189">189</a></span><span class="t">            <span class="nam">axs</span><span class="op">.</span><span class="nam">set_xlabel</span><span class="op">(</span><span class="str">"Time (Snapshots)"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t190" href="#t190">190</a></span><span class="t">            <span class="nam">axs</span><span class="op">.</span><span class="nam">set_ylabel</span><span class="op">(</span><span class="str">f"{self.helpar_name.capitalize()} ({self.hp_unit})"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t191" href="#t191">191</a></span><span class="t">            <span class="nam">axs</span><span class="op">.</span><span class="nam">set_title</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t192" href="#t192">192</a></span><span class="t">                <span class="str">f"Helical Parameter vs Time: {self.helpar_name.capitalize()} "</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t193" href="#t193">193</a></span><span class="t">                <span class="str">"(base pair "</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t194" href="#t194">194</a></span><span class="t">                <span class="str">f"{'step' if self.baselen==1 else ''} {col})"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t195" href="#t195">195</a></span><span class="t">            <span class="nam">fig</span><span class="op">.</span><span class="nam">savefig</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t196" href="#t196">196</a></span><span class="t">                <span class="nam">Path</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span><span class="op">)</span> <span class="op">/</span> <span class="str">f"{series_colfn}.jpg"</span><span class="op">,</span> <span class="nam">format</span><span class="op">=</span><span class="str">"jpg"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t197" href="#t197">197</a></span><span class="t">            <span class="com"># save plot</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t198" href="#t198">198</a></span><span class="t">            <span class="nam">zf</span><span class="op">.</span><span class="nam">write</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t199" href="#t199">199</a></span><span class="t">                <span class="nam">Path</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span><span class="op">)</span> <span class="op">/</span> <span class="str">f"{series_colfn}.jpg"</span><span class="op">,</span> <span class="nam">arcname</span><span class="op">=</span><span class="str">f"{series_colfn}.jpg"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t200" href="#t200">200</a></span><span class="t">            <span class="nam">plt</span><span class="op">.</span><span class="nam">close</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t201" href="#t201">201</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t202" href="#t202">202</a></span><span class="t">            <span class="com"># columns histogram</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t203" href="#t203">203</a></span><span class="t">            <span class="nam">hist_colfn</span> <span class="op">=</span> <span class="str">f"hist_{self.helpar_name}_{col}"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t204" href="#t204">204</a></span><span class="t">            <span class="nam">fig</span><span class="op">,</span> <span class="nam">axs</span> <span class="op">=</span> <span class="nam">plt</span><span class="op">.</span><span class="nam">subplots</span><span class="op">(</span><span class="num">1</span><span class="op">,</span> <span class="num">1</span><span class="op">,</span> <span class="nam">dpi</span><span class="op">=</span><span class="num">300</span><span class="op">,</span> <span class="nam">tight_layout</span><span class="op">=</span><span class="key">True</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t205" href="#t205">205</a></span><span class="t">            <span class="nam">ybins</span><span class="op">,</span> <span class="nam">x</span><span class="op">,</span> <span class="nam">_</span> <span class="op">=</span> <span class="nam">axs</span><span class="op">.</span><span class="nam">hist</span><span class="op">(</span><span class="nam">column_data</span><span class="op">,</span> <span class="nam">bins</span><span class="op">=</span><span class="nam">self</span><span class="op">.</span><span class="nam">bins</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t206" href="#t206">206</a></span><span class="t">            <span class="nam">pd</span><span class="op">.</span><span class="nam">DataFrame</span><span class="op">(</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">helpar_name</span><span class="op">:</span> <span class="nam">x</span><span class="op">[</span><span class="op">:</span><span class="op">-</span><span class="num">1</span><span class="op">]</span><span class="op">,</span> <span class="str">"density"</span><span class="op">:</span> <span class="nam">ybins</span><span class="op">}</span><span class="op">)</span><span class="op">.</span><span class="nam">to_csv</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t207" href="#t207">207</a></span><span class="t">                <span class="nam">Path</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span><span class="op">)</span> <span class="op">/</span> <span class="str">f"{hist_colfn}.csv"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t208" href="#t208">208</a></span><span class="t">                <span class="nam">index</span><span class="op">=</span><span class="key">False</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t209" href="#t209">209</a></span><span class="t">            <span class="com"># save table</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t210" href="#t210">210</a></span><span class="t">            <span class="nam">zf</span><span class="op">.</span><span class="nam">write</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t211" href="#t211">211</a></span><span class="t">                <span class="nam">Path</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span><span class="op">)</span> <span class="op">/</span> <span class="str">f"{hist_colfn}.csv"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t212" href="#t212">212</a></span><span class="t">                <span class="nam">arcname</span><span class="op">=</span><span class="str">f"{hist_colfn}.csv"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t213" href="#t213">213</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t214" href="#t214">214</a></span><span class="t">            <span class="nam">axs</span><span class="op">.</span><span class="nam">set_ylabel</span><span class="op">(</span><span class="str">"Density"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t215" href="#t215">215</a></span><span class="t">            <span class="nam">axs</span><span class="op">.</span><span class="nam">set_xlabel</span><span class="op">(</span><span class="str">f"{self.helpar_name.capitalize()} ({self.hp_unit})"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t216" href="#t216">216</a></span><span class="t">            <span class="nam">fig</span><span class="op">.</span><span class="nam">savefig</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t217" href="#t217">217</a></span><span class="t">                <span class="nam">Path</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span><span class="op">)</span> <span class="op">/</span> <span class="str">f"{hist_colfn}.jpg"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t218" href="#t218">218</a></span><span class="t">                <span class="nam">format</span><span class="op">=</span><span class="str">"jpg"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t219" href="#t219">219</a></span><span class="t">            <span class="com"># save plot</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t220" href="#t220">220</a></span><span class="t">            <span class="nam">zf</span><span class="op">.</span><span class="nam">write</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t221" href="#t221">221</a></span><span class="t">                <span class="nam">Path</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span><span class="op">)</span> <span class="op">/</span> <span class="str">f"{hist_colfn}.jpg"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t222" href="#t222">222</a></span><span class="t">                <span class="nam">arcname</span><span class="op">=</span><span class="str">f"{hist_colfn}.jpg"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t223" href="#t223">223</a></span><span class="t">            <span class="nam">plt</span><span class="op">.</span><span class="nam">close</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t224" href="#t224">224</a></span><span class="t">        <span class="nam">zf</span><span class="op">.</span><span class="nam">close</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t225" href="#t225">225</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t226" href="#t226">226</a></span><span class="t">        <span class="com"># Remove temporary file(s)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t227" href="#t227">227</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_files</span><span class="op">.</span><span class="nam">extend</span><span class="op">(</span><span class="op">[</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t228" href="#t228">228</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"unique_dir"</span><span class="op">)</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t229" href="#t229">229</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t230" href="#t230">230</a></span><span class="t">        <span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t231" href="#t231">231</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">remove_tmp_files</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t232" href="#t232">232</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t233" href="#t233">233</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_arguments</span><span class="op">(</span><span class="nam">output_files_created</span><span class="op">=</span><span class="key">True</span><span class="op">,</span> <span class="nam">raise_exception</span><span class="op">=</span><span class="key">False</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t234" href="#t234">234</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t235" href="#t235">235</a></span><span class="t">        <span class="key">return</span> <span class="num">0</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t236" href="#t236">236</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t237" href="#t237">237</a></span><span class="t"><span class="key">def</span> <span class="nam">dna_timeseries</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t238" href="#t238">238</a></span><span class="t">        <span class="nam">input_ser_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span> <span class="nam">output_zip_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t239" href="#t239">239</a></span><span class="t">        <span class="nam">properties</span><span class="op">:</span> <span class="nam">dict</span> <span class="op">=</span> <span class="key">None</span><span class="op">,</span> <span class="op">**</span><span class="nam">kwargs</span><span class="op">)</span> <span class="op">-></span> <span class="nam">int</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t240" href="#t240">240</a></span><span class="t">    <span class="str">"""Create :class:`HelParTimeSeries &lt;dna.dna_timeseries.HelParTimeSeries>` class and</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t241" href="#t241">241</a></span><span class="t"><span class="str">    execute the :meth:`launch() &lt;dna.dna_timeseries.HelParTimeSeries.launch>` method."""</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t242" href="#t242">242</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t243" href="#t243">243</a></span><span class="t">    <span class="key">return</span> <span class="nam">HelParTimeSeries</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t244" href="#t244">244</a></span><span class="t">        <span class="nam">input_ser_path</span><span class="op">=</span><span class="nam">input_ser_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t245" href="#t245">245</a></span><span class="t">        <span class="nam">output_zip_path</span><span class="op">=</span><span class="nam">output_zip_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t246" href="#t246">246</a></span><span class="t">        <span class="nam">properties</span><span class="op">=</span><span class="nam">properties</span><span class="op">,</span> <span class="op">**</span><span class="nam">kwargs</span><span class="op">)</span><span class="op">.</span><span class="nam">launch</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t247" href="#t247">247</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t237" href="#t237">237</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t238" href="#t238">238</a></span><span class="t"><span class="key">def</span> <span class="nam">dna_timeseries</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t239" href="#t239">239</a></span><span class="t">        <span class="nam">input_ser_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span> <span class="nam">output_zip_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t240" href="#t240">240</a></span><span class="t">        <span class="nam">properties</span><span class="op">:</span> <span class="nam">dict</span> <span class="op">=</span> <span class="key">None</span><span class="op">,</span> <span class="op">**</span><span class="nam">kwargs</span><span class="op">)</span> <span class="op">-></span> <span class="nam">int</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t241" href="#t241">241</a></span><span class="t">    <span class="str">"""Create :class:`HelParTimeSeries &lt;dna.dna_timeseries.HelParTimeSeries>` class and</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t242" href="#t242">242</a></span><span class="t"><span class="str">    execute the :meth:`launch() &lt;dna.dna_timeseries.HelParTimeSeries.launch>` method."""</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t243" href="#t243">243</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t244" href="#t244">244</a></span><span class="t">    <span class="key">return</span> <span class="nam">HelParTimeSeries</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t245" href="#t245">245</a></span><span class="t">        <span class="nam">input_ser_path</span><span class="op">=</span><span class="nam">input_ser_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t246" href="#t246">246</a></span><span class="t">        <span class="nam">output_zip_path</span><span class="op">=</span><span class="nam">output_zip_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t247" href="#t247">247</a></span><span class="t">        <span class="nam">properties</span><span class="op">=</span><span class="nam">properties</span><span class="op">,</span> <span class="op">**</span><span class="nam">kwargs</span><span class="op">)</span><span class="op">.</span><span class="nam">launch</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t248" href="#t248">248</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t249" href="#t249">249</a></span><span class="t"><span class="key">def</span> <span class="nam">main</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t250" href="#t250">250</a></span><span class="t">    <span class="str">"""Command line execution of this building block. Please check the command line documentation."""</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t251" href="#t251">251</a></span><span class="t">    <span class="nam">parser</span> <span class="op">=</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">ArgumentParser</span><span class="op">(</span><span class="nam">description</span><span class="op">=</span><span class="str">'Created time series and histogram plots for each base pair from a helical parameter series file.'</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t252" href="#t252">252</a></span><span class="t">                                     <span class="nam">formatter_class</span><span class="op">=</span><span class="key">lambda</span> <span class="nam">prog</span><span class="op">:</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">RawTextHelpFormatter</span><span class="op">(</span><span class="nam">prog</span><span class="op">,</span> <span class="nam">width</span><span class="op">=</span><span class="num">99999</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t253" href="#t253">253</a></span><span class="t">    <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--config'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">False</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t254" href="#t254">254</a></span><span class="t">                        <span class="nam">help</span><span class="op">=</span><span class="str">'Configuration file'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t255" href="#t255">255</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t256" href="#t256">256</a></span><span class="t">    <span class="nam">required_args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument_group</span><span class="op">(</span><span class="str">'required arguments'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t257" href="#t257">257</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--input_ser_path'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t258" href="#t258">258</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Helical parameter input ser file path. Accepted formats: ser.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t259" href="#t259">259</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--output_zip_path'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t260" href="#t260">260</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Path to output directory.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t261" href="#t261">261</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t262" href="#t262">262</a></span><span class="t">    <span class="nam">args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">parse_args</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t263" href="#t263">263</a></span><span class="t">    <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="op">=</span> <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="key">or</span> <span class="str">"{}"</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t264" href="#t264">264</a></span><span class="t">    <span class="nam">properties</span> <span class="op">=</span> <span class="nam">settings</span><span class="op">.</span><span class="nam">ConfReader</span><span class="op">(</span><span class="nam">config</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">config</span><span class="op">)</span><span class="op">.</span><span class="nam">get_prop_dic</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t265" href="#t265">265</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t266" href="#t266">266</a></span><span class="t">    <span class="nam">dna_timeseries</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t267" href="#t267">267</a></span><span class="t">        <span class="nam">input_ser_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_ser_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t268" href="#t268">268</a></span><span class="t">        <span class="nam">output_zip_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">output_zip_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t269" href="#t269">269</a></span><span class="t">        <span class="nam">properties</span><span class="op">=</span><span class="nam">properties</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t270" href="#t270">270</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t249" href="#t249">249</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t250" href="#t250">250</a></span><span class="t"><span class="key">def</span> <span class="nam">main</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t251" href="#t251">251</a></span><span class="t">    <span class="str">"""Command line execution of this building block. Please check the command line documentation."""</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t252" href="#t252">252</a></span><span class="t">    <span class="nam">parser</span> <span class="op">=</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">ArgumentParser</span><span class="op">(</span><span class="nam">description</span><span class="op">=</span><span class="str">'Created time series and histogram plots for each base pair from a helical parameter series file.'</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t253" href="#t253">253</a></span><span class="t">                                     <span class="nam">formatter_class</span><span class="op">=</span><span class="key">lambda</span> <span class="nam">prog</span><span class="op">:</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">RawTextHelpFormatter</span><span class="op">(</span><span class="nam">prog</span><span class="op">,</span> <span class="nam">width</span><span class="op">=</span><span class="num">99999</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t254" href="#t254">254</a></span><span class="t">    <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--config'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">False</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t255" href="#t255">255</a></span><span class="t">                        <span class="nam">help</span><span class="op">=</span><span class="str">'Configuration file'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t256" href="#t256">256</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t257" href="#t257">257</a></span><span class="t">    <span class="nam">required_args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument_group</span><span class="op">(</span><span class="str">'required arguments'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t258" href="#t258">258</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--input_ser_path'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t259" href="#t259">259</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Helical parameter input ser file path. Accepted formats: ser.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t260" href="#t260">260</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--output_zip_path'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t261" href="#t261">261</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Path to output directory.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t262" href="#t262">262</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t263" href="#t263">263</a></span><span class="t">    <span class="nam">args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">parse_args</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t264" href="#t264">264</a></span><span class="t">    <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="op">=</span> <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="key">or</span> <span class="str">"{}"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t265" href="#t265">265</a></span><span class="t">    <span class="nam">properties</span> <span class="op">=</span> <span class="nam">settings</span><span class="op">.</span><span class="nam">ConfReader</span><span class="op">(</span><span class="nam">config</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">config</span><span class="op">)</span><span class="op">.</span><span class="nam">get_prop_dic</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t266" href="#t266">266</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t267" href="#t267">267</a></span><span class="t">    <span class="nam">dna_timeseries</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t268" href="#t268">268</a></span><span class="t">        <span class="nam">input_ser_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_ser_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t269" href="#t269">269</a></span><span class="t">        <span class="nam">output_zip_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">output_zip_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t270" href="#t270">270</a></span><span class="t">        <span class="nam">properties</span><span class="op">=</span><span class="nam">properties</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t271" href="#t271">271</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t272" href="#t272">272</a></span><span class="t"><span class="key">if</span> <span class="nam">__name__</span> <span class="op">==</span> <span class="str">'__main__'</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t273" href="#t273">273</a></span><span class="t">    <span class="nam">main</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t272" href="#t272">272</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t273" href="#t273">273</a></span><span class="t"><span class="key">if</span> <span class="nam">__name__</span> <span class="op">==</span> <span class="str">'__main__'</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t274" href="#t274">274</a></span><span class="t">    <span class="nam">main</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
 </main>
 <footer>
     <div class="content">
@@ -362,7 +363,7 @@ <h2>
             <a class="nav" href="z_8a2a7f872cf1434f___init___py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.5.1">coverage.py v7.5.1</a>,
-            created at 2024-05-07 09:06 +0000
+            created at 2024-05-24 09:29 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_64e03be4370b7ecc___init___py.html b/coverage/z_64e03be4370b7ecc___init___py.html
index d23da150..ff8caa04 100644
--- a/coverage/z_64e03be4370b7ecc___init___py.html
+++ b/coverage/z_64e03be4370b7ecc___init___py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_64e03be4370b7ecc_intrabpcorr_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.5.1">coverage.py v7.5.1</a>,
-            created at 2024-05-07 09:06 +0000
+            created at 2024-05-24 09:29 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -94,7 +94,7 @@ <h2>
             <a class="nav" href="z_64e03be4370b7ecc_intrabpcorr_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.5.1">coverage.py v7.5.1</a>,
-            created at 2024-05-07 09:06 +0000
+            created at 2024-05-24 09:29 +0000
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 </footer>
diff --git a/coverage/z_64e03be4370b7ecc_intrabpcorr_py.html b/coverage/z_64e03be4370b7ecc_intrabpcorr_py.html
index 9e8b4306..727f5a49 100644
--- a/coverage/z_64e03be4370b7ecc_intrabpcorr_py.html
+++ b/coverage/z_64e03be4370b7ecc_intrabpcorr_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_64e03be4370b7ecc_intrahpcorr_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.5.1">coverage.py v7.5.1</a>,
-            created at 2024-05-07 09:06 +0000
+            created at 2024-05-24 09:29 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -103,314 +103,315 @@ <h2>
     <p class="pln"><span class="n"><a id="t21" href="#t21">21</a></span><span class="t">    <span class="str">"""</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t22" href="#t22">22</a></span><span class="t"><span class="str">    | biobb_dna IntraBasePairCorrelation</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t23" href="#t23">23</a></span><span class="t"><span class="str">    | Calculate correlation between all intra-base pairs of a single sequence and for a single helical parameter.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t24" href="#t24">24</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t25" href="#t25">25</a></span><span class="t"><span class="str">    Args:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t26" href="#t26">26</a></span><span class="t"><span class="str">        input_filename_shear (str): Path to .ser file with data for helical parameter 'shear'. File type: input. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/correlation/canal_output_shear.ser>`_. Accepted formats: ser (edam:format_2330).</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t27" href="#t27">27</a></span><span class="t"><span class="str">        input_filename_stretch (str): Path to .ser file with data for helical parameter 'stretch'. File type: input. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/correlation/canal_output_stretch.ser>`_. Accepted formats: ser (edam:format_2330).</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t28" href="#t28">28</a></span><span class="t"><span class="str">        input_filename_stagger (str): Path to .ser file with data for helical parameter 'stagger'. File type: input. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/correlation/canal_output_stagger.ser>`_. Accepted formats: ser (edam:format_2330).</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t29" href="#t29">29</a></span><span class="t"><span class="str">        input_filename_buckle (str): Path to .ser file with data for helical parameter 'buckle'. File type: input. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/correlation/canal_output_buckle.ser>`_. Accepted formats: ser (edam:format_2330).</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t30" href="#t30">30</a></span><span class="t"><span class="str">        input_filename_propel (str): Path to .ser file with data for helical parameter 'propel'. File type: input. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/correlation/canal_output_propel.ser>`_. Accepted formats: ser (edam:format_2330).</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t31" href="#t31">31</a></span><span class="t"><span class="str">        input_filename_opening (str): Path to .ser file with data for helical parameter 'opening'. File type: input. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/correlation/canal_output_opening.ser>`_. Accepted formats: ser (edam:format_2330).</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t32" href="#t32">32</a></span><span class="t"><span class="str">        output_csv_path (str): Path to directory where output is saved. File type: output. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/reference/correlation/intra_bpcorr_ref.csv>`_. Accepted formats: csv (edam:format_3752).</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t33" href="#t33">33</a></span><span class="t"><span class="str">        output_jpg_path (str): Path to .jpg file where output is saved. File type: output. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/reference/correlation/intra_bpcorr_ref.jpg>`_. Accepted formats: jpg (edam:format_3579).</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t34" href="#t34">34</a></span><span class="t"><span class="str">        properties (dict):</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t35" href="#t35">35</a></span><span class="t"><span class="str">            * **sequence** (*str*) - (None) Nucleic acid sequence for the input .ser file. Length of sequence is expected to be the same as the total number of columns in the .ser file, minus the index column (even if later on a subset of columns is selected with the *seqpos* option).</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t36" href="#t36">36</a></span><span class="t"><span class="str">            * **seqpos** (*list*) - (None) list of sequence positions (columns indices starting by 0) to analyze.  If not specified it will analyse the complete sequence.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t37" href="#t37">37</a></span><span class="t"><span class="str">            * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t38" href="#t38">38</a></span><span class="t"><span class="str">            * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t39" href="#t39">39</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t40" href="#t40">40</a></span><span class="t"><span class="str">    Examples:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t41" href="#t41">41</a></span><span class="t"><span class="str">        This is a use example of how to use the building block from Python::</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t42" href="#t42">42</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t43" href="#t43">43</a></span><span class="t"><span class="str">            from biobb_dna.intrabp_correlations.intrabpcorr import intrabpcorr</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t44" href="#t44">44</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t45" href="#t45">45</a></span><span class="t"><span class="str">            intrabpcorr(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t46" href="#t46">46</a></span><span class="t"><span class="str">                input_filename_shear='path/to/input/shear.ser',</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t47" href="#t47">47</a></span><span class="t"><span class="str">                input_filename_stretch='path/to/input/stretch.ser',</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t48" href="#t48">48</a></span><span class="t"><span class="str">                input_filename_stagger='path/to/input/stagger.ser',</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t49" href="#t49">49</a></span><span class="t"><span class="str">                input_filename_buckle='path/to/input/buckle.ser',</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t50" href="#t50">50</a></span><span class="t"><span class="str">                input_filename_propel='path/to/input/propel.ser',</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t51" href="#t51">51</a></span><span class="t"><span class="str">                input_filename_opening='path/to/input/opening.ser',</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t52" href="#t52">52</a></span><span class="t"><span class="str">                output_csv_path='path/to/output/file.csv',</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t53" href="#t53">53</a></span><span class="t"><span class="str">                output_jpg_path='path/to/output/plot.jpg',</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t54" href="#t54">54</a></span><span class="t"><span class="str">                properties=prop)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t55" href="#t55">55</a></span><span class="t"><span class="str">    Info:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t56" href="#t56">56</a></span><span class="t"><span class="str">        * wrapped_software:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t57" href="#t57">57</a></span><span class="t"><span class="str">            * name: In house</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t58" href="#t58">58</a></span><span class="t"><span class="str">            * license: Apache-2.0</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t59" href="#t59">59</a></span><span class="t"><span class="str">        * ontology:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t60" href="#t60">60</a></span><span class="t"><span class="str">            * name: EDAM</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t61" href="#t61">61</a></span><span class="t"><span class="str">            * schema: http://edamontology.org/EDAM.owl</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t62" href="#t62">62</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t63" href="#t63">63</a></span><span class="t"><span class="str">    """</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t64" href="#t64">64</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t65" href="#t65">65</a></span><span class="t">    <span class="key">def</span> <span class="nam">__init__</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t66" href="#t66">66</a></span><span class="t">            <span class="nam">self</span><span class="op">,</span> <span class="nam">input_filename_shear</span><span class="op">,</span> <span class="nam">input_filename_stretch</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t67" href="#t67">67</a></span><span class="t">            <span class="nam">input_filename_stagger</span><span class="op">,</span> <span class="nam">input_filename_buckle</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t68" href="#t68">68</a></span><span class="t">            <span class="nam">input_filename_propel</span><span class="op">,</span> <span class="nam">input_filename_opening</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t69" href="#t69">69</a></span><span class="t">            <span class="nam">output_csv_path</span><span class="op">,</span> <span class="nam">output_jpg_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t70" href="#t70">70</a></span><span class="t">            <span class="nam">properties</span><span class="op">=</span><span class="key">None</span><span class="op">,</span> <span class="op">**</span><span class="nam">kwargs</span><span class="op">)</span> <span class="op">-></span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t71" href="#t71">71</a></span><span class="t">        <span class="nam">properties</span> <span class="op">=</span> <span class="nam">properties</span> <span class="key">or</span> <span class="op">{</span><span class="op">}</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t72" href="#t72">72</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t73" href="#t73">73</a></span><span class="t">        <span class="com"># Call parent class constructor</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t74" href="#t74">74</a></span><span class="t">        <span class="nam">super</span><span class="op">(</span><span class="op">)</span><span class="op">.</span><span class="nam">__init__</span><span class="op">(</span><span class="nam">properties</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t75" href="#t75">75</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">locals_var_dict</span> <span class="op">=</span> <span class="nam">locals</span><span class="op">(</span><span class="op">)</span><span class="op">.</span><span class="nam">copy</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t76" href="#t76">76</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t77" href="#t77">77</a></span><span class="t">        <span class="com"># Input/Output files</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t78" href="#t78">78</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span> <span class="op">=</span> <span class="op">{</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t79" href="#t79">79</a></span><span class="t">            <span class="str">'in'</span><span class="op">:</span> <span class="op">{</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t80" href="#t80">80</a></span><span class="t">                <span class="str">'input_filename_shear'</span><span class="op">:</span> <span class="nam">input_filename_shear</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t81" href="#t81">81</a></span><span class="t">                <span class="str">'input_filename_stretch'</span><span class="op">:</span> <span class="nam">input_filename_stretch</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t82" href="#t82">82</a></span><span class="t">                <span class="str">'input_filename_stagger'</span><span class="op">:</span> <span class="nam">input_filename_stagger</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t83" href="#t83">83</a></span><span class="t">                <span class="str">'input_filename_buckle'</span><span class="op">:</span> <span class="nam">input_filename_buckle</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t84" href="#t84">84</a></span><span class="t">                <span class="str">'input_filename_propel'</span><span class="op">:</span> <span class="nam">input_filename_propel</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t85" href="#t85">85</a></span><span class="t">                <span class="str">'input_filename_opening'</span><span class="op">:</span> <span class="nam">input_filename_opening</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t86" href="#t86">86</a></span><span class="t">            <span class="op">}</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t87" href="#t87">87</a></span><span class="t">            <span class="str">'out'</span><span class="op">:</span> <span class="op">{</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t88" href="#t88">88</a></span><span class="t">                <span class="str">'output_csv_path'</span><span class="op">:</span> <span class="nam">output_csv_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t89" href="#t89">89</a></span><span class="t">                <span class="str">'output_jpg_path'</span><span class="op">:</span> <span class="nam">output_jpg_path</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t90" href="#t90">90</a></span><span class="t">            <span class="op">}</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t91" href="#t91">91</a></span><span class="t">        <span class="op">}</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t92" href="#t92">92</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t93" href="#t93">93</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">properties</span> <span class="op">=</span> <span class="nam">properties</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t94" href="#t94">94</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"sequence"</span><span class="op">,</span> <span class="key">None</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t95" href="#t95">95</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"seqpos"</span><span class="op">,</span> <span class="key">None</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t96" href="#t96">96</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t97" href="#t97">97</a></span><span class="t">        <span class="com"># Check the properties</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t98" href="#t98">98</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_properties</span><span class="op">(</span><span class="nam">properties</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t99" href="#t99">99</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_arguments</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t100" href="#t100">100</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t101" href="#t101">101</a></span><span class="t">    <span class="op">@</span><span class="nam">launchlogger</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t102" href="#t102">102</a></span><span class="t">    <span class="key">def</span> <span class="nam">launch</span><span class="op">(</span><span class="nam">self</span><span class="op">)</span> <span class="op">-></span> <span class="nam">int</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t103" href="#t103">103</a></span><span class="t">        <span class="str">"""Execute the :class:`HelParCorrelation &lt;intrabp_correlations.intrabpcorr.IntraBasePairCorrelation>` object."""</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t104" href="#t104">104</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t105" href="#t105">105</a></span><span class="t">        <span class="com"># Setup Biobb</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t106" href="#t106">106</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">check_restart</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t107" href="#t107">107</a></span><span class="t">            <span class="key">return</span> <span class="num">0</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t108" href="#t108">108</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">stage_files</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t109" href="#t109">109</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t110" href="#t110">110</a></span><span class="t">        <span class="com"># check sequence</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t111" href="#t111">111</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span> <span class="key">is</span> <span class="key">None</span> <span class="key">or</span> <span class="nam">len</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span><span class="op">)</span> <span class="op">&lt;</span> <span class="num">2</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t112" href="#t112">112</a></span><span class="t">            <span class="key">raise</span> <span class="nam">ValueError</span><span class="op">(</span><span class="str">"sequence is null or too short!"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t113" href="#t113">113</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t114" href="#t114">114</a></span><span class="t">        <span class="com"># check seqpos</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t115" href="#t115">115</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span> <span class="key">is</span> <span class="key">not</span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t116" href="#t116">116</a></span><span class="t">            <span class="key">if</span> <span class="key">not</span> <span class="op">(</span><span class="nam">isinstance</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">,</span> <span class="nam">list</span><span class="op">)</span> <span class="key">and</span> <span class="nam">len</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">)</span> <span class="op">></span> <span class="num">1</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t117" href="#t117">117</a></span><span class="t">                <span class="key">raise</span> <span class="nam">ValueError</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t118" href="#t118">118</a></span><span class="t">                    <span class="str">"seqpos must be a list of at least two integers"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t119" href="#t119">119</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t120" href="#t120">120</a></span><span class="t">        <span class="com"># Creating temporary folder</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t121" href="#t121">121</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span> <span class="op">=</span> <span class="nam">fu</span><span class="op">.</span><span class="nam">create_unique_dir</span><span class="op">(</span><span class="nam">prefix</span><span class="op">=</span><span class="str">"bpcorrelation_"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t122" href="#t122">122</a></span><span class="t">        <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="str">'Creating %s temporary folder'</span> <span class="op">%</span> <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t123" href="#t123">123</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t124" href="#t124">124</a></span><span class="t">        <span class="com"># read input</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t125" href="#t125">125</a></span><span class="t">        <span class="nam">shear</span> <span class="op">=</span> <span class="nam">read_series</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t126" href="#t126">126</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">"in"</span><span class="op">]</span><span class="op">[</span><span class="str">"input_filename_shear"</span><span class="op">]</span><span class="op">,</span> <span class="nam">usecols</span><span class="op">=</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t127" href="#t127">127</a></span><span class="t">        <span class="nam">stretch</span> <span class="op">=</span> <span class="nam">read_series</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t128" href="#t128">128</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">"in"</span><span class="op">]</span><span class="op">[</span><span class="str">"input_filename_stretch"</span><span class="op">]</span><span class="op">,</span> <span class="nam">usecols</span><span class="op">=</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t129" href="#t129">129</a></span><span class="t">        <span class="nam">stagger</span> <span class="op">=</span> <span class="nam">read_series</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t130" href="#t130">130</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">"in"</span><span class="op">]</span><span class="op">[</span><span class="str">"input_filename_stagger"</span><span class="op">]</span><span class="op">,</span> <span class="nam">usecols</span><span class="op">=</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t131" href="#t131">131</a></span><span class="t">        <span class="nam">buckle</span> <span class="op">=</span> <span class="nam">read_series</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t132" href="#t132">132</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">"in"</span><span class="op">]</span><span class="op">[</span><span class="str">"input_filename_buckle"</span><span class="op">]</span><span class="op">,</span> <span class="nam">usecols</span><span class="op">=</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t133" href="#t133">133</a></span><span class="t">        <span class="nam">propel</span> <span class="op">=</span> <span class="nam">read_series</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t134" href="#t134">134</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">"in"</span><span class="op">]</span><span class="op">[</span><span class="str">"input_filename_propel"</span><span class="op">]</span><span class="op">,</span> <span class="nam">usecols</span><span class="op">=</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t135" href="#t135">135</a></span><span class="t">        <span class="nam">opening</span> <span class="op">=</span> <span class="nam">read_series</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t136" href="#t136">136</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">"in"</span><span class="op">]</span><span class="op">[</span><span class="str">"input_filename_opening"</span><span class="op">]</span><span class="op">,</span> <span class="nam">usecols</span><span class="op">=</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t137" href="#t137">137</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t138" href="#t138">138</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span> <span class="key">is</span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t139" href="#t139">139</a></span><span class="t">            <span class="com"># drop first and last columns</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t140" href="#t140">140</a></span><span class="t">            <span class="nam">shear</span> <span class="op">=</span> <span class="nam">shear</span><span class="op">[</span><span class="nam">shear</span><span class="op">.</span><span class="nam">columns</span><span class="op">[</span><span class="num">1</span><span class="op">:</span><span class="op">-</span><span class="num">1</span><span class="op">]</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t141" href="#t141">141</a></span><span class="t">            <span class="nam">stretch</span> <span class="op">=</span> <span class="nam">stretch</span><span class="op">[</span><span class="nam">stretch</span><span class="op">.</span><span class="nam">columns</span><span class="op">[</span><span class="num">1</span><span class="op">:</span><span class="op">-</span><span class="num">1</span><span class="op">]</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t142" href="#t142">142</a></span><span class="t">            <span class="nam">stagger</span> <span class="op">=</span> <span class="nam">stagger</span><span class="op">[</span><span class="nam">stagger</span><span class="op">.</span><span class="nam">columns</span><span class="op">[</span><span class="num">1</span><span class="op">:</span><span class="op">-</span><span class="num">1</span><span class="op">]</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t143" href="#t143">143</a></span><span class="t">            <span class="nam">buckle</span> <span class="op">=</span> <span class="nam">buckle</span><span class="op">[</span><span class="nam">buckle</span><span class="op">.</span><span class="nam">columns</span><span class="op">[</span><span class="num">1</span><span class="op">:</span><span class="op">-</span><span class="num">1</span><span class="op">]</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t144" href="#t144">144</a></span><span class="t">            <span class="nam">propel</span> <span class="op">=</span> <span class="nam">propel</span><span class="op">[</span><span class="nam">propel</span><span class="op">.</span><span class="nam">columns</span><span class="op">[</span><span class="num">1</span><span class="op">:</span><span class="op">-</span><span class="num">1</span><span class="op">]</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t145" href="#t145">145</a></span><span class="t">            <span class="nam">opening</span> <span class="op">=</span> <span class="nam">opening</span><span class="op">[</span><span class="nam">opening</span><span class="op">.</span><span class="nam">columns</span><span class="op">[</span><span class="num">1</span><span class="op">:</span><span class="op">-</span><span class="num">1</span><span class="op">]</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t146" href="#t146">146</a></span><span class="t">            <span class="nam">labels</span> <span class="op">=</span> <span class="op">[</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t147" href="#t147">147</a></span><span class="t">                <span class="str">f"{i+1}_{self.sequence[i:i+1]}"</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">range</span><span class="op">(</span><span class="num">1</span><span class="op">,</span> <span class="nam">len</span><span class="op">(</span><span class="nam">shear</span><span class="op">.</span><span class="nam">columns</span><span class="op">)</span> <span class="op">+</span> <span class="num">1</span><span class="op">)</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t148" href="#t148">148</a></span><span class="t">            <span class="nam">corr_index</span> <span class="op">=</span> <span class="op">[</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t149" href="#t149">149</a></span><span class="t">                <span class="str">f"{self.sequence[i:i+2]}"</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">range</span><span class="op">(</span><span class="num">1</span><span class="op">,</span> <span class="nam">len</span><span class="op">(</span><span class="nam">shear</span><span class="op">.</span><span class="nam">columns</span><span class="op">)</span> <span class="op">+</span> <span class="num">1</span><span class="op">)</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t150" href="#t150">150</a></span><span class="t">        <span class="key">else</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t151" href="#t151">151</a></span><span class="t">            <span class="nam">labels</span> <span class="op">=</span> <span class="op">[</span><span class="str">f"{i+1}_{self.sequence[i:i+1]}"</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t152" href="#t152">152</a></span><span class="t">            <span class="nam">corr_index</span> <span class="op">=</span> <span class="op">[</span><span class="str">f"{self.sequence[i:i+2]}"</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t153" href="#t153">153</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t154" href="#t154">154</a></span><span class="t">        <span class="com"># rename duplicated subunits</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t155" href="#t155">155</a></span><span class="t">        <span class="nam">shear</span><span class="op">.</span><span class="nam">columns</span> <span class="op">=</span> <span class="nam">labels</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t156" href="#t156">156</a></span><span class="t">        <span class="nam">stretch</span><span class="op">.</span><span class="nam">columns</span> <span class="op">=</span> <span class="nam">labels</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t157" href="#t157">157</a></span><span class="t">        <span class="nam">stagger</span><span class="op">.</span><span class="nam">columns</span> <span class="op">=</span> <span class="nam">labels</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t158" href="#t158">158</a></span><span class="t">        <span class="nam">buckle</span><span class="op">.</span><span class="nam">columns</span> <span class="op">=</span> <span class="nam">labels</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t159" href="#t159">159</a></span><span class="t">        <span class="nam">propel</span><span class="op">.</span><span class="nam">columns</span> <span class="op">=</span> <span class="nam">labels</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t160" href="#t160">160</a></span><span class="t">        <span class="nam">opening</span><span class="op">.</span><span class="nam">columns</span> <span class="op">=</span> <span class="nam">labels</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t161" href="#t161">161</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t162" href="#t162">162</a></span><span class="t">        <span class="com"># set names to each dataset</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t163" href="#t163">163</a></span><span class="t">        <span class="nam">shear</span><span class="op">.</span><span class="nam">name</span> <span class="op">=</span> <span class="str">"shear"</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t164" href="#t164">164</a></span><span class="t">        <span class="nam">stretch</span><span class="op">.</span><span class="nam">name</span> <span class="op">=</span> <span class="str">"stretch"</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t165" href="#t165">165</a></span><span class="t">        <span class="nam">stagger</span><span class="op">.</span><span class="nam">name</span> <span class="op">=</span> <span class="str">"stagger"</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t166" href="#t166">166</a></span><span class="t">        <span class="nam">buckle</span><span class="op">.</span><span class="nam">name</span> <span class="op">=</span> <span class="str">"buckle"</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t167" href="#t167">167</a></span><span class="t">        <span class="nam">propel</span><span class="op">.</span><span class="nam">name</span> <span class="op">=</span> <span class="str">"propel"</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t168" href="#t168">168</a></span><span class="t">        <span class="nam">opening</span><span class="op">.</span><span class="nam">name</span> <span class="op">=</span> <span class="str">"opening"</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t169" href="#t169">169</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t170" href="#t170">170</a></span><span class="t">        <span class="com"># get correlation between neighboring basepairs among all helical parameters</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t171" href="#t171">171</a></span><span class="t">        <span class="nam">results</span> <span class="op">=</span> <span class="op">{</span><span class="op">}</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t172" href="#t172">172</a></span><span class="t">        <span class="nam">datasets</span> <span class="op">=</span> <span class="op">[</span><span class="nam">shear</span><span class="op">,</span> <span class="nam">stretch</span><span class="op">,</span> <span class="nam">stagger</span><span class="op">,</span> <span class="nam">buckle</span><span class="op">,</span> <span class="nam">propel</span><span class="op">,</span> <span class="nam">opening</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t173" href="#t173">173</a></span><span class="t">        <span class="key">for</span> <span class="nam">ser1</span><span class="op">,</span> <span class="nam">ser2</span> <span class="key">in</span> <span class="nam">product</span><span class="op">(</span><span class="nam">datasets</span><span class="op">,</span> <span class="nam">datasets</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t174" href="#t174">174</a></span><span class="t">            <span class="nam">ser2_shifted</span> <span class="op">=</span> <span class="nam">ser2</span><span class="op">.</span><span class="nam">shift</span><span class="op">(</span><span class="nam">axis</span><span class="op">=</span><span class="num">1</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t175" href="#t175">175</a></span><span class="t">            <span class="nam">ser2_shifted</span><span class="op">[</span><span class="nam">labels</span><span class="op">[</span><span class="num">0</span><span class="op">]</span><span class="op">]</span> <span class="op">=</span> <span class="nam">ser2</span><span class="op">[</span><span class="nam">labels</span><span class="op">[</span><span class="op">-</span><span class="num">1</span><span class="op">]</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t176" href="#t176">176</a></span><span class="t">            <span class="key">if</span> <span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t177" href="#t177">177</a></span><span class="t">                    <span class="nam">ser1</span><span class="op">.</span><span class="nam">name</span> <span class="key">in</span> <span class="nam">constants</span><span class="op">.</span><span class="nam">hp_angular</span> <span class="key">and</span> <span class="nam">ser2</span><span class="op">.</span><span class="nam">name</span> <span class="key">in</span> <span class="nam">constants</span><span class="op">.</span><span class="nam">hp_angular</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t178" href="#t178">178</a></span><span class="t">                <span class="nam">method</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">circular</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t179" href="#t179">179</a></span><span class="t">            <span class="key">elif</span> <span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t180" href="#t180">180</a></span><span class="t">                <span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t181" href="#t181">181</a></span><span class="t">                    <span class="nam">ser1</span><span class="op">.</span><span class="nam">name</span> <span class="key">in</span> <span class="nam">constants</span><span class="op">.</span><span class="nam">hp_angular</span> <span class="key">and</span> <span class="key">not</span> <span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t182" href="#t182">182</a></span><span class="t">                        <span class="nam">ser2</span><span class="op">.</span><span class="nam">name</span> <span class="key">in</span> <span class="nam">constants</span><span class="op">.</span><span class="nam">hp_angular</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t183" href="#t183">183</a></span><span class="t">                <span class="op">)</span> <span class="key">or</span> <span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t184" href="#t184">184</a></span><span class="t">                    <span class="nam">ser2</span><span class="op">.</span><span class="nam">name</span> <span class="key">in</span> <span class="nam">constants</span><span class="op">.</span><span class="nam">hp_angular</span> <span class="key">and</span> <span class="key">not</span> <span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t185" href="#t185">185</a></span><span class="t">                        <span class="nam">ser1</span><span class="op">.</span><span class="nam">name</span> <span class="key">in</span> <span class="nam">constants</span><span class="op">.</span><span class="nam">hp_angular</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t186" href="#t186">186</a></span><span class="t">                <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t187" href="#t187">187</a></span><span class="t">            <span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t188" href="#t188">188</a></span><span class="t">                <span class="nam">method</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">circlineal</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t189" href="#t189">189</a></span><span class="t">            <span class="key">else</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t190" href="#t190">190</a></span><span class="t">                <span class="nam">method</span> <span class="op">=</span> <span class="str">"pearson"</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t191" href="#t191">191</a></span><span class="t">            <span class="nam">corr_data</span> <span class="op">=</span> <span class="nam">ser1</span><span class="op">.</span><span class="nam">corrwith</span><span class="op">(</span><span class="nam">ser2_shifted</span><span class="op">,</span> <span class="nam">method</span><span class="op">=</span><span class="nam">method</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t192" href="#t192">192</a></span><span class="t">            <span class="nam">corr_data</span><span class="op">.</span><span class="nam">index</span> <span class="op">=</span> <span class="nam">corr_index</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t193" href="#t193">193</a></span><span class="t">            <span class="nam">results</span><span class="op">[</span><span class="str">f"{ser1.name}/{ser2.name}"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">corr_data</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t194" href="#t194">194</a></span><span class="t">        <span class="nam">result_df</span> <span class="op">=</span> <span class="nam">pd</span><span class="op">.</span><span class="nam">DataFrame</span><span class="op">.</span><span class="nam">from_dict</span><span class="op">(</span><span class="nam">results</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t195" href="#t195">195</a></span><span class="t">        <span class="nam">result_df</span><span class="op">.</span><span class="nam">index</span> <span class="op">=</span> <span class="nam">corr_index</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t196" href="#t196">196</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t197" href="#t197">197</a></span><span class="t">        <span class="com"># save csv data</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t198" href="#t198">198</a></span><span class="t">        <span class="nam">result_df</span><span class="op">.</span><span class="nam">to_csv</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">"out"</span><span class="op">]</span><span class="op">[</span><span class="str">"output_csv_path"</span><span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t199" href="#t199">199</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t200" href="#t200">200</a></span><span class="t">        <span class="com"># create heatmap</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t201" href="#t201">201</a></span><span class="t">        <span class="nam">cmap</span> <span class="op">=</span> <span class="nam">plt</span><span class="op">.</span><span class="nam">get_cmap</span><span class="op">(</span><span class="str">"bwr"</span><span class="op">)</span><span class="op">.</span><span class="nam">copy</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t202" href="#t202">202</a></span><span class="t">        <span class="nam">bounds</span> <span class="op">=</span> <span class="op">[</span><span class="op">-</span><span class="num">1</span><span class="op">,</span> <span class="op">-</span><span class="num">.8</span><span class="op">,</span> <span class="op">-</span><span class="num">.6</span><span class="op">,</span> <span class="op">-</span><span class="num">.4</span><span class="op">,</span> <span class="op">-</span><span class="num">.2</span><span class="op">,</span> <span class="num">.2</span><span class="op">,</span> <span class="num">.4</span><span class="op">,</span> <span class="num">.6</span><span class="op">,</span> <span class="num">.8</span><span class="op">,</span> <span class="num">1</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t203" href="#t203">203</a></span><span class="t">        <span class="nam">num</span> <span class="op">=</span> <span class="nam">cmap</span><span class="op">.</span><span class="nam">N</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t204" href="#t204">204</a></span><span class="t">        <span class="nam">norm</span> <span class="op">=</span> <span class="nam">mpl</span><span class="op">.</span><span class="nam">colors</span><span class="op">.</span><span class="nam">BoundaryNorm</span><span class="op">(</span><span class="nam">bounds</span><span class="op">,</span> <span class="nam">num</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t205" href="#t205">205</a></span><span class="t">        <span class="nam">cmap</span><span class="op">.</span><span class="nam">set_bad</span><span class="op">(</span><span class="nam">color</span><span class="op">=</span><span class="str">"gainsboro"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t206" href="#t206">206</a></span><span class="t">        <span class="nam">fig</span><span class="op">,</span> <span class="nam">ax</span> <span class="op">=</span> <span class="nam">plt</span><span class="op">.</span><span class="nam">subplots</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t207" href="#t207">207</a></span><span class="t">            <span class="num">1</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t24" href="#t24">24</a></span><span class="t"><span class="str">    | Calculate correlation between neighboring base pairs and pairs of helical parameters.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t25" href="#t25">25</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t26" href="#t26">26</a></span><span class="t"><span class="str">    Args:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t27" href="#t27">27</a></span><span class="t"><span class="str">        input_filename_shear (str): Path to .ser file with data for helical parameter 'shear'. File type: input. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/correlation/canal_output_shear.ser>`_. Accepted formats: ser (edam:format_2330).</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t28" href="#t28">28</a></span><span class="t"><span class="str">        input_filename_stretch (str): Path to .ser file with data for helical parameter 'stretch'. File type: input. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/correlation/canal_output_stretch.ser>`_. Accepted formats: ser (edam:format_2330).</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t29" href="#t29">29</a></span><span class="t"><span class="str">        input_filename_stagger (str): Path to .ser file with data for helical parameter 'stagger'. File type: input. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/correlation/canal_output_stagger.ser>`_. Accepted formats: ser (edam:format_2330).</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t30" href="#t30">30</a></span><span class="t"><span class="str">        input_filename_buckle (str): Path to .ser file with data for helical parameter 'buckle'. File type: input. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/correlation/canal_output_buckle.ser>`_. Accepted formats: ser (edam:format_2330).</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t31" href="#t31">31</a></span><span class="t"><span class="str">        input_filename_propel (str): Path to .ser file with data for helical parameter 'propel'. File type: input. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/correlation/canal_output_propel.ser>`_. Accepted formats: ser (edam:format_2330).</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t32" href="#t32">32</a></span><span class="t"><span class="str">        input_filename_opening (str): Path to .ser file with data for helical parameter 'opening'. File type: input. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/correlation/canal_output_opening.ser>`_. Accepted formats: ser (edam:format_2330).</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t33" href="#t33">33</a></span><span class="t"><span class="str">        output_csv_path (str): Path to directory where output is saved. File type: output. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/reference/correlation/intra_bpcorr_ref.csv>`_. Accepted formats: csv (edam:format_3752).</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t34" href="#t34">34</a></span><span class="t"><span class="str">        output_jpg_path (str): Path to .jpg file where output is saved. File type: output. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/reference/correlation/intra_bpcorr_ref.jpg>`_. Accepted formats: jpg (edam:format_3579).</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t35" href="#t35">35</a></span><span class="t"><span class="str">        properties (dict):</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t36" href="#t36">36</a></span><span class="t"><span class="str">            * **sequence** (*str*) - (None) Nucleic acid sequence for the input .ser file. Length of sequence is expected to be the same as the total number of columns in the .ser file, minus the index column (even if later on a subset of columns is selected with the *seqpos* option).</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t37" href="#t37">37</a></span><span class="t"><span class="str">            * **seqpos** (*list*) - (None) list of sequence positions (columns indices starting by 0) to analyze.  If not specified it will analyse the complete sequence.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t38" href="#t38">38</a></span><span class="t"><span class="str">            * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t39" href="#t39">39</a></span><span class="t"><span class="str">            * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t40" href="#t40">40</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t41" href="#t41">41</a></span><span class="t"><span class="str">    Examples:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t42" href="#t42">42</a></span><span class="t"><span class="str">        This is a use example of how to use the building block from Python::</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t43" href="#t43">43</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t44" href="#t44">44</a></span><span class="t"><span class="str">            from biobb_dna.intrabp_correlations.intrabpcorr import intrabpcorr</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t45" href="#t45">45</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t46" href="#t46">46</a></span><span class="t"><span class="str">            intrabpcorr(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t47" href="#t47">47</a></span><span class="t"><span class="str">                input_filename_shear='path/to/input/shear.ser',</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t48" href="#t48">48</a></span><span class="t"><span class="str">                input_filename_stretch='path/to/input/stretch.ser',</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t49" href="#t49">49</a></span><span class="t"><span class="str">                input_filename_stagger='path/to/input/stagger.ser',</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t50" href="#t50">50</a></span><span class="t"><span class="str">                input_filename_buckle='path/to/input/buckle.ser',</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t51" href="#t51">51</a></span><span class="t"><span class="str">                input_filename_propel='path/to/input/propel.ser',</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t52" href="#t52">52</a></span><span class="t"><span class="str">                input_filename_opening='path/to/input/opening.ser',</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t53" href="#t53">53</a></span><span class="t"><span class="str">                output_csv_path='path/to/output/file.csv',</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t54" href="#t54">54</a></span><span class="t"><span class="str">                output_jpg_path='path/to/output/plot.jpg',</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t55" href="#t55">55</a></span><span class="t"><span class="str">                properties=prop)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t56" href="#t56">56</a></span><span class="t"><span class="str">    Info:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t57" href="#t57">57</a></span><span class="t"><span class="str">        * wrapped_software:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t58" href="#t58">58</a></span><span class="t"><span class="str">            * name: In house</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t59" href="#t59">59</a></span><span class="t"><span class="str">            * license: Apache-2.0</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t60" href="#t60">60</a></span><span class="t"><span class="str">        * ontology:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t61" href="#t61">61</a></span><span class="t"><span class="str">            * name: EDAM</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t62" href="#t62">62</a></span><span class="t"><span class="str">            * schema: http://edamontology.org/EDAM.owl</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t63" href="#t63">63</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t64" href="#t64">64</a></span><span class="t"><span class="str">    """</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t65" href="#t65">65</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t66" href="#t66">66</a></span><span class="t">    <span class="key">def</span> <span class="nam">__init__</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t67" href="#t67">67</a></span><span class="t">            <span class="nam">self</span><span class="op">,</span> <span class="nam">input_filename_shear</span><span class="op">,</span> <span class="nam">input_filename_stretch</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t68" href="#t68">68</a></span><span class="t">            <span class="nam">input_filename_stagger</span><span class="op">,</span> <span class="nam">input_filename_buckle</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t69" href="#t69">69</a></span><span class="t">            <span class="nam">input_filename_propel</span><span class="op">,</span> <span class="nam">input_filename_opening</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t70" href="#t70">70</a></span><span class="t">            <span class="nam">output_csv_path</span><span class="op">,</span> <span class="nam">output_jpg_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t71" href="#t71">71</a></span><span class="t">            <span class="nam">properties</span><span class="op">=</span><span class="key">None</span><span class="op">,</span> <span class="op">**</span><span class="nam">kwargs</span><span class="op">)</span> <span class="op">-></span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t72" href="#t72">72</a></span><span class="t">        <span class="nam">properties</span> <span class="op">=</span> <span class="nam">properties</span> <span class="key">or</span> <span class="op">{</span><span class="op">}</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t73" href="#t73">73</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t74" href="#t74">74</a></span><span class="t">        <span class="com"># Call parent class constructor</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t75" href="#t75">75</a></span><span class="t">        <span class="nam">super</span><span class="op">(</span><span class="op">)</span><span class="op">.</span><span class="nam">__init__</span><span class="op">(</span><span class="nam">properties</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t76" href="#t76">76</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">locals_var_dict</span> <span class="op">=</span> <span class="nam">locals</span><span class="op">(</span><span class="op">)</span><span class="op">.</span><span class="nam">copy</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t77" href="#t77">77</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t78" href="#t78">78</a></span><span class="t">        <span class="com"># Input/Output files</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t79" href="#t79">79</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span> <span class="op">=</span> <span class="op">{</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t80" href="#t80">80</a></span><span class="t">            <span class="str">'in'</span><span class="op">:</span> <span class="op">{</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t81" href="#t81">81</a></span><span class="t">                <span class="str">'input_filename_shear'</span><span class="op">:</span> <span class="nam">input_filename_shear</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t82" href="#t82">82</a></span><span class="t">                <span class="str">'input_filename_stretch'</span><span class="op">:</span> <span class="nam">input_filename_stretch</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t83" href="#t83">83</a></span><span class="t">                <span class="str">'input_filename_stagger'</span><span class="op">:</span> <span class="nam">input_filename_stagger</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t84" href="#t84">84</a></span><span class="t">                <span class="str">'input_filename_buckle'</span><span class="op">:</span> <span class="nam">input_filename_buckle</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t85" href="#t85">85</a></span><span class="t">                <span class="str">'input_filename_propel'</span><span class="op">:</span> <span class="nam">input_filename_propel</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t86" href="#t86">86</a></span><span class="t">                <span class="str">'input_filename_opening'</span><span class="op">:</span> <span class="nam">input_filename_opening</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t87" href="#t87">87</a></span><span class="t">            <span class="op">}</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t88" href="#t88">88</a></span><span class="t">            <span class="str">'out'</span><span class="op">:</span> <span class="op">{</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t89" href="#t89">89</a></span><span class="t">                <span class="str">'output_csv_path'</span><span class="op">:</span> <span class="nam">output_csv_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t90" href="#t90">90</a></span><span class="t">                <span class="str">'output_jpg_path'</span><span class="op">:</span> <span class="nam">output_jpg_path</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t91" href="#t91">91</a></span><span class="t">            <span class="op">}</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t92" href="#t92">92</a></span><span class="t">        <span class="op">}</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t93" href="#t93">93</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t94" href="#t94">94</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">properties</span> <span class="op">=</span> <span class="nam">properties</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t95" href="#t95">95</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"sequence"</span><span class="op">,</span> <span class="key">None</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t96" href="#t96">96</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"seqpos"</span><span class="op">,</span> <span class="key">None</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t97" href="#t97">97</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t98" href="#t98">98</a></span><span class="t">        <span class="com"># Check the properties</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t99" href="#t99">99</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_properties</span><span class="op">(</span><span class="nam">properties</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t100" href="#t100">100</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_arguments</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t101" href="#t101">101</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t102" href="#t102">102</a></span><span class="t">    <span class="op">@</span><span class="nam">launchlogger</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t103" href="#t103">103</a></span><span class="t">    <span class="key">def</span> <span class="nam">launch</span><span class="op">(</span><span class="nam">self</span><span class="op">)</span> <span class="op">-></span> <span class="nam">int</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t104" href="#t104">104</a></span><span class="t">        <span class="str">"""Execute the :class:`HelParCorrelation &lt;intrabp_correlations.intrabpcorr.IntraBasePairCorrelation>` object."""</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t105" href="#t105">105</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t106" href="#t106">106</a></span><span class="t">        <span class="com"># Setup Biobb</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t107" href="#t107">107</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">check_restart</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t108" href="#t108">108</a></span><span class="t">            <span class="key">return</span> <span class="num">0</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t109" href="#t109">109</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">stage_files</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t110" href="#t110">110</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t111" href="#t111">111</a></span><span class="t">        <span class="com"># check sequence</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t112" href="#t112">112</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span> <span class="key">is</span> <span class="key">None</span> <span class="key">or</span> <span class="nam">len</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span><span class="op">)</span> <span class="op">&lt;</span> <span class="num">2</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t113" href="#t113">113</a></span><span class="t">            <span class="key">raise</span> <span class="nam">ValueError</span><span class="op">(</span><span class="str">"sequence is null or too short!"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t114" href="#t114">114</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t115" href="#t115">115</a></span><span class="t">        <span class="com"># check seqpos</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t116" href="#t116">116</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span> <span class="key">is</span> <span class="key">not</span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t117" href="#t117">117</a></span><span class="t">            <span class="key">if</span> <span class="key">not</span> <span class="op">(</span><span class="nam">isinstance</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">,</span> <span class="nam">list</span><span class="op">)</span> <span class="key">and</span> <span class="nam">len</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">)</span> <span class="op">></span> <span class="num">1</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t118" href="#t118">118</a></span><span class="t">                <span class="key">raise</span> <span class="nam">ValueError</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t119" href="#t119">119</a></span><span class="t">                    <span class="str">"seqpos must be a list of at least two integers"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t120" href="#t120">120</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t121" href="#t121">121</a></span><span class="t">        <span class="com"># Creating temporary folder</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t122" href="#t122">122</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span> <span class="op">=</span> <span class="nam">fu</span><span class="op">.</span><span class="nam">create_unique_dir</span><span class="op">(</span><span class="nam">prefix</span><span class="op">=</span><span class="str">"bpcorrelation_"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t123" href="#t123">123</a></span><span class="t">        <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="str">'Creating %s temporary folder'</span> <span class="op">%</span> <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t124" href="#t124">124</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t125" href="#t125">125</a></span><span class="t">        <span class="com"># read input</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t126" href="#t126">126</a></span><span class="t">        <span class="nam">shear</span> <span class="op">=</span> <span class="nam">read_series</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t127" href="#t127">127</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">"in"</span><span class="op">]</span><span class="op">[</span><span class="str">"input_filename_shear"</span><span class="op">]</span><span class="op">,</span> <span class="nam">usecols</span><span class="op">=</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t128" href="#t128">128</a></span><span class="t">        <span class="nam">stretch</span> <span class="op">=</span> <span class="nam">read_series</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t129" href="#t129">129</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">"in"</span><span class="op">]</span><span class="op">[</span><span class="str">"input_filename_stretch"</span><span class="op">]</span><span class="op">,</span> <span class="nam">usecols</span><span class="op">=</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t130" href="#t130">130</a></span><span class="t">        <span class="nam">stagger</span> <span class="op">=</span> <span class="nam">read_series</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t131" href="#t131">131</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">"in"</span><span class="op">]</span><span class="op">[</span><span class="str">"input_filename_stagger"</span><span class="op">]</span><span class="op">,</span> <span class="nam">usecols</span><span class="op">=</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t132" href="#t132">132</a></span><span class="t">        <span class="nam">buckle</span> <span class="op">=</span> <span class="nam">read_series</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t133" href="#t133">133</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">"in"</span><span class="op">]</span><span class="op">[</span><span class="str">"input_filename_buckle"</span><span class="op">]</span><span class="op">,</span> <span class="nam">usecols</span><span class="op">=</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t134" href="#t134">134</a></span><span class="t">        <span class="nam">propel</span> <span class="op">=</span> <span class="nam">read_series</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t135" href="#t135">135</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">"in"</span><span class="op">]</span><span class="op">[</span><span class="str">"input_filename_propel"</span><span class="op">]</span><span class="op">,</span> <span class="nam">usecols</span><span class="op">=</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t136" href="#t136">136</a></span><span class="t">        <span class="nam">opening</span> <span class="op">=</span> <span class="nam">read_series</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t137" href="#t137">137</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">"in"</span><span class="op">]</span><span class="op">[</span><span class="str">"input_filename_opening"</span><span class="op">]</span><span class="op">,</span> <span class="nam">usecols</span><span class="op">=</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t138" href="#t138">138</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t139" href="#t139">139</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span> <span class="key">is</span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t140" href="#t140">140</a></span><span class="t">            <span class="com"># drop first and last columns</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t141" href="#t141">141</a></span><span class="t">            <span class="nam">shear</span> <span class="op">=</span> <span class="nam">shear</span><span class="op">[</span><span class="nam">shear</span><span class="op">.</span><span class="nam">columns</span><span class="op">[</span><span class="num">1</span><span class="op">:</span><span class="op">-</span><span class="num">1</span><span class="op">]</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t142" href="#t142">142</a></span><span class="t">            <span class="nam">stretch</span> <span class="op">=</span> <span class="nam">stretch</span><span class="op">[</span><span class="nam">stretch</span><span class="op">.</span><span class="nam">columns</span><span class="op">[</span><span class="num">1</span><span class="op">:</span><span class="op">-</span><span class="num">1</span><span class="op">]</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t143" href="#t143">143</a></span><span class="t">            <span class="nam">stagger</span> <span class="op">=</span> <span class="nam">stagger</span><span class="op">[</span><span class="nam">stagger</span><span class="op">.</span><span class="nam">columns</span><span class="op">[</span><span class="num">1</span><span class="op">:</span><span class="op">-</span><span class="num">1</span><span class="op">]</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t144" href="#t144">144</a></span><span class="t">            <span class="nam">buckle</span> <span class="op">=</span> <span class="nam">buckle</span><span class="op">[</span><span class="nam">buckle</span><span class="op">.</span><span class="nam">columns</span><span class="op">[</span><span class="num">1</span><span class="op">:</span><span class="op">-</span><span class="num">1</span><span class="op">]</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t145" href="#t145">145</a></span><span class="t">            <span class="nam">propel</span> <span class="op">=</span> <span class="nam">propel</span><span class="op">[</span><span class="nam">propel</span><span class="op">.</span><span class="nam">columns</span><span class="op">[</span><span class="num">1</span><span class="op">:</span><span class="op">-</span><span class="num">1</span><span class="op">]</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t146" href="#t146">146</a></span><span class="t">            <span class="nam">opening</span> <span class="op">=</span> <span class="nam">opening</span><span class="op">[</span><span class="nam">opening</span><span class="op">.</span><span class="nam">columns</span><span class="op">[</span><span class="num">1</span><span class="op">:</span><span class="op">-</span><span class="num">1</span><span class="op">]</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t147" href="#t147">147</a></span><span class="t">            <span class="nam">labels</span> <span class="op">=</span> <span class="op">[</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t148" href="#t148">148</a></span><span class="t">                <span class="str">f"{i+1}_{self.sequence[i:i+1]}"</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">range</span><span class="op">(</span><span class="num">1</span><span class="op">,</span> <span class="nam">len</span><span class="op">(</span><span class="nam">shear</span><span class="op">.</span><span class="nam">columns</span><span class="op">)</span> <span class="op">+</span> <span class="num">1</span><span class="op">)</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t149" href="#t149">149</a></span><span class="t">            <span class="nam">corr_index</span> <span class="op">=</span> <span class="op">[</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t150" href="#t150">150</a></span><span class="t">                <span class="str">f"{self.sequence[i:i+2]}"</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">range</span><span class="op">(</span><span class="num">1</span><span class="op">,</span> <span class="nam">len</span><span class="op">(</span><span class="nam">shear</span><span class="op">.</span><span class="nam">columns</span><span class="op">)</span> <span class="op">+</span> <span class="num">1</span><span class="op">)</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t151" href="#t151">151</a></span><span class="t">        <span class="key">else</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t152" href="#t152">152</a></span><span class="t">            <span class="nam">labels</span> <span class="op">=</span> <span class="op">[</span><span class="str">f"{i+1}_{self.sequence[i:i+1]}"</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t153" href="#t153">153</a></span><span class="t">            <span class="nam">corr_index</span> <span class="op">=</span> <span class="op">[</span><span class="str">f"{self.sequence[i:i+2]}"</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t154" href="#t154">154</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t155" href="#t155">155</a></span><span class="t">        <span class="com"># rename duplicated subunits</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t156" href="#t156">156</a></span><span class="t">        <span class="nam">shear</span><span class="op">.</span><span class="nam">columns</span> <span class="op">=</span> <span class="nam">labels</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t157" href="#t157">157</a></span><span class="t">        <span class="nam">stretch</span><span class="op">.</span><span class="nam">columns</span> <span class="op">=</span> <span class="nam">labels</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t158" href="#t158">158</a></span><span class="t">        <span class="nam">stagger</span><span class="op">.</span><span class="nam">columns</span> <span class="op">=</span> <span class="nam">labels</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t159" href="#t159">159</a></span><span class="t">        <span class="nam">buckle</span><span class="op">.</span><span class="nam">columns</span> <span class="op">=</span> <span class="nam">labels</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t160" href="#t160">160</a></span><span class="t">        <span class="nam">propel</span><span class="op">.</span><span class="nam">columns</span> <span class="op">=</span> <span class="nam">labels</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t161" href="#t161">161</a></span><span class="t">        <span class="nam">opening</span><span class="op">.</span><span class="nam">columns</span> <span class="op">=</span> <span class="nam">labels</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t162" href="#t162">162</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t163" href="#t163">163</a></span><span class="t">        <span class="com"># set names to each dataset</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t164" href="#t164">164</a></span><span class="t">        <span class="nam">shear</span><span class="op">.</span><span class="nam">name</span> <span class="op">=</span> <span class="str">"shear"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t165" href="#t165">165</a></span><span class="t">        <span class="nam">stretch</span><span class="op">.</span><span class="nam">name</span> <span class="op">=</span> <span class="str">"stretch"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t166" href="#t166">166</a></span><span class="t">        <span class="nam">stagger</span><span class="op">.</span><span class="nam">name</span> <span class="op">=</span> <span class="str">"stagger"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t167" href="#t167">167</a></span><span class="t">        <span class="nam">buckle</span><span class="op">.</span><span class="nam">name</span> <span class="op">=</span> <span class="str">"buckle"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t168" href="#t168">168</a></span><span class="t">        <span class="nam">propel</span><span class="op">.</span><span class="nam">name</span> <span class="op">=</span> <span class="str">"propel"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t169" href="#t169">169</a></span><span class="t">        <span class="nam">opening</span><span class="op">.</span><span class="nam">name</span> <span class="op">=</span> <span class="str">"opening"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t170" href="#t170">170</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t171" href="#t171">171</a></span><span class="t">        <span class="com"># get correlation between neighboring basepairs among all helical parameters</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t172" href="#t172">172</a></span><span class="t">        <span class="nam">results</span> <span class="op">=</span> <span class="op">{</span><span class="op">}</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t173" href="#t173">173</a></span><span class="t">        <span class="nam">datasets</span> <span class="op">=</span> <span class="op">[</span><span class="nam">shear</span><span class="op">,</span> <span class="nam">stretch</span><span class="op">,</span> <span class="nam">stagger</span><span class="op">,</span> <span class="nam">buckle</span><span class="op">,</span> <span class="nam">propel</span><span class="op">,</span> <span class="nam">opening</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t174" href="#t174">174</a></span><span class="t">        <span class="key">for</span> <span class="nam">ser1</span><span class="op">,</span> <span class="nam">ser2</span> <span class="key">in</span> <span class="nam">product</span><span class="op">(</span><span class="nam">datasets</span><span class="op">,</span> <span class="nam">datasets</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t175" href="#t175">175</a></span><span class="t">            <span class="nam">ser2_shifted</span> <span class="op">=</span> <span class="nam">ser2</span><span class="op">.</span><span class="nam">shift</span><span class="op">(</span><span class="nam">axis</span><span class="op">=</span><span class="num">1</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t176" href="#t176">176</a></span><span class="t">            <span class="nam">ser2_shifted</span><span class="op">[</span><span class="nam">labels</span><span class="op">[</span><span class="num">0</span><span class="op">]</span><span class="op">]</span> <span class="op">=</span> <span class="nam">ser2</span><span class="op">[</span><span class="nam">labels</span><span class="op">[</span><span class="op">-</span><span class="num">1</span><span class="op">]</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t177" href="#t177">177</a></span><span class="t">            <span class="key">if</span> <span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t178" href="#t178">178</a></span><span class="t">                    <span class="nam">ser1</span><span class="op">.</span><span class="nam">name</span> <span class="key">in</span> <span class="nam">constants</span><span class="op">.</span><span class="nam">hp_angular</span> <span class="key">and</span> <span class="nam">ser2</span><span class="op">.</span><span class="nam">name</span> <span class="key">in</span> <span class="nam">constants</span><span class="op">.</span><span class="nam">hp_angular</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t179" href="#t179">179</a></span><span class="t">                <span class="nam">method</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">circular</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t180" href="#t180">180</a></span><span class="t">            <span class="key">elif</span> <span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t181" href="#t181">181</a></span><span class="t">                <span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t182" href="#t182">182</a></span><span class="t">                    <span class="nam">ser1</span><span class="op">.</span><span class="nam">name</span> <span class="key">in</span> <span class="nam">constants</span><span class="op">.</span><span class="nam">hp_angular</span> <span class="key">and</span> <span class="key">not</span> <span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t183" href="#t183">183</a></span><span class="t">                        <span class="nam">ser2</span><span class="op">.</span><span class="nam">name</span> <span class="key">in</span> <span class="nam">constants</span><span class="op">.</span><span class="nam">hp_angular</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t184" href="#t184">184</a></span><span class="t">                <span class="op">)</span> <span class="key">or</span> <span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t185" href="#t185">185</a></span><span class="t">                    <span class="nam">ser2</span><span class="op">.</span><span class="nam">name</span> <span class="key">in</span> <span class="nam">constants</span><span class="op">.</span><span class="nam">hp_angular</span> <span class="key">and</span> <span class="key">not</span> <span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t186" href="#t186">186</a></span><span class="t">                        <span class="nam">ser1</span><span class="op">.</span><span class="nam">name</span> <span class="key">in</span> <span class="nam">constants</span><span class="op">.</span><span class="nam">hp_angular</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t187" href="#t187">187</a></span><span class="t">                <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t188" href="#t188">188</a></span><span class="t">            <span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t189" href="#t189">189</a></span><span class="t">                <span class="nam">method</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">circlineal</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t190" href="#t190">190</a></span><span class="t">            <span class="key">else</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t191" href="#t191">191</a></span><span class="t">                <span class="nam">method</span> <span class="op">=</span> <span class="str">"pearson"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t192" href="#t192">192</a></span><span class="t">            <span class="nam">corr_data</span> <span class="op">=</span> <span class="nam">ser1</span><span class="op">.</span><span class="nam">corrwith</span><span class="op">(</span><span class="nam">ser2_shifted</span><span class="op">,</span> <span class="nam">method</span><span class="op">=</span><span class="nam">method</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t193" href="#t193">193</a></span><span class="t">            <span class="nam">corr_data</span><span class="op">.</span><span class="nam">index</span> <span class="op">=</span> <span class="nam">corr_index</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t194" href="#t194">194</a></span><span class="t">            <span class="nam">results</span><span class="op">[</span><span class="str">f"{ser1.name}/{ser2.name}"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">corr_data</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t195" href="#t195">195</a></span><span class="t">        <span class="nam">result_df</span> <span class="op">=</span> <span class="nam">pd</span><span class="op">.</span><span class="nam">DataFrame</span><span class="op">.</span><span class="nam">from_dict</span><span class="op">(</span><span class="nam">results</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t196" href="#t196">196</a></span><span class="t">        <span class="nam">result_df</span><span class="op">.</span><span class="nam">index</span> <span class="op">=</span> <span class="nam">corr_index</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t197" href="#t197">197</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t198" href="#t198">198</a></span><span class="t">        <span class="com"># save csv data</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t199" href="#t199">199</a></span><span class="t">        <span class="nam">result_df</span><span class="op">.</span><span class="nam">to_csv</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">"out"</span><span class="op">]</span><span class="op">[</span><span class="str">"output_csv_path"</span><span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t200" href="#t200">200</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t201" href="#t201">201</a></span><span class="t">        <span class="com"># create heatmap</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t202" href="#t202">202</a></span><span class="t">        <span class="nam">cmap</span> <span class="op">=</span> <span class="nam">plt</span><span class="op">.</span><span class="nam">get_cmap</span><span class="op">(</span><span class="str">"bwr"</span><span class="op">)</span><span class="op">.</span><span class="nam">copy</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t203" href="#t203">203</a></span><span class="t">        <span class="nam">bounds</span> <span class="op">=</span> <span class="op">[</span><span class="op">-</span><span class="num">1</span><span class="op">,</span> <span class="op">-</span><span class="num">.8</span><span class="op">,</span> <span class="op">-</span><span class="num">.6</span><span class="op">,</span> <span class="op">-</span><span class="num">.4</span><span class="op">,</span> <span class="op">-</span><span class="num">.2</span><span class="op">,</span> <span class="num">.2</span><span class="op">,</span> <span class="num">.4</span><span class="op">,</span> <span class="num">.6</span><span class="op">,</span> <span class="num">.8</span><span class="op">,</span> <span class="num">1</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t204" href="#t204">204</a></span><span class="t">        <span class="nam">num</span> <span class="op">=</span> <span class="nam">cmap</span><span class="op">.</span><span class="nam">N</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t205" href="#t205">205</a></span><span class="t">        <span class="nam">norm</span> <span class="op">=</span> <span class="nam">mpl</span><span class="op">.</span><span class="nam">colors</span><span class="op">.</span><span class="nam">BoundaryNorm</span><span class="op">(</span><span class="nam">bounds</span><span class="op">,</span> <span class="nam">num</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t206" href="#t206">206</a></span><span class="t">        <span class="nam">cmap</span><span class="op">.</span><span class="nam">set_bad</span><span class="op">(</span><span class="nam">color</span><span class="op">=</span><span class="str">"gainsboro"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t207" href="#t207">207</a></span><span class="t">        <span class="nam">fig</span><span class="op">,</span> <span class="nam">ax</span> <span class="op">=</span> <span class="nam">plt</span><span class="op">.</span><span class="nam">subplots</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t208" href="#t208">208</a></span><span class="t">            <span class="num">1</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t209" href="#t209">209</a></span><span class="t">            <span class="nam">dpi</span><span class="op">=</span><span class="num">300</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t210" href="#t210">210</a></span><span class="t">            <span class="nam">figsize</span><span class="op">=</span><span class="op">(</span><span class="num">7.5</span><span class="op">,</span> <span class="num">5</span><span class="op">)</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t211" href="#t211">211</a></span><span class="t">            <span class="nam">tight_layout</span><span class="op">=</span><span class="key">True</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t212" href="#t212">212</a></span><span class="t">        <span class="nam">im</span> <span class="op">=</span> <span class="nam">ax</span><span class="op">.</span><span class="nam">imshow</span><span class="op">(</span><span class="nam">result_df</span><span class="op">,</span> <span class="nam">cmap</span><span class="op">=</span><span class="nam">cmap</span><span class="op">,</span> <span class="nam">norm</span><span class="op">=</span><span class="nam">norm</span><span class="op">,</span> <span class="nam">aspect</span><span class="op">=</span><span class="str">'auto'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t213" href="#t213">213</a></span><span class="t">        <span class="nam">plt</span><span class="op">.</span><span class="nam">colorbar</span><span class="op">(</span><span class="nam">im</span><span class="op">,</span> <span class="nam">ticks</span><span class="op">=</span><span class="op">[</span><span class="op">-</span><span class="num">1</span><span class="op">,</span> <span class="op">-</span><span class="num">.8</span><span class="op">,</span> <span class="op">-</span><span class="num">.6</span><span class="op">,</span> <span class="op">-</span><span class="num">.4</span><span class="op">,</span> <span class="op">-</span><span class="num">.2</span><span class="op">,</span> <span class="num">.2</span><span class="op">,</span> <span class="num">.4</span><span class="op">,</span> <span class="num">.6</span><span class="op">,</span> <span class="num">.8</span><span class="op">,</span> <span class="num">1</span><span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t214" href="#t214">214</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t215" href="#t215">215</a></span><span class="t">        <span class="com"># axes</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t216" href="#t216">216</a></span><span class="t">        <span class="nam">xlocs</span> <span class="op">=</span> <span class="nam">np</span><span class="op">.</span><span class="nam">arange</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">result_df</span><span class="op">.</span><span class="nam">columns</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t217" href="#t217">217</a></span><span class="t">        <span class="nam">_</span> <span class="op">=</span> <span class="nam">ax</span><span class="op">.</span><span class="nam">set_xticks</span><span class="op">(</span><span class="nam">xlocs</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t218" href="#t218">218</a></span><span class="t">        <span class="nam">_</span> <span class="op">=</span> <span class="nam">ax</span><span class="op">.</span><span class="nam">set_xticklabels</span><span class="op">(</span><span class="nam">result_df</span><span class="op">.</span><span class="nam">columns</span><span class="op">.</span><span class="nam">to_list</span><span class="op">(</span><span class="op">)</span><span class="op">,</span> <span class="nam">rotation</span><span class="op">=</span><span class="num">90</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t219" href="#t219">219</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t220" href="#t220">220</a></span><span class="t">        <span class="nam">ylocs</span> <span class="op">=</span> <span class="nam">np</span><span class="op">.</span><span class="nam">arange</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">result_df</span><span class="op">.</span><span class="nam">index</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t221" href="#t221">221</a></span><span class="t">        <span class="nam">_</span> <span class="op">=</span> <span class="nam">ax</span><span class="op">.</span><span class="nam">set_yticks</span><span class="op">(</span><span class="nam">ylocs</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t222" href="#t222">222</a></span><span class="t">        <span class="nam">_</span> <span class="op">=</span> <span class="nam">ax</span><span class="op">.</span><span class="nam">set_yticklabels</span><span class="op">(</span><span class="nam">result_df</span><span class="op">.</span><span class="nam">index</span><span class="op">.</span><span class="nam">to_list</span><span class="op">(</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t223" href="#t223">223</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t224" href="#t224">224</a></span><span class="t">        <span class="nam">ax</span><span class="op">.</span><span class="nam">set_title</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t225" href="#t225">225</a></span><span class="t">            <span class="str">"Correlation for neighboring basepairs "</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t226" href="#t226">226</a></span><span class="t">            <span class="str">"and pairs of helical parameters"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t227" href="#t227">227</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t228" href="#t228">228</a></span><span class="t">        <span class="nam">fig</span><span class="op">.</span><span class="nam">tight_layout</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t229" href="#t229">229</a></span><span class="t">        <span class="nam">fig</span><span class="op">.</span><span class="nam">savefig</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t230" href="#t230">230</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'out'</span><span class="op">]</span><span class="op">[</span><span class="str">'output_jpg_path'</span><span class="op">]</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t231" href="#t231">231</a></span><span class="t">            <span class="nam">format</span><span class="op">=</span><span class="str">"jpg"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t232" href="#t232">232</a></span><span class="t">        <span class="nam">plt</span><span class="op">.</span><span class="nam">close</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t233" href="#t233">233</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t234" href="#t234">234</a></span><span class="t">        <span class="com"># Remove temporary file(s)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t235" href="#t235">235</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_files</span><span class="op">.</span><span class="nam">extend</span><span class="op">(</span><span class="op">[</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t236" href="#t236">236</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"unique_dir"</span><span class="op">)</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t237" href="#t237">237</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t238" href="#t238">238</a></span><span class="t">        <span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t239" href="#t239">239</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">remove_tmp_files</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t240" href="#t240">240</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t241" href="#t241">241</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_arguments</span><span class="op">(</span><span class="nam">output_files_created</span><span class="op">=</span><span class="key">True</span><span class="op">,</span> <span class="nam">raise_exception</span><span class="op">=</span><span class="key">False</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t242" href="#t242">242</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t243" href="#t243">243</a></span><span class="t">        <span class="key">return</span> <span class="num">0</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t244" href="#t244">244</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t245" href="#t245">245</a></span><span class="t">    <span class="op">@</span><span class="nam">staticmethod</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t246" href="#t246">246</a></span><span class="t">    <span class="key">def</span> <span class="nam">circular</span><span class="op">(</span><span class="nam">x1</span><span class="op">,</span> <span class="nam">x2</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t247" href="#t247">247</a></span><span class="t">        <span class="nam">x1</span> <span class="op">=</span> <span class="nam">x1</span> <span class="op">*</span> <span class="nam">np</span><span class="op">.</span><span class="nam">pi</span> <span class="op">/</span> <span class="num">180</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t248" href="#t248">248</a></span><span class="t">        <span class="nam">x2</span> <span class="op">=</span> <span class="nam">x2</span> <span class="op">*</span> <span class="nam">np</span><span class="op">.</span><span class="nam">pi</span> <span class="op">/</span> <span class="num">180</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t249" href="#t249">249</a></span><span class="t">        <span class="nam">diff_1</span> <span class="op">=</span> <span class="nam">np</span><span class="op">.</span><span class="nam">sin</span><span class="op">(</span><span class="nam">x1</span> <span class="op">-</span> <span class="nam">x1</span><span class="op">.</span><span class="nam">mean</span><span class="op">(</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t250" href="#t250">250</a></span><span class="t">        <span class="nam">diff_2</span> <span class="op">=</span> <span class="nam">np</span><span class="op">.</span><span class="nam">sin</span><span class="op">(</span><span class="nam">x2</span> <span class="op">-</span> <span class="nam">x2</span><span class="op">.</span><span class="nam">mean</span><span class="op">(</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t251" href="#t251">251</a></span><span class="t">        <span class="nam">num</span> <span class="op">=</span> <span class="op">(</span><span class="nam">diff_1</span> <span class="op">*</span> <span class="nam">diff_2</span><span class="op">)</span><span class="op">.</span><span class="nam">sum</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t252" href="#t252">252</a></span><span class="t">        <span class="nam">den</span> <span class="op">=</span> <span class="nam">np</span><span class="op">.</span><span class="nam">sqrt</span><span class="op">(</span><span class="op">(</span><span class="nam">diff_1</span> <span class="op">**</span> <span class="num">2</span><span class="op">)</span><span class="op">.</span><span class="nam">sum</span><span class="op">(</span><span class="op">)</span> <span class="op">*</span> <span class="op">(</span><span class="nam">diff_2</span> <span class="op">**</span> <span class="num">2</span><span class="op">)</span><span class="op">.</span><span class="nam">sum</span><span class="op">(</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t253" href="#t253">253</a></span><span class="t">        <span class="key">return</span> <span class="nam">num</span> <span class="op">/</span> <span class="nam">den</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t254" href="#t254">254</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t255" href="#t255">255</a></span><span class="t">    <span class="op">@</span><span class="nam">staticmethod</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t256" href="#t256">256</a></span><span class="t">    <span class="key">def</span> <span class="nam">circlineal</span><span class="op">(</span><span class="nam">x1</span><span class="op">,</span> <span class="nam">x2</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t257" href="#t257">257</a></span><span class="t">        <span class="nam">x2</span> <span class="op">=</span> <span class="nam">x2</span> <span class="op">*</span> <span class="nam">np</span><span class="op">.</span><span class="nam">pi</span> <span class="op">/</span> <span class="num">180</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t258" href="#t258">258</a></span><span class="t">        <span class="nam">rc</span> <span class="op">=</span> <span class="nam">np</span><span class="op">.</span><span class="nam">corrcoef</span><span class="op">(</span><span class="nam">x1</span><span class="op">,</span> <span class="nam">np</span><span class="op">.</span><span class="nam">cos</span><span class="op">(</span><span class="nam">x2</span><span class="op">)</span><span class="op">)</span><span class="op">[</span><span class="num">1</span><span class="op">,</span> <span class="num">0</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t259" href="#t259">259</a></span><span class="t">        <span class="nam">rs</span> <span class="op">=</span> <span class="nam">np</span><span class="op">.</span><span class="nam">corrcoef</span><span class="op">(</span><span class="nam">x1</span><span class="op">,</span> <span class="nam">np</span><span class="op">.</span><span class="nam">sin</span><span class="op">(</span><span class="nam">x2</span><span class="op">)</span><span class="op">)</span><span class="op">[</span><span class="num">1</span><span class="op">,</span> <span class="num">0</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t260" href="#t260">260</a></span><span class="t">        <span class="nam">rcs</span> <span class="op">=</span> <span class="nam">np</span><span class="op">.</span><span class="nam">corrcoef</span><span class="op">(</span><span class="nam">np</span><span class="op">.</span><span class="nam">sin</span><span class="op">(</span><span class="nam">x2</span><span class="op">)</span><span class="op">,</span> <span class="nam">np</span><span class="op">.</span><span class="nam">cos</span><span class="op">(</span><span class="nam">x2</span><span class="op">)</span><span class="op">)</span><span class="op">[</span><span class="num">1</span><span class="op">,</span> <span class="num">0</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t261" href="#t261">261</a></span><span class="t">        <span class="nam">num</span> <span class="op">=</span> <span class="op">(</span><span class="nam">rc</span> <span class="op">**</span> <span class="num">2</span><span class="op">)</span> <span class="op">+</span> <span class="op">(</span><span class="nam">rs</span> <span class="op">**</span> <span class="num">2</span><span class="op">)</span> <span class="op">-</span> <span class="num">2</span> <span class="op">*</span> <span class="nam">rc</span> <span class="op">*</span> <span class="nam">rs</span> <span class="op">*</span> <span class="nam">rcs</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t262" href="#t262">262</a></span><span class="t">        <span class="nam">den</span> <span class="op">=</span> <span class="num">1</span> <span class="op">-</span> <span class="op">(</span><span class="nam">rcs</span> <span class="op">**</span> <span class="num">2</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t263" href="#t263">263</a></span><span class="t">        <span class="nam">correlation</span> <span class="op">=</span> <span class="nam">np</span><span class="op">.</span><span class="nam">sqrt</span><span class="op">(</span><span class="nam">num</span> <span class="op">/</span> <span class="nam">den</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t264" href="#t264">264</a></span><span class="t">        <span class="key">if</span> <span class="nam">np</span><span class="op">.</span><span class="nam">corrcoef</span><span class="op">(</span><span class="nam">x1</span><span class="op">,</span> <span class="nam">x2</span><span class="op">)</span><span class="op">[</span><span class="num">1</span><span class="op">,</span> <span class="num">0</span><span class="op">]</span> <span class="op">&lt;</span> <span class="num">0</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t265" href="#t265">265</a></span><span class="t">            <span class="nam">correlation</span> <span class="op">*=</span> <span class="op">-</span><span class="num">1</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t266" href="#t266">266</a></span><span class="t">        <span class="key">return</span> <span class="nam">correlation</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t267" href="#t267">267</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t209" href="#t209">209</a></span><span class="t">            <span class="num">1</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t210" href="#t210">210</a></span><span class="t">            <span class="nam">dpi</span><span class="op">=</span><span class="num">300</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t211" href="#t211">211</a></span><span class="t">            <span class="nam">figsize</span><span class="op">=</span><span class="op">(</span><span class="num">7.5</span><span class="op">,</span> <span class="num">5</span><span class="op">)</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t212" href="#t212">212</a></span><span class="t">            <span class="nam">tight_layout</span><span class="op">=</span><span class="key">True</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t213" href="#t213">213</a></span><span class="t">        <span class="nam">im</span> <span class="op">=</span> <span class="nam">ax</span><span class="op">.</span><span class="nam">imshow</span><span class="op">(</span><span class="nam">result_df</span><span class="op">,</span> <span class="nam">cmap</span><span class="op">=</span><span class="nam">cmap</span><span class="op">,</span> <span class="nam">norm</span><span class="op">=</span><span class="nam">norm</span><span class="op">,</span> <span class="nam">aspect</span><span class="op">=</span><span class="str">'auto'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t214" href="#t214">214</a></span><span class="t">        <span class="nam">plt</span><span class="op">.</span><span class="nam">colorbar</span><span class="op">(</span><span class="nam">im</span><span class="op">,</span> <span class="nam">ticks</span><span class="op">=</span><span class="op">[</span><span class="op">-</span><span class="num">1</span><span class="op">,</span> <span class="op">-</span><span class="num">.8</span><span class="op">,</span> <span class="op">-</span><span class="num">.6</span><span class="op">,</span> <span class="op">-</span><span class="num">.4</span><span class="op">,</span> <span class="op">-</span><span class="num">.2</span><span class="op">,</span> <span class="num">.2</span><span class="op">,</span> <span class="num">.4</span><span class="op">,</span> <span class="num">.6</span><span class="op">,</span> <span class="num">.8</span><span class="op">,</span> <span class="num">1</span><span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t215" href="#t215">215</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t216" href="#t216">216</a></span><span class="t">        <span class="com"># axes</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t217" href="#t217">217</a></span><span class="t">        <span class="nam">xlocs</span> <span class="op">=</span> <span class="nam">np</span><span class="op">.</span><span class="nam">arange</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">result_df</span><span class="op">.</span><span class="nam">columns</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t218" href="#t218">218</a></span><span class="t">        <span class="nam">_</span> <span class="op">=</span> <span class="nam">ax</span><span class="op">.</span><span class="nam">set_xticks</span><span class="op">(</span><span class="nam">xlocs</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t219" href="#t219">219</a></span><span class="t">        <span class="nam">_</span> <span class="op">=</span> <span class="nam">ax</span><span class="op">.</span><span class="nam">set_xticklabels</span><span class="op">(</span><span class="nam">result_df</span><span class="op">.</span><span class="nam">columns</span><span class="op">.</span><span class="nam">to_list</span><span class="op">(</span><span class="op">)</span><span class="op">,</span> <span class="nam">rotation</span><span class="op">=</span><span class="num">90</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t220" href="#t220">220</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t221" href="#t221">221</a></span><span class="t">        <span class="nam">ylocs</span> <span class="op">=</span> <span class="nam">np</span><span class="op">.</span><span class="nam">arange</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">result_df</span><span class="op">.</span><span class="nam">index</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t222" href="#t222">222</a></span><span class="t">        <span class="nam">_</span> <span class="op">=</span> <span class="nam">ax</span><span class="op">.</span><span class="nam">set_yticks</span><span class="op">(</span><span class="nam">ylocs</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t223" href="#t223">223</a></span><span class="t">        <span class="nam">_</span> <span class="op">=</span> <span class="nam">ax</span><span class="op">.</span><span class="nam">set_yticklabels</span><span class="op">(</span><span class="nam">result_df</span><span class="op">.</span><span class="nam">index</span><span class="op">.</span><span class="nam">to_list</span><span class="op">(</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t224" href="#t224">224</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t225" href="#t225">225</a></span><span class="t">        <span class="nam">ax</span><span class="op">.</span><span class="nam">set_title</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t226" href="#t226">226</a></span><span class="t">            <span class="str">"Correlation for neighboring basepairs "</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t227" href="#t227">227</a></span><span class="t">            <span class="str">"and pairs of helical parameters"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t228" href="#t228">228</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t229" href="#t229">229</a></span><span class="t">        <span class="nam">fig</span><span class="op">.</span><span class="nam">tight_layout</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t230" href="#t230">230</a></span><span class="t">        <span class="nam">fig</span><span class="op">.</span><span class="nam">savefig</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t231" href="#t231">231</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'out'</span><span class="op">]</span><span class="op">[</span><span class="str">'output_jpg_path'</span><span class="op">]</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t232" href="#t232">232</a></span><span class="t">            <span class="nam">format</span><span class="op">=</span><span class="str">"jpg"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t233" href="#t233">233</a></span><span class="t">        <span class="nam">plt</span><span class="op">.</span><span class="nam">close</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t234" href="#t234">234</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t235" href="#t235">235</a></span><span class="t">        <span class="com"># Remove temporary file(s)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t236" href="#t236">236</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_files</span><span class="op">.</span><span class="nam">extend</span><span class="op">(</span><span class="op">[</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t237" href="#t237">237</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"unique_dir"</span><span class="op">)</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t238" href="#t238">238</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t239" href="#t239">239</a></span><span class="t">        <span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t240" href="#t240">240</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">remove_tmp_files</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t241" href="#t241">241</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t242" href="#t242">242</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_arguments</span><span class="op">(</span><span class="nam">output_files_created</span><span class="op">=</span><span class="key">True</span><span class="op">,</span> <span class="nam">raise_exception</span><span class="op">=</span><span class="key">False</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t243" href="#t243">243</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t244" href="#t244">244</a></span><span class="t">        <span class="key">return</span> <span class="num">0</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t245" href="#t245">245</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t246" href="#t246">246</a></span><span class="t">    <span class="op">@</span><span class="nam">staticmethod</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t247" href="#t247">247</a></span><span class="t">    <span class="key">def</span> <span class="nam">circular</span><span class="op">(</span><span class="nam">x1</span><span class="op">,</span> <span class="nam">x2</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t248" href="#t248">248</a></span><span class="t">        <span class="nam">x1</span> <span class="op">=</span> <span class="nam">x1</span> <span class="op">*</span> <span class="nam">np</span><span class="op">.</span><span class="nam">pi</span> <span class="op">/</span> <span class="num">180</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t249" href="#t249">249</a></span><span class="t">        <span class="nam">x2</span> <span class="op">=</span> <span class="nam">x2</span> <span class="op">*</span> <span class="nam">np</span><span class="op">.</span><span class="nam">pi</span> <span class="op">/</span> <span class="num">180</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t250" href="#t250">250</a></span><span class="t">        <span class="nam">diff_1</span> <span class="op">=</span> <span class="nam">np</span><span class="op">.</span><span class="nam">sin</span><span class="op">(</span><span class="nam">x1</span> <span class="op">-</span> <span class="nam">x1</span><span class="op">.</span><span class="nam">mean</span><span class="op">(</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t251" href="#t251">251</a></span><span class="t">        <span class="nam">diff_2</span> <span class="op">=</span> <span class="nam">np</span><span class="op">.</span><span class="nam">sin</span><span class="op">(</span><span class="nam">x2</span> <span class="op">-</span> <span class="nam">x2</span><span class="op">.</span><span class="nam">mean</span><span class="op">(</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t252" href="#t252">252</a></span><span class="t">        <span class="nam">num</span> <span class="op">=</span> <span class="op">(</span><span class="nam">diff_1</span> <span class="op">*</span> <span class="nam">diff_2</span><span class="op">)</span><span class="op">.</span><span class="nam">sum</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t253" href="#t253">253</a></span><span class="t">        <span class="nam">den</span> <span class="op">=</span> <span class="nam">np</span><span class="op">.</span><span class="nam">sqrt</span><span class="op">(</span><span class="op">(</span><span class="nam">diff_1</span> <span class="op">**</span> <span class="num">2</span><span class="op">)</span><span class="op">.</span><span class="nam">sum</span><span class="op">(</span><span class="op">)</span> <span class="op">*</span> <span class="op">(</span><span class="nam">diff_2</span> <span class="op">**</span> <span class="num">2</span><span class="op">)</span><span class="op">.</span><span class="nam">sum</span><span class="op">(</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t254" href="#t254">254</a></span><span class="t">        <span class="key">return</span> <span class="nam">num</span> <span class="op">/</span> <span class="nam">den</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t255" href="#t255">255</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t256" href="#t256">256</a></span><span class="t">    <span class="op">@</span><span class="nam">staticmethod</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t257" href="#t257">257</a></span><span class="t">    <span class="key">def</span> <span class="nam">circlineal</span><span class="op">(</span><span class="nam">x1</span><span class="op">,</span> <span class="nam">x2</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t258" href="#t258">258</a></span><span class="t">        <span class="nam">x2</span> <span class="op">=</span> <span class="nam">x2</span> <span class="op">*</span> <span class="nam">np</span><span class="op">.</span><span class="nam">pi</span> <span class="op">/</span> <span class="num">180</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t259" href="#t259">259</a></span><span class="t">        <span class="nam">rc</span> <span class="op">=</span> <span class="nam">np</span><span class="op">.</span><span class="nam">corrcoef</span><span class="op">(</span><span class="nam">x1</span><span class="op">,</span> <span class="nam">np</span><span class="op">.</span><span class="nam">cos</span><span class="op">(</span><span class="nam">x2</span><span class="op">)</span><span class="op">)</span><span class="op">[</span><span class="num">1</span><span class="op">,</span> <span class="num">0</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t260" href="#t260">260</a></span><span class="t">        <span class="nam">rs</span> <span class="op">=</span> <span class="nam">np</span><span class="op">.</span><span class="nam">corrcoef</span><span class="op">(</span><span class="nam">x1</span><span class="op">,</span> <span class="nam">np</span><span class="op">.</span><span class="nam">sin</span><span class="op">(</span><span class="nam">x2</span><span class="op">)</span><span class="op">)</span><span class="op">[</span><span class="num">1</span><span class="op">,</span> <span class="num">0</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t261" href="#t261">261</a></span><span class="t">        <span class="nam">rcs</span> <span class="op">=</span> <span class="nam">np</span><span class="op">.</span><span class="nam">corrcoef</span><span class="op">(</span><span class="nam">np</span><span class="op">.</span><span class="nam">sin</span><span class="op">(</span><span class="nam">x2</span><span class="op">)</span><span class="op">,</span> <span class="nam">np</span><span class="op">.</span><span class="nam">cos</span><span class="op">(</span><span class="nam">x2</span><span class="op">)</span><span class="op">)</span><span class="op">[</span><span class="num">1</span><span class="op">,</span> <span class="num">0</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t262" href="#t262">262</a></span><span class="t">        <span class="nam">num</span> <span class="op">=</span> <span class="op">(</span><span class="nam">rc</span> <span class="op">**</span> <span class="num">2</span><span class="op">)</span> <span class="op">+</span> <span class="op">(</span><span class="nam">rs</span> <span class="op">**</span> <span class="num">2</span><span class="op">)</span> <span class="op">-</span> <span class="num">2</span> <span class="op">*</span> <span class="nam">rc</span> <span class="op">*</span> <span class="nam">rs</span> <span class="op">*</span> <span class="nam">rcs</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t263" href="#t263">263</a></span><span class="t">        <span class="nam">den</span> <span class="op">=</span> <span class="num">1</span> <span class="op">-</span> <span class="op">(</span><span class="nam">rcs</span> <span class="op">**</span> <span class="num">2</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t264" href="#t264">264</a></span><span class="t">        <span class="nam">correlation</span> <span class="op">=</span> <span class="nam">np</span><span class="op">.</span><span class="nam">sqrt</span><span class="op">(</span><span class="nam">num</span> <span class="op">/</span> <span class="nam">den</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t265" href="#t265">265</a></span><span class="t">        <span class="key">if</span> <span class="nam">np</span><span class="op">.</span><span class="nam">corrcoef</span><span class="op">(</span><span class="nam">x1</span><span class="op">,</span> <span class="nam">x2</span><span class="op">)</span><span class="op">[</span><span class="num">1</span><span class="op">,</span> <span class="num">0</span><span class="op">]</span> <span class="op">&lt;</span> <span class="num">0</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t266" href="#t266">266</a></span><span class="t">            <span class="nam">correlation</span> <span class="op">*=</span> <span class="op">-</span><span class="num">1</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t267" href="#t267">267</a></span><span class="t">        <span class="key">return</span> <span class="nam">correlation</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t268" href="#t268">268</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t269" href="#t269">269</a></span><span class="t"><span class="key">def</span> <span class="nam">intrabpcorr</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t270" href="#t270">270</a></span><span class="t">        <span class="nam">input_filename_shear</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span> <span class="nam">input_filename_stretch</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t271" href="#t271">271</a></span><span class="t">        <span class="nam">input_filename_stagger</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span> <span class="nam">input_filename_buckle</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t272" href="#t272">272</a></span><span class="t">        <span class="nam">input_filename_propel</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span> <span class="nam">input_filename_opening</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t273" href="#t273">273</a></span><span class="t">        <span class="nam">output_csv_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span> <span class="nam">output_jpg_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t274" href="#t274">274</a></span><span class="t">        <span class="nam">properties</span><span class="op">:</span> <span class="nam">dict</span> <span class="op">=</span> <span class="key">None</span><span class="op">,</span> <span class="op">**</span><span class="nam">kwargs</span><span class="op">)</span> <span class="op">-></span> <span class="nam">int</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t275" href="#t275">275</a></span><span class="t">    <span class="str">"""Create :class:`HelParCorrelation &lt;intrabp_correlations.intrabpcorr.IntraBasePairCorrelation>` class and</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t276" href="#t276">276</a></span><span class="t"><span class="str">    execute the :meth:`launch() &lt;intrabp_correlations.intrabpcorr.IntraBasePairCorrelation.launch>` method."""</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t277" href="#t277">277</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t278" href="#t278">278</a></span><span class="t">    <span class="key">return</span> <span class="nam">IntraBasePairCorrelation</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t279" href="#t279">279</a></span><span class="t">        <span class="nam">input_filename_shear</span><span class="op">=</span><span class="nam">input_filename_shear</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t280" href="#t280">280</a></span><span class="t">        <span class="nam">input_filename_stretch</span><span class="op">=</span><span class="nam">input_filename_stretch</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t281" href="#t281">281</a></span><span class="t">        <span class="nam">input_filename_stagger</span><span class="op">=</span><span class="nam">input_filename_stagger</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t282" href="#t282">282</a></span><span class="t">        <span class="nam">input_filename_buckle</span><span class="op">=</span><span class="nam">input_filename_buckle</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t283" href="#t283">283</a></span><span class="t">        <span class="nam">input_filename_propel</span><span class="op">=</span><span class="nam">input_filename_propel</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t284" href="#t284">284</a></span><span class="t">        <span class="nam">input_filename_opening</span><span class="op">=</span><span class="nam">input_filename_opening</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t285" href="#t285">285</a></span><span class="t">        <span class="nam">output_csv_path</span><span class="op">=</span><span class="nam">output_csv_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t286" href="#t286">286</a></span><span class="t">        <span class="nam">output_jpg_path</span><span class="op">=</span><span class="nam">output_jpg_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t287" href="#t287">287</a></span><span class="t">        <span class="nam">properties</span><span class="op">=</span><span class="nam">properties</span><span class="op">,</span> <span class="op">**</span><span class="nam">kwargs</span><span class="op">)</span><span class="op">.</span><span class="nam">launch</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t288" href="#t288">288</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t269" href="#t269">269</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t270" href="#t270">270</a></span><span class="t"><span class="key">def</span> <span class="nam">intrabpcorr</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t271" href="#t271">271</a></span><span class="t">        <span class="nam">input_filename_shear</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span> <span class="nam">input_filename_stretch</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t272" href="#t272">272</a></span><span class="t">        <span class="nam">input_filename_stagger</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span> <span class="nam">input_filename_buckle</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t273" href="#t273">273</a></span><span class="t">        <span class="nam">input_filename_propel</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span> <span class="nam">input_filename_opening</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t274" href="#t274">274</a></span><span class="t">        <span class="nam">output_csv_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span> <span class="nam">output_jpg_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t275" href="#t275">275</a></span><span class="t">        <span class="nam">properties</span><span class="op">:</span> <span class="nam">dict</span> <span class="op">=</span> <span class="key">None</span><span class="op">,</span> <span class="op">**</span><span class="nam">kwargs</span><span class="op">)</span> <span class="op">-></span> <span class="nam">int</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t276" href="#t276">276</a></span><span class="t">    <span class="str">"""Create :class:`HelParCorrelation &lt;intrabp_correlations.intrabpcorr.IntraBasePairCorrelation>` class and</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t277" href="#t277">277</a></span><span class="t"><span class="str">    execute the :meth:`launch() &lt;intrabp_correlations.intrabpcorr.IntraBasePairCorrelation.launch>` method."""</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t278" href="#t278">278</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t279" href="#t279">279</a></span><span class="t">    <span class="key">return</span> <span class="nam">IntraBasePairCorrelation</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t280" href="#t280">280</a></span><span class="t">        <span class="nam">input_filename_shear</span><span class="op">=</span><span class="nam">input_filename_shear</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t281" href="#t281">281</a></span><span class="t">        <span class="nam">input_filename_stretch</span><span class="op">=</span><span class="nam">input_filename_stretch</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t282" href="#t282">282</a></span><span class="t">        <span class="nam">input_filename_stagger</span><span class="op">=</span><span class="nam">input_filename_stagger</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t283" href="#t283">283</a></span><span class="t">        <span class="nam">input_filename_buckle</span><span class="op">=</span><span class="nam">input_filename_buckle</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t284" href="#t284">284</a></span><span class="t">        <span class="nam">input_filename_propel</span><span class="op">=</span><span class="nam">input_filename_propel</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t285" href="#t285">285</a></span><span class="t">        <span class="nam">input_filename_opening</span><span class="op">=</span><span class="nam">input_filename_opening</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t286" href="#t286">286</a></span><span class="t">        <span class="nam">output_csv_path</span><span class="op">=</span><span class="nam">output_csv_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t287" href="#t287">287</a></span><span class="t">        <span class="nam">output_jpg_path</span><span class="op">=</span><span class="nam">output_jpg_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t288" href="#t288">288</a></span><span class="t">        <span class="nam">properties</span><span class="op">=</span><span class="nam">properties</span><span class="op">,</span> <span class="op">**</span><span class="nam">kwargs</span><span class="op">)</span><span class="op">.</span><span class="nam">launch</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t289" href="#t289">289</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t290" href="#t290">290</a></span><span class="t"><span class="key">def</span> <span class="nam">main</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t291" href="#t291">291</a></span><span class="t">    <span class="str">"""Command line execution of this building block. Please check the command line documentation."""</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t292" href="#t292">292</a></span><span class="t">    <span class="nam">parser</span> <span class="op">=</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">ArgumentParser</span><span class="op">(</span><span class="nam">description</span><span class="op">=</span><span class="str">'Load .ser file from Canal output and calculate correlation between base pairs of the corresponding sequence.'</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t293" href="#t293">293</a></span><span class="t">                                     <span class="nam">formatter_class</span><span class="op">=</span><span class="key">lambda</span> <span class="nam">prog</span><span class="op">:</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">RawTextHelpFormatter</span><span class="op">(</span><span class="nam">prog</span><span class="op">,</span> <span class="nam">width</span><span class="op">=</span><span class="num">99999</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t294" href="#t294">294</a></span><span class="t">    <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--config'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">False</span><span class="op">,</span> <span class="nam">help</span><span class="op">=</span><span class="str">'Configuration file'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t295" href="#t295">295</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t296" href="#t296">296</a></span><span class="t">    <span class="nam">required_args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument_group</span><span class="op">(</span><span class="str">'required arguments'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t297" href="#t297">297</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--input_filename_shear'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t298" href="#t298">298</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Path to ser file for helical parameter shear. Accepted formats: ser.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t299" href="#t299">299</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--input_filename_stretch'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t300" href="#t300">300</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Path to ser file for helical parameter stretch. Accepted formats: ser.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t301" href="#t301">301</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--input_filename_stagger'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t302" href="#t302">302</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Path to ser file for helical parameter stagger. Accepted formats: ser.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t303" href="#t303">303</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--input_filename_buckle'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t304" href="#t304">304</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Path to ser file for helical parameter buckle. Accepted formats: ser.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t305" href="#t305">305</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--input_filename_propel'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t306" href="#t306">306</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Path to ser file for helical parameter propel. Accepted formats: ser.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t307" href="#t307">307</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--input_filename_opening'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t308" href="#t308">308</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Path to ser file for helical parameter opening. Accepted formats: ser.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t309" href="#t309">309</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--output_csv_path'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t310" href="#t310">310</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Path to output file. Accepted formats: csv.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t311" href="#t311">311</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--output_jpg_path'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t312" href="#t312">312</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Path to output plot. Accepted formats: jpg.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t313" href="#t313">313</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t314" href="#t314">314</a></span><span class="t">    <span class="nam">args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">parse_args</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t315" href="#t315">315</a></span><span class="t">    <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="op">=</span> <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="key">or</span> <span class="str">"{}"</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t316" href="#t316">316</a></span><span class="t">    <span class="nam">properties</span> <span class="op">=</span> <span class="nam">settings</span><span class="op">.</span><span class="nam">ConfReader</span><span class="op">(</span><span class="nam">config</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">config</span><span class="op">)</span><span class="op">.</span><span class="nam">get_prop_dic</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t317" href="#t317">317</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t318" href="#t318">318</a></span><span class="t">    <span class="nam">intrabpcorr</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t319" href="#t319">319</a></span><span class="t">        <span class="nam">input_filename_shear</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_filename_shear</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t320" href="#t320">320</a></span><span class="t">        <span class="nam">input_filename_stretch</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_filename_stretch</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t321" href="#t321">321</a></span><span class="t">        <span class="nam">input_filename_stagger</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_filename_stagger</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t322" href="#t322">322</a></span><span class="t">        <span class="nam">input_filename_buckle</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_filename_buckle</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t323" href="#t323">323</a></span><span class="t">        <span class="nam">input_filename_propel</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_filename_propel</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t324" href="#t324">324</a></span><span class="t">        <span class="nam">input_filename_opening</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_filename_opening</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t325" href="#t325">325</a></span><span class="t">        <span class="nam">output_csv_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">output_csv_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t326" href="#t326">326</a></span><span class="t">        <span class="nam">output_jpg_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">output_jpg_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t327" href="#t327">327</a></span><span class="t">        <span class="nam">properties</span><span class="op">=</span><span class="nam">properties</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t328" href="#t328">328</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t290" href="#t290">290</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t291" href="#t291">291</a></span><span class="t"><span class="key">def</span> <span class="nam">main</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t292" href="#t292">292</a></span><span class="t">    <span class="str">"""Command line execution of this building block. Please check the command line documentation."""</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t293" href="#t293">293</a></span><span class="t">    <span class="nam">parser</span> <span class="op">=</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">ArgumentParser</span><span class="op">(</span><span class="nam">description</span><span class="op">=</span><span class="str">'Load .ser file from Canal output and calculate correlation between base pairs of the corresponding sequence.'</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t294" href="#t294">294</a></span><span class="t">                                     <span class="nam">formatter_class</span><span class="op">=</span><span class="key">lambda</span> <span class="nam">prog</span><span class="op">:</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">RawTextHelpFormatter</span><span class="op">(</span><span class="nam">prog</span><span class="op">,</span> <span class="nam">width</span><span class="op">=</span><span class="num">99999</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t295" href="#t295">295</a></span><span class="t">    <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--config'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">False</span><span class="op">,</span> <span class="nam">help</span><span class="op">=</span><span class="str">'Configuration file'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t296" href="#t296">296</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t297" href="#t297">297</a></span><span class="t">    <span class="nam">required_args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument_group</span><span class="op">(</span><span class="str">'required arguments'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t298" href="#t298">298</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--input_filename_shear'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t299" href="#t299">299</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Path to ser file for helical parameter shear. Accepted formats: ser.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t300" href="#t300">300</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--input_filename_stretch'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t301" href="#t301">301</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Path to ser file for helical parameter stretch. Accepted formats: ser.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t302" href="#t302">302</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--input_filename_stagger'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t303" href="#t303">303</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Path to ser file for helical parameter stagger. Accepted formats: ser.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t304" href="#t304">304</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--input_filename_buckle'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t305" href="#t305">305</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Path to ser file for helical parameter buckle. Accepted formats: ser.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t306" href="#t306">306</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--input_filename_propel'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t307" href="#t307">307</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Path to ser file for helical parameter propel. Accepted formats: ser.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t308" href="#t308">308</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--input_filename_opening'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t309" href="#t309">309</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Path to ser file for helical parameter opening. Accepted formats: ser.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t310" href="#t310">310</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--output_csv_path'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t311" href="#t311">311</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Path to output file. Accepted formats: csv.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t312" href="#t312">312</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--output_jpg_path'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t313" href="#t313">313</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Path to output plot. Accepted formats: jpg.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t314" href="#t314">314</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t315" href="#t315">315</a></span><span class="t">    <span class="nam">args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">parse_args</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t316" href="#t316">316</a></span><span class="t">    <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="op">=</span> <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="key">or</span> <span class="str">"{}"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t317" href="#t317">317</a></span><span class="t">    <span class="nam">properties</span> <span class="op">=</span> <span class="nam">settings</span><span class="op">.</span><span class="nam">ConfReader</span><span class="op">(</span><span class="nam">config</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">config</span><span class="op">)</span><span class="op">.</span><span class="nam">get_prop_dic</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t318" href="#t318">318</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t319" href="#t319">319</a></span><span class="t">    <span class="nam">intrabpcorr</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t320" href="#t320">320</a></span><span class="t">        <span class="nam">input_filename_shear</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_filename_shear</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t321" href="#t321">321</a></span><span class="t">        <span class="nam">input_filename_stretch</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_filename_stretch</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t322" href="#t322">322</a></span><span class="t">        <span class="nam">input_filename_stagger</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_filename_stagger</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t323" href="#t323">323</a></span><span class="t">        <span class="nam">input_filename_buckle</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_filename_buckle</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t324" href="#t324">324</a></span><span class="t">        <span class="nam">input_filename_propel</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_filename_propel</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t325" href="#t325">325</a></span><span class="t">        <span class="nam">input_filename_opening</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_filename_opening</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t326" href="#t326">326</a></span><span class="t">        <span class="nam">output_csv_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">output_csv_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t327" href="#t327">327</a></span><span class="t">        <span class="nam">output_jpg_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">output_jpg_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t328" href="#t328">328</a></span><span class="t">        <span class="nam">properties</span><span class="op">=</span><span class="nam">properties</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t329" href="#t329">329</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t330" href="#t330">330</a></span><span class="t"><span class="key">if</span> <span class="nam">__name__</span> <span class="op">==</span> <span class="str">'__main__'</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t331" href="#t331">331</a></span><span class="t">    <span class="nam">main</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t330" href="#t330">330</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t331" href="#t331">331</a></span><span class="t"><span class="key">if</span> <span class="nam">__name__</span> <span class="op">==</span> <span class="str">'__main__'</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t332" href="#t332">332</a></span><span class="t">    <span class="nam">main</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
 </main>
 <footer>
     <div class="content">
@@ -420,7 +421,7 @@ <h2>
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+            created at 2024-05-24 09:29 +0000
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+            created at 2024-05-24 09:29 +0000
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@@ -100,314 +100,315 @@ <h2>
     <p class="pln"><span class="n"><a id="t18" href="#t18">18</a></span><span class="t">    <span class="str">"""</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t19" href="#t19">19</a></span><span class="t"><span class="str">    | biobb_dna IntraHelParCorrelation</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t20" href="#t20">20</a></span><span class="t"><span class="str">    | Calculate correlation between helical parameters for a single intra-base pair.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t21" href="#t21">21</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t22" href="#t22">22</a></span><span class="t"><span class="str">    Args:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t23" href="#t23">23</a></span><span class="t"><span class="str">        input_filename_shear (str): Path to .csv file with data for helical parameter 'shear'. File type: input. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/correlation/series_shear_A.csv>`_. Accepted formats: csv (edam:format_3752).</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t24" href="#t24">24</a></span><span class="t"><span class="str">        input_filename_stretch (str): Path to .csv file with data for helical parameter 'stretch'. File type: input. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/correlation/series_stretch_A.csv>`_. Accepted formats: csv (edam:format_3752).</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t25" href="#t25">25</a></span><span class="t"><span class="str">        input_filename_stagger (str): Path to .csv file with data for helical parameter 'stagger'. File type: input. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/correlation/series_stagger_A.csv>`_. Accepted formats: csv (edam:format_3752).</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t26" href="#t26">26</a></span><span class="t"><span class="str">        input_filename_buckle (str): Path to .csv file with data for helical parameter 'buckle'. File type: input. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/correlation/series_buckle_A.csv>`_. Accepted formats: csv (edam:format_3752).</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t27" href="#t27">27</a></span><span class="t"><span class="str">        input_filename_propel (str): Path to .csv file with data for helical parameter 'propeller'. File type: input. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/correlation/series_propel_A.csv>`_. Accepted formats: csv (edam:format_3752).</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t28" href="#t28">28</a></span><span class="t"><span class="str">        input_filename_opening (str): Path to .csv file with data for helical parameter 'opening'. File type: input. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/correlation/series_opening_A.csv>`_. Accepted formats: csv (edam:format_3752).</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t29" href="#t29">29</a></span><span class="t"><span class="str">        output_csv_path (str): Path to directory where output is saved. File type: output. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/reference/correlation/intra_hpcorr_ref.csv>`_. Accepted formats: csv (edam:format_3752).</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t30" href="#t30">30</a></span><span class="t"><span class="str">        output_jpg_path (str): Path to .jpg file where output is saved. File type: output. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/reference/correlation/intra_hpcorr_ref.jpg>`_. Accepted formats: jpg (edam:format_3579).</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t31" href="#t31">31</a></span><span class="t"><span class="str">        properties (dict):</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t32" href="#t32">32</a></span><span class="t"><span class="str">            * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t33" href="#t33">33</a></span><span class="t"><span class="str">            * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t34" href="#t34">34</a></span><span class="t"><span class="str">            * **base** (*str*) - (None) Name of base analyzed.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t35" href="#t35">35</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t36" href="#t36">36</a></span><span class="t"><span class="str">    Examples:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t37" href="#t37">37</a></span><span class="t"><span class="str">        This is a use example of how to use the building block from Python::</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t38" href="#t38">38</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t39" href="#t39">39</a></span><span class="t"><span class="str">            from biobb_dna.intrabp_correlations.intrahpcorr import intrahpcorr</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t40" href="#t40">40</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t41" href="#t41">41</a></span><span class="t"><span class="str">            prop = {</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t42" href="#t42">42</a></span><span class="t"><span class="str">                'base': 'A',</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t43" href="#t43">43</a></span><span class="t"><span class="str">            }</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t44" href="#t44">44</a></span><span class="t"><span class="str">            intrahpcorr(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t45" href="#t45">45</a></span><span class="t"><span class="str">                input_filename_shear='path/to/shear.csv',</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t46" href="#t46">46</a></span><span class="t"><span class="str">                input_filename_stretch='path/to/stretch.csv',</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t47" href="#t47">47</a></span><span class="t"><span class="str">                input_filename_stagger='path/to/stagger.csv',</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t48" href="#t48">48</a></span><span class="t"><span class="str">                input_filename_buckle='path/to/buckle.csv',</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t49" href="#t49">49</a></span><span class="t"><span class="str">                input_filename_propel='path/to/propel.csv',</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t50" href="#t50">50</a></span><span class="t"><span class="str">                input_filename_opening='path/to/opening.csv',</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t51" href="#t51">51</a></span><span class="t"><span class="str">                output_csv_path='path/to/output/file.csv',</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t52" href="#t52">52</a></span><span class="t"><span class="str">                output_jpg_path='path/to/output/file.jpg',</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t53" href="#t53">53</a></span><span class="t"><span class="str">                properties=prop)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t54" href="#t54">54</a></span><span class="t"><span class="str">    Info:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t55" href="#t55">55</a></span><span class="t"><span class="str">        * wrapped_software:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t56" href="#t56">56</a></span><span class="t"><span class="str">            * name: In house</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t57" href="#t57">57</a></span><span class="t"><span class="str">            * license: Apache-2.0</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t58" href="#t58">58</a></span><span class="t"><span class="str">        * ontology:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t59" href="#t59">59</a></span><span class="t"><span class="str">            * name: EDAM</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t60" href="#t60">60</a></span><span class="t"><span class="str">            * schema: http://edamontology.org/EDAM.owl</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t61" href="#t61">61</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t62" href="#t62">62</a></span><span class="t"><span class="str">    """</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t63" href="#t63">63</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t64" href="#t64">64</a></span><span class="t">    <span class="key">def</span> <span class="nam">__init__</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t65" href="#t65">65</a></span><span class="t">            <span class="nam">self</span><span class="op">,</span> <span class="nam">input_filename_shear</span><span class="op">,</span> <span class="nam">input_filename_stretch</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t66" href="#t66">66</a></span><span class="t">            <span class="nam">input_filename_stagger</span><span class="op">,</span> <span class="nam">input_filename_buckle</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t67" href="#t67">67</a></span><span class="t">            <span class="nam">input_filename_propel</span><span class="op">,</span> <span class="nam">input_filename_opening</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t68" href="#t68">68</a></span><span class="t">            <span class="nam">output_csv_path</span><span class="op">,</span> <span class="nam">output_jpg_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t69" href="#t69">69</a></span><span class="t">            <span class="nam">properties</span><span class="op">=</span><span class="key">None</span><span class="op">,</span> <span class="op">**</span><span class="nam">kwargs</span><span class="op">)</span> <span class="op">-></span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t70" href="#t70">70</a></span><span class="t">        <span class="nam">properties</span> <span class="op">=</span> <span class="nam">properties</span> <span class="key">or</span> <span class="op">{</span><span class="op">}</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t71" href="#t71">71</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t72" href="#t72">72</a></span><span class="t">        <span class="com"># Call parent class constructor</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t73" href="#t73">73</a></span><span class="t">        <span class="nam">super</span><span class="op">(</span><span class="op">)</span><span class="op">.</span><span class="nam">__init__</span><span class="op">(</span><span class="nam">properties</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t74" href="#t74">74</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">locals_var_dict</span> <span class="op">=</span> <span class="nam">locals</span><span class="op">(</span><span class="op">)</span><span class="op">.</span><span class="nam">copy</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t75" href="#t75">75</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t76" href="#t76">76</a></span><span class="t">        <span class="com"># Input/Output files</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t77" href="#t77">77</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span> <span class="op">=</span> <span class="op">{</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t78" href="#t78">78</a></span><span class="t">            <span class="str">'in'</span><span class="op">:</span> <span class="op">{</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t79" href="#t79">79</a></span><span class="t">                <span class="str">'input_filename_shear'</span><span class="op">:</span> <span class="nam">input_filename_shear</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t80" href="#t80">80</a></span><span class="t">                <span class="str">'input_filename_stretch'</span><span class="op">:</span> <span class="nam">input_filename_stretch</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t81" href="#t81">81</a></span><span class="t">                <span class="str">'input_filename_stagger'</span><span class="op">:</span> <span class="nam">input_filename_stagger</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t82" href="#t82">82</a></span><span class="t">                <span class="str">'input_filename_buckle'</span><span class="op">:</span> <span class="nam">input_filename_buckle</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t83" href="#t83">83</a></span><span class="t">                <span class="str">'input_filename_propel'</span><span class="op">:</span> <span class="nam">input_filename_propel</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t84" href="#t84">84</a></span><span class="t">                <span class="str">'input_filename_opening'</span><span class="op">:</span> <span class="nam">input_filename_opening</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t85" href="#t85">85</a></span><span class="t">            <span class="op">}</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t86" href="#t86">86</a></span><span class="t">            <span class="str">'out'</span><span class="op">:</span> <span class="op">{</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t87" href="#t87">87</a></span><span class="t">                <span class="str">'output_csv_path'</span><span class="op">:</span> <span class="nam">output_csv_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t88" href="#t88">88</a></span><span class="t">                <span class="str">'output_jpg_path'</span><span class="op">:</span> <span class="nam">output_jpg_path</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t89" href="#t89">89</a></span><span class="t">            <span class="op">}</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t90" href="#t90">90</a></span><span class="t">        <span class="op">}</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t91" href="#t91">91</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t92" href="#t92">92</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">properties</span> <span class="op">=</span> <span class="nam">properties</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t93" href="#t93">93</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">base</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"base"</span><span class="op">,</span> <span class="key">None</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t94" href="#t94">94</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t95" href="#t95">95</a></span><span class="t">        <span class="com"># Check the properties</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t96" href="#t96">96</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_properties</span><span class="op">(</span><span class="nam">properties</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t97" href="#t97">97</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_arguments</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t98" href="#t98">98</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t99" href="#t99">99</a></span><span class="t">    <span class="op">@</span><span class="nam">launchlogger</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t100" href="#t100">100</a></span><span class="t">    <span class="key">def</span> <span class="nam">launch</span><span class="op">(</span><span class="nam">self</span><span class="op">)</span> <span class="op">-></span> <span class="nam">int</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t101" href="#t101">101</a></span><span class="t">        <span class="str">"""Execute the :class:`IntraHelParCorrelation &lt;intrabp_correlations.intrahpcorr.IntraHelParCorrelation>` object."""</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t102" href="#t102">102</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t103" href="#t103">103</a></span><span class="t">        <span class="com"># Setup Biobb</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t104" href="#t104">104</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">check_restart</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t105" href="#t105">105</a></span><span class="t">            <span class="key">return</span> <span class="num">0</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t106" href="#t106">106</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">stage_files</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t107" href="#t107">107</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t108" href="#t108">108</a></span><span class="t">        <span class="com"># Creating temporary folder</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t109" href="#t109">109</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span> <span class="op">=</span> <span class="nam">fu</span><span class="op">.</span><span class="nam">create_unique_dir</span><span class="op">(</span><span class="nam">prefix</span><span class="op">=</span><span class="str">"hpcorrelation_"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t110" href="#t110">110</a></span><span class="t">        <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="str">'Creating %s temporary folder'</span> <span class="op">%</span> <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t111" href="#t111">111</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t112" href="#t112">112</a></span><span class="t">        <span class="com"># read input</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t113" href="#t113">113</a></span><span class="t">        <span class="nam">shear</span> <span class="op">=</span> <span class="nam">load_data</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">"in"</span><span class="op">]</span><span class="op">[</span><span class="str">"input_filename_shear"</span><span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t114" href="#t114">114</a></span><span class="t">        <span class="nam">stretch</span> <span class="op">=</span> <span class="nam">load_data</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">"in"</span><span class="op">]</span><span class="op">[</span><span class="str">"input_filename_stretch"</span><span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t115" href="#t115">115</a></span><span class="t">        <span class="nam">stagger</span> <span class="op">=</span> <span class="nam">load_data</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">"in"</span><span class="op">]</span><span class="op">[</span><span class="str">"input_filename_stagger"</span><span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t116" href="#t116">116</a></span><span class="t">        <span class="nam">buckle</span> <span class="op">=</span> <span class="nam">load_data</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">"in"</span><span class="op">]</span><span class="op">[</span><span class="str">"input_filename_buckle"</span><span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t117" href="#t117">117</a></span><span class="t">        <span class="nam">propel</span> <span class="op">=</span> <span class="nam">load_data</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">"in"</span><span class="op">]</span><span class="op">[</span><span class="str">"input_filename_propel"</span><span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t118" href="#t118">118</a></span><span class="t">        <span class="nam">opening</span> <span class="op">=</span> <span class="nam">load_data</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">"in"</span><span class="op">]</span><span class="op">[</span><span class="str">"input_filename_opening"</span><span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t119" href="#t119">119</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t120" href="#t120">120</a></span><span class="t">        <span class="com"># get base</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t121" href="#t121">121</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">base</span> <span class="key">is</span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t122" href="#t122">122</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">base</span> <span class="op">=</span> <span class="nam">shear</span><span class="op">.</span><span class="nam">columns</span><span class="op">[</span><span class="num">0</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t123" href="#t123">123</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t124" href="#t124">124</a></span><span class="t">        <span class="com"># make matrix</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t125" href="#t125">125</a></span><span class="t">        <span class="com"># coordinates = ["shear", "stretch", "stagger", "buckle", "propel", "opening"]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t126" href="#t126">126</a></span><span class="t">        <span class="nam">coordinates</span> <span class="op">=</span> <span class="op">[</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t127" href="#t127">127</a></span><span class="t">            <span class="str">"shear"</span><span class="op">,</span> <span class="str">"stretch"</span><span class="op">,</span> <span class="str">"stagger"</span><span class="op">,</span> <span class="str">"buckle"</span><span class="op">,</span> <span class="str">"propel"</span><span class="op">,</span> <span class="str">"opening"</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t128" href="#t128">128</a></span><span class="t">        <span class="nam">corr_matrix</span> <span class="op">=</span> <span class="nam">pd</span><span class="op">.</span><span class="nam">DataFrame</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t129" href="#t129">129</a></span><span class="t">            <span class="nam">np</span><span class="op">.</span><span class="nam">eye</span><span class="op">(</span><span class="num">6</span><span class="op">,</span> <span class="num">6</span><span class="op">)</span><span class="op">,</span> <span class="nam">index</span><span class="op">=</span><span class="nam">coordinates</span><span class="op">,</span> <span class="nam">columns</span><span class="op">=</span><span class="nam">coordinates</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t130" href="#t130">130</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t131" href="#t131">131</a></span><span class="t">        <span class="com"># shear</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t132" href="#t132">132</a></span><span class="t">        <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"shear"</span><span class="op">]</span><span class="op">[</span><span class="str">"stretch"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">shear</span><span class="op">.</span><span class="nam">corrwith</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t133" href="#t133">133</a></span><span class="t">            <span class="nam">stretch</span><span class="op">,</span> <span class="nam">method</span><span class="op">=</span><span class="str">"pearson"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t134" href="#t134">134</a></span><span class="t">        <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"shear"</span><span class="op">]</span><span class="op">[</span><span class="str">"stagger"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">shear</span><span class="op">.</span><span class="nam">corrwith</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t135" href="#t135">135</a></span><span class="t">            <span class="nam">stagger</span><span class="op">,</span> <span class="nam">method</span><span class="op">=</span><span class="str">"pearson"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t136" href="#t136">136</a></span><span class="t">        <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"shear"</span><span class="op">]</span><span class="op">[</span><span class="str">"buckle"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">shear</span><span class="op">.</span><span class="nam">corrwith</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t137" href="#t137">137</a></span><span class="t">            <span class="nam">buckle</span><span class="op">,</span> <span class="nam">method</span><span class="op">=</span><span class="nam">self</span><span class="op">.</span><span class="nam">circlineal</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t138" href="#t138">138</a></span><span class="t">        <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"shear"</span><span class="op">]</span><span class="op">[</span><span class="str">"propel"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">shear</span><span class="op">.</span><span class="nam">corrwith</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t139" href="#t139">139</a></span><span class="t">            <span class="nam">propel</span><span class="op">,</span> <span class="nam">method</span><span class="op">=</span><span class="nam">self</span><span class="op">.</span><span class="nam">circlineal</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t140" href="#t140">140</a></span><span class="t">        <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"shear"</span><span class="op">]</span><span class="op">[</span><span class="str">"opening"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">shear</span><span class="op">.</span><span class="nam">corrwith</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t141" href="#t141">141</a></span><span class="t">            <span class="nam">opening</span><span class="op">,</span> <span class="nam">method</span><span class="op">=</span><span class="nam">self</span><span class="op">.</span><span class="nam">circlineal</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t142" href="#t142">142</a></span><span class="t">        <span class="com"># symmetric values</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t143" href="#t143">143</a></span><span class="t">        <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"stretch"</span><span class="op">]</span><span class="op">[</span><span class="str">"shear"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"shear"</span><span class="op">]</span><span class="op">[</span><span class="str">"stretch"</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t144" href="#t144">144</a></span><span class="t">        <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"stagger"</span><span class="op">]</span><span class="op">[</span><span class="str">"shear"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"shear"</span><span class="op">]</span><span class="op">[</span><span class="str">"stagger"</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t145" href="#t145">145</a></span><span class="t">        <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"buckle"</span><span class="op">]</span><span class="op">[</span><span class="str">"shear"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"shear"</span><span class="op">]</span><span class="op">[</span><span class="str">"buckle"</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t146" href="#t146">146</a></span><span class="t">        <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"propel"</span><span class="op">]</span><span class="op">[</span><span class="str">"shear"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"shear"</span><span class="op">]</span><span class="op">[</span><span class="str">"propel"</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t147" href="#t147">147</a></span><span class="t">        <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"opening"</span><span class="op">]</span><span class="op">[</span><span class="str">"shear"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"shear"</span><span class="op">]</span><span class="op">[</span><span class="str">"opening"</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t148" href="#t148">148</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t149" href="#t149">149</a></span><span class="t">        <span class="com"># stretch</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t150" href="#t150">150</a></span><span class="t">        <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"stretch"</span><span class="op">]</span><span class="op">[</span><span class="str">"stagger"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">stretch</span><span class="op">.</span><span class="nam">corrwith</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t151" href="#t151">151</a></span><span class="t">            <span class="nam">stagger</span><span class="op">,</span> <span class="nam">method</span><span class="op">=</span><span class="str">"pearson"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t152" href="#t152">152</a></span><span class="t">        <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"stretch"</span><span class="op">]</span><span class="op">[</span><span class="str">"buckle"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">stretch</span><span class="op">.</span><span class="nam">corrwith</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t153" href="#t153">153</a></span><span class="t">            <span class="nam">buckle</span><span class="op">,</span> <span class="nam">method</span><span class="op">=</span><span class="nam">self</span><span class="op">.</span><span class="nam">circlineal</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t154" href="#t154">154</a></span><span class="t">        <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"stretch"</span><span class="op">]</span><span class="op">[</span><span class="str">"propel"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">stretch</span><span class="op">.</span><span class="nam">corrwith</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t155" href="#t155">155</a></span><span class="t">            <span class="nam">propel</span><span class="op">,</span> <span class="nam">method</span><span class="op">=</span><span class="nam">self</span><span class="op">.</span><span class="nam">circlineal</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t156" href="#t156">156</a></span><span class="t">        <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"stretch"</span><span class="op">]</span><span class="op">[</span><span class="str">"opening"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">stretch</span><span class="op">.</span><span class="nam">corrwith</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t157" href="#t157">157</a></span><span class="t">            <span class="nam">opening</span><span class="op">,</span> <span class="nam">method</span><span class="op">=</span><span class="nam">self</span><span class="op">.</span><span class="nam">circlineal</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t158" href="#t158">158</a></span><span class="t">        <span class="com"># symmetric values</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t159" href="#t159">159</a></span><span class="t">        <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"stagger"</span><span class="op">]</span><span class="op">[</span><span class="str">"stretch"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"stretch"</span><span class="op">]</span><span class="op">[</span><span class="str">"stagger"</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t160" href="#t160">160</a></span><span class="t">        <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"buckle"</span><span class="op">]</span><span class="op">[</span><span class="str">"stretch"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"stretch"</span><span class="op">]</span><span class="op">[</span><span class="str">"buckle"</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t161" href="#t161">161</a></span><span class="t">        <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"propel"</span><span class="op">]</span><span class="op">[</span><span class="str">"stretch"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"stretch"</span><span class="op">]</span><span class="op">[</span><span class="str">"propel"</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t162" href="#t162">162</a></span><span class="t">        <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"opening"</span><span class="op">]</span><span class="op">[</span><span class="str">"stretch"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"stretch"</span><span class="op">]</span><span class="op">[</span><span class="str">"opening"</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t163" href="#t163">163</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t164" href="#t164">164</a></span><span class="t">        <span class="com"># stagger</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t165" href="#t165">165</a></span><span class="t">        <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"stagger"</span><span class="op">]</span><span class="op">[</span><span class="str">"buckle"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">stagger</span><span class="op">.</span><span class="nam">corrwith</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t166" href="#t166">166</a></span><span class="t">            <span class="nam">buckle</span><span class="op">,</span> <span class="nam">method</span><span class="op">=</span><span class="nam">self</span><span class="op">.</span><span class="nam">circlineal</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t167" href="#t167">167</a></span><span class="t">        <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"stagger"</span><span class="op">]</span><span class="op">[</span><span class="str">"propel"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">stagger</span><span class="op">.</span><span class="nam">corrwith</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t168" href="#t168">168</a></span><span class="t">            <span class="nam">propel</span><span class="op">,</span> <span class="nam">method</span><span class="op">=</span><span class="nam">self</span><span class="op">.</span><span class="nam">circlineal</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t169" href="#t169">169</a></span><span class="t">        <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"stagger"</span><span class="op">]</span><span class="op">[</span><span class="str">"opening"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">stagger</span><span class="op">.</span><span class="nam">corrwith</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t170" href="#t170">170</a></span><span class="t">            <span class="nam">opening</span><span class="op">,</span> <span class="nam">method</span><span class="op">=</span><span class="nam">self</span><span class="op">.</span><span class="nam">circlineal</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t171" href="#t171">171</a></span><span class="t">        <span class="com"># symmetric values</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t172" href="#t172">172</a></span><span class="t">        <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"buckle"</span><span class="op">]</span><span class="op">[</span><span class="str">"stagger"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"stagger"</span><span class="op">]</span><span class="op">[</span><span class="str">"buckle"</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t173" href="#t173">173</a></span><span class="t">        <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"propel"</span><span class="op">]</span><span class="op">[</span><span class="str">"stagger"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"stagger"</span><span class="op">]</span><span class="op">[</span><span class="str">"propel"</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t174" href="#t174">174</a></span><span class="t">        <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"opening"</span><span class="op">]</span><span class="op">[</span><span class="str">"stagger"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"stagger"</span><span class="op">]</span><span class="op">[</span><span class="str">"opening"</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t175" href="#t175">175</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t176" href="#t176">176</a></span><span class="t">        <span class="com"># buckle</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t177" href="#t177">177</a></span><span class="t">        <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"buckle"</span><span class="op">]</span><span class="op">[</span><span class="str">"propel"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">buckle</span><span class="op">.</span><span class="nam">corrwith</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t178" href="#t178">178</a></span><span class="t">            <span class="nam">propel</span><span class="op">,</span> <span class="nam">method</span><span class="op">=</span><span class="nam">self</span><span class="op">.</span><span class="nam">circular</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t179" href="#t179">179</a></span><span class="t">        <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"buckle"</span><span class="op">]</span><span class="op">[</span><span class="str">"opening"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">buckle</span><span class="op">.</span><span class="nam">corrwith</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t180" href="#t180">180</a></span><span class="t">            <span class="nam">opening</span><span class="op">,</span> <span class="nam">method</span><span class="op">=</span><span class="nam">self</span><span class="op">.</span><span class="nam">circular</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t181" href="#t181">181</a></span><span class="t">        <span class="com"># symmetric values</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t182" href="#t182">182</a></span><span class="t">        <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"propel"</span><span class="op">]</span><span class="op">[</span><span class="str">"buckle"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"buckle"</span><span class="op">]</span><span class="op">[</span><span class="str">"propel"</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t183" href="#t183">183</a></span><span class="t">        <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"opening"</span><span class="op">]</span><span class="op">[</span><span class="str">"buckle"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"buckle"</span><span class="op">]</span><span class="op">[</span><span class="str">"opening"</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t184" href="#t184">184</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t185" href="#t185">185</a></span><span class="t">        <span class="com"># propel</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t186" href="#t186">186</a></span><span class="t">        <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"propel"</span><span class="op">]</span><span class="op">[</span><span class="str">"opening"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">propel</span><span class="op">.</span><span class="nam">corrwith</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t187" href="#t187">187</a></span><span class="t">            <span class="nam">opening</span><span class="op">,</span> <span class="nam">method</span><span class="op">=</span><span class="nam">self</span><span class="op">.</span><span class="nam">circular</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t188" href="#t188">188</a></span><span class="t">        <span class="com"># symmetric values</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t189" href="#t189">189</a></span><span class="t">        <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"opening"</span><span class="op">]</span><span class="op">[</span><span class="str">"propel"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"propel"</span><span class="op">]</span><span class="op">[</span><span class="str">"opening"</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t190" href="#t190">190</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t191" href="#t191">191</a></span><span class="t">        <span class="com"># save csv data</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t192" href="#t192">192</a></span><span class="t">        <span class="nam">corr_matrix</span><span class="op">.</span><span class="nam">to_csv</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">"out"</span><span class="op">]</span><span class="op">[</span><span class="str">"output_csv_path"</span><span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t193" href="#t193">193</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t194" href="#t194">194</a></span><span class="t">        <span class="com"># create heatmap</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t195" href="#t195">195</a></span><span class="t">        <span class="nam">fig</span><span class="op">,</span> <span class="nam">axs</span> <span class="op">=</span> <span class="nam">plt</span><span class="op">.</span><span class="nam">subplots</span><span class="op">(</span><span class="num">1</span><span class="op">,</span> <span class="num">1</span><span class="op">,</span> <span class="nam">dpi</span><span class="op">=</span><span class="num">300</span><span class="op">,</span> <span class="nam">tight_layout</span><span class="op">=</span><span class="key">True</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t196" href="#t196">196</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">pcolor</span><span class="op">(</span><span class="nam">corr_matrix</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t197" href="#t197">197</a></span><span class="t">        <span class="com"># Loop over data dimensions and create text annotations.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t198" href="#t198">198</a></span><span class="t">        <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">range</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">corr_matrix</span><span class="op">)</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t199" href="#t199">199</a></span><span class="t">            <span class="key">for</span> <span class="nam">j</span> <span class="key">in</span> <span class="nam">range</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">corr_matrix</span><span class="op">)</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t200" href="#t200">200</a></span><span class="t">                <span class="nam">axs</span><span class="op">.</span><span class="nam">text</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t201" href="#t201">201</a></span><span class="t">                    <span class="nam">j</span><span class="op">+</span><span class="num">.5</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t202" href="#t202">202</a></span><span class="t">                    <span class="nam">i</span><span class="op">+</span><span class="num">.5</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t203" href="#t203">203</a></span><span class="t">                    <span class="str">f"{corr_matrix[coordinates[j]].loc[coordinates[i]]:.2f}"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t204" href="#t204">204</a></span><span class="t">                    <span class="nam">ha</span><span class="op">=</span><span class="str">"center"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t205" href="#t205">205</a></span><span class="t">                    <span class="nam">va</span><span class="op">=</span><span class="str">"center"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t206" href="#t206">206</a></span><span class="t">                    <span class="nam">color</span><span class="op">=</span><span class="str">"w"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t207" href="#t207">207</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_xticks</span><span class="op">(</span><span class="op">[</span><span class="nam">i</span> <span class="op">+</span> <span class="num">0.5</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">range</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">corr_matrix</span><span class="op">)</span><span class="op">)</span><span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t208" href="#t208">208</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_xticklabels</span><span class="op">(</span><span class="nam">corr_matrix</span><span class="op">.</span><span class="nam">columns</span><span class="op">,</span> <span class="nam">rotation</span><span class="op">=</span><span class="num">90</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t209" href="#t209">209</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_yticks</span><span class="op">(</span><span class="op">[</span><span class="nam">i</span><span class="op">+</span><span class="num">0.5</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">range</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">corr_matrix</span><span class="op">)</span><span class="op">)</span><span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t210" href="#t210">210</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_yticklabels</span><span class="op">(</span><span class="nam">corr_matrix</span><span class="op">.</span><span class="nam">index</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t211" href="#t211">211</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_title</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t212" href="#t212">212</a></span><span class="t">            <span class="str">"Helical Parameter Correlation "</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t213" href="#t213">213</a></span><span class="t">            <span class="str">f"for Base Pair Step \'{self.base}\'"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t214" href="#t214">214</a></span><span class="t">        <span class="nam">fig</span><span class="op">.</span><span class="nam">tight_layout</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t215" href="#t215">215</a></span><span class="t">        <span class="nam">fig</span><span class="op">.</span><span class="nam">savefig</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t216" href="#t216">216</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'out'</span><span class="op">]</span><span class="op">[</span><span class="str">'output_jpg_path'</span><span class="op">]</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t217" href="#t217">217</a></span><span class="t">            <span class="nam">format</span><span class="op">=</span><span class="str">"jpg"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t218" href="#t218">218</a></span><span class="t">        <span class="nam">plt</span><span class="op">.</span><span class="nam">close</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t219" href="#t219">219</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t220" href="#t220">220</a></span><span class="t">        <span class="com"># Remove temporary file(s)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t221" href="#t221">221</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_files</span><span class="op">.</span><span class="nam">extend</span><span class="op">(</span><span class="op">[</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t222" href="#t222">222</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"unique_dir"</span><span class="op">)</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t223" href="#t223">223</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t224" href="#t224">224</a></span><span class="t">        <span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t225" href="#t225">225</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">remove_tmp_files</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t226" href="#t226">226</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t227" href="#t227">227</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_arguments</span><span class="op">(</span><span class="nam">output_files_created</span><span class="op">=</span><span class="key">True</span><span class="op">,</span> <span class="nam">raise_exception</span><span class="op">=</span><span class="key">False</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t228" href="#t228">228</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t229" href="#t229">229</a></span><span class="t">        <span class="key">return</span> <span class="num">0</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t230" href="#t230">230</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t231" href="#t231">231</a></span><span class="t">    <span class="key">def</span> <span class="nam">get_corr_method</span><span class="op">(</span><span class="nam">self</span><span class="op">,</span> <span class="nam">corrtype1</span><span class="op">,</span> <span class="nam">corrtype2</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t232" href="#t232">232</a></span><span class="t">        <span class="key">if</span> <span class="nam">corrtype1</span> <span class="op">==</span> <span class="str">"circular"</span> <span class="key">and</span> <span class="nam">corrtype2</span> <span class="op">==</span> <span class="str">"linear"</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t233" href="#t233">233</a></span><span class="t">            <span class="nam">method</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">circlineal</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t234" href="#t234">234</a></span><span class="t">        <span class="key">if</span> <span class="nam">corrtype1</span> <span class="op">==</span> <span class="str">"linear"</span> <span class="key">and</span> <span class="nam">corrtype2</span> <span class="op">==</span> <span class="str">"circular"</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t235" href="#t235">235</a></span><span class="t">            <span class="nam">method</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">circlineal</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t236" href="#t236">236</a></span><span class="t">        <span class="key">elif</span> <span class="nam">corrtype1</span> <span class="op">==</span> <span class="str">"circular"</span> <span class="key">and</span> <span class="nam">corrtype2</span> <span class="op">==</span> <span class="str">"circular"</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t237" href="#t237">237</a></span><span class="t">            <span class="nam">method</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">circular</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t238" href="#t238">238</a></span><span class="t">        <span class="key">else</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t239" href="#t239">239</a></span><span class="t">            <span class="nam">method</span> <span class="op">=</span> <span class="str">"pearson"</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t240" href="#t240">240</a></span><span class="t">        <span class="key">return</span> <span class="nam">method</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t241" href="#t241">241</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t242" href="#t242">242</a></span><span class="t">    <span class="op">@</span><span class="nam">staticmethod</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t243" href="#t243">243</a></span><span class="t">    <span class="key">def</span> <span class="nam">circular</span><span class="op">(</span><span class="nam">x1</span><span class="op">,</span> <span class="nam">x2</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t244" href="#t244">244</a></span><span class="t">        <span class="nam">x1</span> <span class="op">=</span> <span class="nam">x1</span> <span class="op">*</span> <span class="nam">np</span><span class="op">.</span><span class="nam">pi</span> <span class="op">/</span> <span class="num">180</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t245" href="#t245">245</a></span><span class="t">        <span class="nam">x2</span> <span class="op">=</span> <span class="nam">x2</span> <span class="op">*</span> <span class="nam">np</span><span class="op">.</span><span class="nam">pi</span> <span class="op">/</span> <span class="num">180</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t246" href="#t246">246</a></span><span class="t">        <span class="nam">diff_1</span> <span class="op">=</span> <span class="nam">np</span><span class="op">.</span><span class="nam">sin</span><span class="op">(</span><span class="nam">x1</span> <span class="op">-</span> <span class="nam">x1</span><span class="op">.</span><span class="nam">mean</span><span class="op">(</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t247" href="#t247">247</a></span><span class="t">        <span class="nam">diff_2</span> <span class="op">=</span> <span class="nam">np</span><span class="op">.</span><span class="nam">sin</span><span class="op">(</span><span class="nam">x2</span> <span class="op">-</span> <span class="nam">x2</span><span class="op">.</span><span class="nam">mean</span><span class="op">(</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t248" href="#t248">248</a></span><span class="t">        <span class="nam">num</span> <span class="op">=</span> <span class="op">(</span><span class="nam">diff_1</span> <span class="op">*</span> <span class="nam">diff_2</span><span class="op">)</span><span class="op">.</span><span class="nam">sum</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t249" href="#t249">249</a></span><span class="t">        <span class="nam">den</span> <span class="op">=</span> <span class="nam">np</span><span class="op">.</span><span class="nam">sqrt</span><span class="op">(</span><span class="op">(</span><span class="nam">diff_1</span> <span class="op">**</span> <span class="num">2</span><span class="op">)</span><span class="op">.</span><span class="nam">sum</span><span class="op">(</span><span class="op">)</span> <span class="op">*</span> <span class="op">(</span><span class="nam">diff_2</span> <span class="op">**</span> <span class="num">2</span><span class="op">)</span><span class="op">.</span><span class="nam">sum</span><span class="op">(</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t250" href="#t250">250</a></span><span class="t">        <span class="key">return</span> <span class="nam">num</span> <span class="op">/</span> <span class="nam">den</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t251" href="#t251">251</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t252" href="#t252">252</a></span><span class="t">    <span class="op">@</span><span class="nam">staticmethod</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t253" href="#t253">253</a></span><span class="t">    <span class="key">def</span> <span class="nam">circlineal</span><span class="op">(</span><span class="nam">x1</span><span class="op">,</span> <span class="nam">x2</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t254" href="#t254">254</a></span><span class="t">        <span class="nam">x2</span> <span class="op">=</span> <span class="nam">x2</span> <span class="op">*</span> <span class="nam">np</span><span class="op">.</span><span class="nam">pi</span> <span class="op">/</span> <span class="num">180</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t255" href="#t255">255</a></span><span class="t">        <span class="nam">rc</span> <span class="op">=</span> <span class="nam">np</span><span class="op">.</span><span class="nam">corrcoef</span><span class="op">(</span><span class="nam">x1</span><span class="op">,</span> <span class="nam">np</span><span class="op">.</span><span class="nam">cos</span><span class="op">(</span><span class="nam">x2</span><span class="op">)</span><span class="op">)</span><span class="op">[</span><span class="num">1</span><span class="op">,</span> <span class="num">0</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t256" href="#t256">256</a></span><span class="t">        <span class="nam">rs</span> <span class="op">=</span> <span class="nam">np</span><span class="op">.</span><span class="nam">corrcoef</span><span class="op">(</span><span class="nam">x1</span><span class="op">,</span> <span class="nam">np</span><span class="op">.</span><span class="nam">sin</span><span class="op">(</span><span class="nam">x2</span><span class="op">)</span><span class="op">)</span><span class="op">[</span><span class="num">1</span><span class="op">,</span> <span class="num">0</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t257" href="#t257">257</a></span><span class="t">        <span class="nam">rcs</span> <span class="op">=</span> <span class="nam">np</span><span class="op">.</span><span class="nam">corrcoef</span><span class="op">(</span><span class="nam">np</span><span class="op">.</span><span class="nam">sin</span><span class="op">(</span><span class="nam">x2</span><span class="op">)</span><span class="op">,</span> <span class="nam">np</span><span class="op">.</span><span class="nam">cos</span><span class="op">(</span><span class="nam">x2</span><span class="op">)</span><span class="op">)</span><span class="op">[</span><span class="num">1</span><span class="op">,</span> <span class="num">0</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t258" href="#t258">258</a></span><span class="t">        <span class="nam">num</span> <span class="op">=</span> <span class="op">(</span><span class="nam">rc</span> <span class="op">**</span> <span class="num">2</span><span class="op">)</span> <span class="op">+</span> <span class="op">(</span><span class="nam">rs</span> <span class="op">**</span> <span class="num">2</span><span class="op">)</span> <span class="op">-</span> <span class="num">2</span> <span class="op">*</span> <span class="nam">rc</span> <span class="op">*</span> <span class="nam">rs</span> <span class="op">*</span> <span class="nam">rcs</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t259" href="#t259">259</a></span><span class="t">        <span class="nam">den</span> <span class="op">=</span> <span class="num">1</span> <span class="op">-</span> <span class="op">(</span><span class="nam">rcs</span> <span class="op">**</span> <span class="num">2</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t260" href="#t260">260</a></span><span class="t">        <span class="nam">correlation</span> <span class="op">=</span> <span class="nam">np</span><span class="op">.</span><span class="nam">sqrt</span><span class="op">(</span><span class="nam">num</span> <span class="op">/</span> <span class="nam">den</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t261" href="#t261">261</a></span><span class="t">        <span class="key">if</span> <span class="nam">np</span><span class="op">.</span><span class="nam">corrcoef</span><span class="op">(</span><span class="nam">x1</span><span class="op">,</span> <span class="nam">x2</span><span class="op">)</span><span class="op">[</span><span class="num">1</span><span class="op">,</span> <span class="num">0</span><span class="op">]</span> <span class="op">&lt;</span> <span class="num">0</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t262" href="#t262">262</a></span><span class="t">            <span class="nam">correlation</span> <span class="op">*=</span> <span class="op">-</span><span class="num">1</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t263" href="#t263">263</a></span><span class="t">        <span class="key">return</span> <span class="nam">correlation</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t264" href="#t264">264</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t21" href="#t21">21</a></span><span class="t"><span class="str">    | Calculate correlation between helical parameters for a single intra-base pair.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t22" href="#t22">22</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t23" href="#t23">23</a></span><span class="t"><span class="str">    Args:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t24" href="#t24">24</a></span><span class="t"><span class="str">        input_filename_shear (str): Path to .csv file with data for helical parameter 'shear'. File type: input. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/correlation/series_shear_A.csv>`_. Accepted formats: csv (edam:format_3752).</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t25" href="#t25">25</a></span><span class="t"><span class="str">        input_filename_stretch (str): Path to .csv file with data for helical parameter 'stretch'. File type: input. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/correlation/series_stretch_A.csv>`_. Accepted formats: csv (edam:format_3752).</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t26" href="#t26">26</a></span><span class="t"><span class="str">        input_filename_stagger (str): Path to .csv file with data for helical parameter 'stagger'. File type: input. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/correlation/series_stagger_A.csv>`_. Accepted formats: csv (edam:format_3752).</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t27" href="#t27">27</a></span><span class="t"><span class="str">        input_filename_buckle (str): Path to .csv file with data for helical parameter 'buckle'. File type: input. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/correlation/series_buckle_A.csv>`_. Accepted formats: csv (edam:format_3752).</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t28" href="#t28">28</a></span><span class="t"><span class="str">        input_filename_propel (str): Path to .csv file with data for helical parameter 'propeller'. File type: input. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/correlation/series_propel_A.csv>`_. Accepted formats: csv (edam:format_3752).</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t29" href="#t29">29</a></span><span class="t"><span class="str">        input_filename_opening (str): Path to .csv file with data for helical parameter 'opening'. File type: input. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/correlation/series_opening_A.csv>`_. Accepted formats: csv (edam:format_3752).</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t30" href="#t30">30</a></span><span class="t"><span class="str">        output_csv_path (str): Path to directory where output is saved. File type: output. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/reference/correlation/intra_hpcorr_ref.csv>`_. Accepted formats: csv (edam:format_3752).</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t31" href="#t31">31</a></span><span class="t"><span class="str">        output_jpg_path (str): Path to .jpg file where output is saved. File type: output. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/reference/correlation/intra_hpcorr_ref.jpg>`_. Accepted formats: jpg (edam:format_3579).</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t32" href="#t32">32</a></span><span class="t"><span class="str">        properties (dict):</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t33" href="#t33">33</a></span><span class="t"><span class="str">            * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t34" href="#t34">34</a></span><span class="t"><span class="str">            * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t35" href="#t35">35</a></span><span class="t"><span class="str">            * **base** (*str*) - (None) Name of base analyzed.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t36" href="#t36">36</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t37" href="#t37">37</a></span><span class="t"><span class="str">    Examples:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t38" href="#t38">38</a></span><span class="t"><span class="str">        This is a use example of how to use the building block from Python::</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t39" href="#t39">39</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t40" href="#t40">40</a></span><span class="t"><span class="str">            from biobb_dna.intrabp_correlations.intrahpcorr import intrahpcorr</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t41" href="#t41">41</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t42" href="#t42">42</a></span><span class="t"><span class="str">            prop = {</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t43" href="#t43">43</a></span><span class="t"><span class="str">                'base': 'A',</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t44" href="#t44">44</a></span><span class="t"><span class="str">            }</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t45" href="#t45">45</a></span><span class="t"><span class="str">            intrahpcorr(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t46" href="#t46">46</a></span><span class="t"><span class="str">                input_filename_shear='path/to/shear.csv',</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t47" href="#t47">47</a></span><span class="t"><span class="str">                input_filename_stretch='path/to/stretch.csv',</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t48" href="#t48">48</a></span><span class="t"><span class="str">                input_filename_stagger='path/to/stagger.csv',</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t49" href="#t49">49</a></span><span class="t"><span class="str">                input_filename_buckle='path/to/buckle.csv',</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t50" href="#t50">50</a></span><span class="t"><span class="str">                input_filename_propel='path/to/propel.csv',</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t51" href="#t51">51</a></span><span class="t"><span class="str">                input_filename_opening='path/to/opening.csv',</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t52" href="#t52">52</a></span><span class="t"><span class="str">                output_csv_path='path/to/output/file.csv',</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t53" href="#t53">53</a></span><span class="t"><span class="str">                output_jpg_path='path/to/output/file.jpg',</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t54" href="#t54">54</a></span><span class="t"><span class="str">                properties=prop)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t55" href="#t55">55</a></span><span class="t"><span class="str">    Info:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t56" href="#t56">56</a></span><span class="t"><span class="str">        * wrapped_software:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t57" href="#t57">57</a></span><span class="t"><span class="str">            * name: In house</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t58" href="#t58">58</a></span><span class="t"><span class="str">            * license: Apache-2.0</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t59" href="#t59">59</a></span><span class="t"><span class="str">        * ontology:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t60" href="#t60">60</a></span><span class="t"><span class="str">            * name: EDAM</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t61" href="#t61">61</a></span><span class="t"><span class="str">            * schema: http://edamontology.org/EDAM.owl</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t62" href="#t62">62</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t63" href="#t63">63</a></span><span class="t"><span class="str">    """</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t64" href="#t64">64</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t65" href="#t65">65</a></span><span class="t">    <span class="key">def</span> <span class="nam">__init__</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t66" href="#t66">66</a></span><span class="t">            <span class="nam">self</span><span class="op">,</span> <span class="nam">input_filename_shear</span><span class="op">,</span> <span class="nam">input_filename_stretch</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t67" href="#t67">67</a></span><span class="t">            <span class="nam">input_filename_stagger</span><span class="op">,</span> <span class="nam">input_filename_buckle</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t68" href="#t68">68</a></span><span class="t">            <span class="nam">input_filename_propel</span><span class="op">,</span> <span class="nam">input_filename_opening</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t69" href="#t69">69</a></span><span class="t">            <span class="nam">output_csv_path</span><span class="op">,</span> <span class="nam">output_jpg_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t70" href="#t70">70</a></span><span class="t">            <span class="nam">properties</span><span class="op">=</span><span class="key">None</span><span class="op">,</span> <span class="op">**</span><span class="nam">kwargs</span><span class="op">)</span> <span class="op">-></span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t71" href="#t71">71</a></span><span class="t">        <span class="nam">properties</span> <span class="op">=</span> <span class="nam">properties</span> <span class="key">or</span> <span class="op">{</span><span class="op">}</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t72" href="#t72">72</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t73" href="#t73">73</a></span><span class="t">        <span class="com"># Call parent class constructor</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t74" href="#t74">74</a></span><span class="t">        <span class="nam">super</span><span class="op">(</span><span class="op">)</span><span class="op">.</span><span class="nam">__init__</span><span class="op">(</span><span class="nam">properties</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t75" href="#t75">75</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">locals_var_dict</span> <span class="op">=</span> <span class="nam">locals</span><span class="op">(</span><span class="op">)</span><span class="op">.</span><span class="nam">copy</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t76" href="#t76">76</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t77" href="#t77">77</a></span><span class="t">        <span class="com"># Input/Output files</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t78" href="#t78">78</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span> <span class="op">=</span> <span class="op">{</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t79" href="#t79">79</a></span><span class="t">            <span class="str">'in'</span><span class="op">:</span> <span class="op">{</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t80" href="#t80">80</a></span><span class="t">                <span class="str">'input_filename_shear'</span><span class="op">:</span> <span class="nam">input_filename_shear</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t81" href="#t81">81</a></span><span class="t">                <span class="str">'input_filename_stretch'</span><span class="op">:</span> <span class="nam">input_filename_stretch</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t82" href="#t82">82</a></span><span class="t">                <span class="str">'input_filename_stagger'</span><span class="op">:</span> <span class="nam">input_filename_stagger</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t83" href="#t83">83</a></span><span class="t">                <span class="str">'input_filename_buckle'</span><span class="op">:</span> <span class="nam">input_filename_buckle</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t84" href="#t84">84</a></span><span class="t">                <span class="str">'input_filename_propel'</span><span class="op">:</span> <span class="nam">input_filename_propel</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t85" href="#t85">85</a></span><span class="t">                <span class="str">'input_filename_opening'</span><span class="op">:</span> <span class="nam">input_filename_opening</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t86" href="#t86">86</a></span><span class="t">            <span class="op">}</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t87" href="#t87">87</a></span><span class="t">            <span class="str">'out'</span><span class="op">:</span> <span class="op">{</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t88" href="#t88">88</a></span><span class="t">                <span class="str">'output_csv_path'</span><span class="op">:</span> <span class="nam">output_csv_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t89" href="#t89">89</a></span><span class="t">                <span class="str">'output_jpg_path'</span><span class="op">:</span> <span class="nam">output_jpg_path</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t90" href="#t90">90</a></span><span class="t">            <span class="op">}</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t91" href="#t91">91</a></span><span class="t">        <span class="op">}</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t92" href="#t92">92</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t93" href="#t93">93</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">properties</span> <span class="op">=</span> <span class="nam">properties</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t94" href="#t94">94</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">base</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"base"</span><span class="op">,</span> <span class="key">None</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t95" href="#t95">95</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t96" href="#t96">96</a></span><span class="t">        <span class="com"># Check the properties</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t97" href="#t97">97</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_properties</span><span class="op">(</span><span class="nam">properties</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t98" href="#t98">98</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_arguments</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t99" href="#t99">99</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t100" href="#t100">100</a></span><span class="t">    <span class="op">@</span><span class="nam">launchlogger</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t101" href="#t101">101</a></span><span class="t">    <span class="key">def</span> <span class="nam">launch</span><span class="op">(</span><span class="nam">self</span><span class="op">)</span> <span class="op">-></span> <span class="nam">int</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t102" href="#t102">102</a></span><span class="t">        <span class="str">"""Execute the :class:`IntraHelParCorrelation &lt;intrabp_correlations.intrahpcorr.IntraHelParCorrelation>` object."""</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t103" href="#t103">103</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t104" href="#t104">104</a></span><span class="t">        <span class="com"># Setup Biobb</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t105" href="#t105">105</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">check_restart</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t106" href="#t106">106</a></span><span class="t">            <span class="key">return</span> <span class="num">0</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t107" href="#t107">107</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">stage_files</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t108" href="#t108">108</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t109" href="#t109">109</a></span><span class="t">        <span class="com"># Creating temporary folder</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t110" href="#t110">110</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span> <span class="op">=</span> <span class="nam">fu</span><span class="op">.</span><span class="nam">create_unique_dir</span><span class="op">(</span><span class="nam">prefix</span><span class="op">=</span><span class="str">"hpcorrelation_"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t111" href="#t111">111</a></span><span class="t">        <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="str">'Creating %s temporary folder'</span> <span class="op">%</span> <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t112" href="#t112">112</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t113" href="#t113">113</a></span><span class="t">        <span class="com"># read input</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t114" href="#t114">114</a></span><span class="t">        <span class="nam">shear</span> <span class="op">=</span> <span class="nam">load_data</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">"in"</span><span class="op">]</span><span class="op">[</span><span class="str">"input_filename_shear"</span><span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t115" href="#t115">115</a></span><span class="t">        <span class="nam">stretch</span> <span class="op">=</span> <span class="nam">load_data</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">"in"</span><span class="op">]</span><span class="op">[</span><span class="str">"input_filename_stretch"</span><span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t116" href="#t116">116</a></span><span class="t">        <span class="nam">stagger</span> <span class="op">=</span> <span class="nam">load_data</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">"in"</span><span class="op">]</span><span class="op">[</span><span class="str">"input_filename_stagger"</span><span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t117" href="#t117">117</a></span><span class="t">        <span class="nam">buckle</span> <span class="op">=</span> <span class="nam">load_data</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">"in"</span><span class="op">]</span><span class="op">[</span><span class="str">"input_filename_buckle"</span><span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t118" href="#t118">118</a></span><span class="t">        <span class="nam">propel</span> <span class="op">=</span> <span class="nam">load_data</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">"in"</span><span class="op">]</span><span class="op">[</span><span class="str">"input_filename_propel"</span><span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t119" href="#t119">119</a></span><span class="t">        <span class="nam">opening</span> <span class="op">=</span> <span class="nam">load_data</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">"in"</span><span class="op">]</span><span class="op">[</span><span class="str">"input_filename_opening"</span><span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t120" href="#t120">120</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t121" href="#t121">121</a></span><span class="t">        <span class="com"># get base</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t122" href="#t122">122</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">base</span> <span class="key">is</span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t123" href="#t123">123</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">base</span> <span class="op">=</span> <span class="nam">shear</span><span class="op">.</span><span class="nam">columns</span><span class="op">[</span><span class="num">0</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t124" href="#t124">124</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t125" href="#t125">125</a></span><span class="t">        <span class="com"># make matrix</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t126" href="#t126">126</a></span><span class="t">        <span class="com"># coordinates = ["shear", "stretch", "stagger", "buckle", "propel", "opening"]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t127" href="#t127">127</a></span><span class="t">        <span class="nam">coordinates</span> <span class="op">=</span> <span class="op">[</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t128" href="#t128">128</a></span><span class="t">            <span class="str">"shear"</span><span class="op">,</span> <span class="str">"stretch"</span><span class="op">,</span> <span class="str">"stagger"</span><span class="op">,</span> <span class="str">"buckle"</span><span class="op">,</span> <span class="str">"propel"</span><span class="op">,</span> <span class="str">"opening"</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t129" href="#t129">129</a></span><span class="t">        <span class="nam">corr_matrix</span> <span class="op">=</span> <span class="nam">pd</span><span class="op">.</span><span class="nam">DataFrame</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t130" href="#t130">130</a></span><span class="t">            <span class="nam">np</span><span class="op">.</span><span class="nam">eye</span><span class="op">(</span><span class="num">6</span><span class="op">,</span> <span class="num">6</span><span class="op">)</span><span class="op">,</span> <span class="nam">index</span><span class="op">=</span><span class="nam">coordinates</span><span class="op">,</span> <span class="nam">columns</span><span class="op">=</span><span class="nam">coordinates</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t131" href="#t131">131</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t132" href="#t132">132</a></span><span class="t">        <span class="com"># shear</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t133" href="#t133">133</a></span><span class="t">        <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"shear"</span><span class="op">]</span><span class="op">[</span><span class="str">"stretch"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">shear</span><span class="op">.</span><span class="nam">corrwith</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t134" href="#t134">134</a></span><span class="t">            <span class="nam">stretch</span><span class="op">,</span> <span class="nam">method</span><span class="op">=</span><span class="str">"pearson"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t135" href="#t135">135</a></span><span class="t">        <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"shear"</span><span class="op">]</span><span class="op">[</span><span class="str">"stagger"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">shear</span><span class="op">.</span><span class="nam">corrwith</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t136" href="#t136">136</a></span><span class="t">            <span class="nam">stagger</span><span class="op">,</span> <span class="nam">method</span><span class="op">=</span><span class="str">"pearson"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t137" href="#t137">137</a></span><span class="t">        <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"shear"</span><span class="op">]</span><span class="op">[</span><span class="str">"buckle"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">shear</span><span class="op">.</span><span class="nam">corrwith</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t138" href="#t138">138</a></span><span class="t">            <span class="nam">buckle</span><span class="op">,</span> <span class="nam">method</span><span class="op">=</span><span class="nam">self</span><span class="op">.</span><span class="nam">circlineal</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t139" href="#t139">139</a></span><span class="t">        <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"shear"</span><span class="op">]</span><span class="op">[</span><span class="str">"propel"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">shear</span><span class="op">.</span><span class="nam">corrwith</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t140" href="#t140">140</a></span><span class="t">            <span class="nam">propel</span><span class="op">,</span> <span class="nam">method</span><span class="op">=</span><span class="nam">self</span><span class="op">.</span><span class="nam">circlineal</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t141" href="#t141">141</a></span><span class="t">        <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"shear"</span><span class="op">]</span><span class="op">[</span><span class="str">"opening"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">shear</span><span class="op">.</span><span class="nam">corrwith</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t142" href="#t142">142</a></span><span class="t">            <span class="nam">opening</span><span class="op">,</span> <span class="nam">method</span><span class="op">=</span><span class="nam">self</span><span class="op">.</span><span class="nam">circlineal</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t143" href="#t143">143</a></span><span class="t">        <span class="com"># symmetric values</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t144" href="#t144">144</a></span><span class="t">        <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"stretch"</span><span class="op">]</span><span class="op">[</span><span class="str">"shear"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"shear"</span><span class="op">]</span><span class="op">[</span><span class="str">"stretch"</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t145" href="#t145">145</a></span><span class="t">        <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"stagger"</span><span class="op">]</span><span class="op">[</span><span class="str">"shear"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"shear"</span><span class="op">]</span><span class="op">[</span><span class="str">"stagger"</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t146" href="#t146">146</a></span><span class="t">        <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"buckle"</span><span class="op">]</span><span class="op">[</span><span class="str">"shear"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"shear"</span><span class="op">]</span><span class="op">[</span><span class="str">"buckle"</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t147" href="#t147">147</a></span><span class="t">        <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"propel"</span><span class="op">]</span><span class="op">[</span><span class="str">"shear"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"shear"</span><span class="op">]</span><span class="op">[</span><span class="str">"propel"</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t148" href="#t148">148</a></span><span class="t">        <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"opening"</span><span class="op">]</span><span class="op">[</span><span class="str">"shear"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"shear"</span><span class="op">]</span><span class="op">[</span><span class="str">"opening"</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t149" href="#t149">149</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t150" href="#t150">150</a></span><span class="t">        <span class="com"># stretch</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t151" href="#t151">151</a></span><span class="t">        <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"stretch"</span><span class="op">]</span><span class="op">[</span><span class="str">"stagger"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">stretch</span><span class="op">.</span><span class="nam">corrwith</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t152" href="#t152">152</a></span><span class="t">            <span class="nam">stagger</span><span class="op">,</span> <span class="nam">method</span><span class="op">=</span><span class="str">"pearson"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t153" href="#t153">153</a></span><span class="t">        <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"stretch"</span><span class="op">]</span><span class="op">[</span><span class="str">"buckle"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">stretch</span><span class="op">.</span><span class="nam">corrwith</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t154" href="#t154">154</a></span><span class="t">            <span class="nam">buckle</span><span class="op">,</span> <span class="nam">method</span><span class="op">=</span><span class="nam">self</span><span class="op">.</span><span class="nam">circlineal</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t155" href="#t155">155</a></span><span class="t">        <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"stretch"</span><span class="op">]</span><span class="op">[</span><span class="str">"propel"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">stretch</span><span class="op">.</span><span class="nam">corrwith</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t156" href="#t156">156</a></span><span class="t">            <span class="nam">propel</span><span class="op">,</span> <span class="nam">method</span><span class="op">=</span><span class="nam">self</span><span class="op">.</span><span class="nam">circlineal</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t157" href="#t157">157</a></span><span class="t">        <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"stretch"</span><span class="op">]</span><span class="op">[</span><span class="str">"opening"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">stretch</span><span class="op">.</span><span class="nam">corrwith</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t158" href="#t158">158</a></span><span class="t">            <span class="nam">opening</span><span class="op">,</span> <span class="nam">method</span><span class="op">=</span><span class="nam">self</span><span class="op">.</span><span class="nam">circlineal</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t159" href="#t159">159</a></span><span class="t">        <span class="com"># symmetric values</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t160" href="#t160">160</a></span><span class="t">        <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"stagger"</span><span class="op">]</span><span class="op">[</span><span class="str">"stretch"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"stretch"</span><span class="op">]</span><span class="op">[</span><span class="str">"stagger"</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t161" href="#t161">161</a></span><span class="t">        <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"buckle"</span><span class="op">]</span><span class="op">[</span><span class="str">"stretch"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"stretch"</span><span class="op">]</span><span class="op">[</span><span class="str">"buckle"</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t162" href="#t162">162</a></span><span class="t">        <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"propel"</span><span class="op">]</span><span class="op">[</span><span class="str">"stretch"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"stretch"</span><span class="op">]</span><span class="op">[</span><span class="str">"propel"</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t163" href="#t163">163</a></span><span class="t">        <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"opening"</span><span class="op">]</span><span class="op">[</span><span class="str">"stretch"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"stretch"</span><span class="op">]</span><span class="op">[</span><span class="str">"opening"</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t164" href="#t164">164</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t165" href="#t165">165</a></span><span class="t">        <span class="com"># stagger</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t166" href="#t166">166</a></span><span class="t">        <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"stagger"</span><span class="op">]</span><span class="op">[</span><span class="str">"buckle"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">stagger</span><span class="op">.</span><span class="nam">corrwith</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t167" href="#t167">167</a></span><span class="t">            <span class="nam">buckle</span><span class="op">,</span> <span class="nam">method</span><span class="op">=</span><span class="nam">self</span><span class="op">.</span><span class="nam">circlineal</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t168" href="#t168">168</a></span><span class="t">        <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"stagger"</span><span class="op">]</span><span class="op">[</span><span class="str">"propel"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">stagger</span><span class="op">.</span><span class="nam">corrwith</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t169" href="#t169">169</a></span><span class="t">            <span class="nam">propel</span><span class="op">,</span> <span class="nam">method</span><span class="op">=</span><span class="nam">self</span><span class="op">.</span><span class="nam">circlineal</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t170" href="#t170">170</a></span><span class="t">        <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"stagger"</span><span class="op">]</span><span class="op">[</span><span class="str">"opening"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">stagger</span><span class="op">.</span><span class="nam">corrwith</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t171" href="#t171">171</a></span><span class="t">            <span class="nam">opening</span><span class="op">,</span> <span class="nam">method</span><span class="op">=</span><span class="nam">self</span><span class="op">.</span><span class="nam">circlineal</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t172" href="#t172">172</a></span><span class="t">        <span class="com"># symmetric values</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t173" href="#t173">173</a></span><span class="t">        <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"buckle"</span><span class="op">]</span><span class="op">[</span><span class="str">"stagger"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"stagger"</span><span class="op">]</span><span class="op">[</span><span class="str">"buckle"</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t174" href="#t174">174</a></span><span class="t">        <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"propel"</span><span class="op">]</span><span class="op">[</span><span class="str">"stagger"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"stagger"</span><span class="op">]</span><span class="op">[</span><span class="str">"propel"</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t175" href="#t175">175</a></span><span class="t">        <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"opening"</span><span class="op">]</span><span class="op">[</span><span class="str">"stagger"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"stagger"</span><span class="op">]</span><span class="op">[</span><span class="str">"opening"</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t176" href="#t176">176</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t177" href="#t177">177</a></span><span class="t">        <span class="com"># buckle</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t178" href="#t178">178</a></span><span class="t">        <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"buckle"</span><span class="op">]</span><span class="op">[</span><span class="str">"propel"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">buckle</span><span class="op">.</span><span class="nam">corrwith</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t179" href="#t179">179</a></span><span class="t">            <span class="nam">propel</span><span class="op">,</span> <span class="nam">method</span><span class="op">=</span><span class="nam">self</span><span class="op">.</span><span class="nam">circular</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t180" href="#t180">180</a></span><span class="t">        <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"buckle"</span><span class="op">]</span><span class="op">[</span><span class="str">"opening"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">buckle</span><span class="op">.</span><span class="nam">corrwith</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t181" href="#t181">181</a></span><span class="t">            <span class="nam">opening</span><span class="op">,</span> <span class="nam">method</span><span class="op">=</span><span class="nam">self</span><span class="op">.</span><span class="nam">circular</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t182" href="#t182">182</a></span><span class="t">        <span class="com"># symmetric values</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t183" href="#t183">183</a></span><span class="t">        <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"propel"</span><span class="op">]</span><span class="op">[</span><span class="str">"buckle"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"buckle"</span><span class="op">]</span><span class="op">[</span><span class="str">"propel"</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t184" href="#t184">184</a></span><span class="t">        <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"opening"</span><span class="op">]</span><span class="op">[</span><span class="str">"buckle"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"buckle"</span><span class="op">]</span><span class="op">[</span><span class="str">"opening"</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t185" href="#t185">185</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t186" href="#t186">186</a></span><span class="t">        <span class="com"># propel</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t187" href="#t187">187</a></span><span class="t">        <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"propel"</span><span class="op">]</span><span class="op">[</span><span class="str">"opening"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">propel</span><span class="op">.</span><span class="nam">corrwith</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t188" href="#t188">188</a></span><span class="t">            <span class="nam">opening</span><span class="op">,</span> <span class="nam">method</span><span class="op">=</span><span class="nam">self</span><span class="op">.</span><span class="nam">circular</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t189" href="#t189">189</a></span><span class="t">        <span class="com"># symmetric values</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t190" href="#t190">190</a></span><span class="t">        <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"opening"</span><span class="op">]</span><span class="op">[</span><span class="str">"propel"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"propel"</span><span class="op">]</span><span class="op">[</span><span class="str">"opening"</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t191" href="#t191">191</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t192" href="#t192">192</a></span><span class="t">        <span class="com"># save csv data</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t193" href="#t193">193</a></span><span class="t">        <span class="nam">corr_matrix</span><span class="op">.</span><span class="nam">to_csv</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">"out"</span><span class="op">]</span><span class="op">[</span><span class="str">"output_csv_path"</span><span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t194" href="#t194">194</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t195" href="#t195">195</a></span><span class="t">        <span class="com"># create heatmap</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t196" href="#t196">196</a></span><span class="t">        <span class="nam">fig</span><span class="op">,</span> <span class="nam">axs</span> <span class="op">=</span> <span class="nam">plt</span><span class="op">.</span><span class="nam">subplots</span><span class="op">(</span><span class="num">1</span><span class="op">,</span> <span class="num">1</span><span class="op">,</span> <span class="nam">dpi</span><span class="op">=</span><span class="num">300</span><span class="op">,</span> <span class="nam">tight_layout</span><span class="op">=</span><span class="key">True</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t197" href="#t197">197</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">pcolor</span><span class="op">(</span><span class="nam">corr_matrix</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t198" href="#t198">198</a></span><span class="t">        <span class="com"># Loop over data dimensions and create text annotations.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t199" href="#t199">199</a></span><span class="t">        <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">range</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">corr_matrix</span><span class="op">)</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t200" href="#t200">200</a></span><span class="t">            <span class="key">for</span> <span class="nam">j</span> <span class="key">in</span> <span class="nam">range</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">corr_matrix</span><span class="op">)</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t201" href="#t201">201</a></span><span class="t">                <span class="nam">axs</span><span class="op">.</span><span class="nam">text</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t202" href="#t202">202</a></span><span class="t">                    <span class="nam">j</span><span class="op">+</span><span class="num">.5</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t203" href="#t203">203</a></span><span class="t">                    <span class="nam">i</span><span class="op">+</span><span class="num">.5</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t204" href="#t204">204</a></span><span class="t">                    <span class="str">f"{corr_matrix[coordinates[j]].loc[coordinates[i]]:.2f}"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t205" href="#t205">205</a></span><span class="t">                    <span class="nam">ha</span><span class="op">=</span><span class="str">"center"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t206" href="#t206">206</a></span><span class="t">                    <span class="nam">va</span><span class="op">=</span><span class="str">"center"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t207" href="#t207">207</a></span><span class="t">                    <span class="nam">color</span><span class="op">=</span><span class="str">"w"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t208" href="#t208">208</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_xticks</span><span class="op">(</span><span class="op">[</span><span class="nam">i</span> <span class="op">+</span> <span class="num">0.5</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">range</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">corr_matrix</span><span class="op">)</span><span class="op">)</span><span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t209" href="#t209">209</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_xticklabels</span><span class="op">(</span><span class="nam">corr_matrix</span><span class="op">.</span><span class="nam">columns</span><span class="op">,</span> <span class="nam">rotation</span><span class="op">=</span><span class="num">90</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t210" href="#t210">210</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_yticks</span><span class="op">(</span><span class="op">[</span><span class="nam">i</span><span class="op">+</span><span class="num">0.5</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">range</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">corr_matrix</span><span class="op">)</span><span class="op">)</span><span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t211" href="#t211">211</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_yticklabels</span><span class="op">(</span><span class="nam">corr_matrix</span><span class="op">.</span><span class="nam">index</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t212" href="#t212">212</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_title</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t213" href="#t213">213</a></span><span class="t">            <span class="str">"Helical Parameter Correlation "</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t214" href="#t214">214</a></span><span class="t">            <span class="str">f"for Base Pair Step \'{self.base}\'"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t215" href="#t215">215</a></span><span class="t">        <span class="nam">fig</span><span class="op">.</span><span class="nam">tight_layout</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t216" href="#t216">216</a></span><span class="t">        <span class="nam">fig</span><span class="op">.</span><span class="nam">savefig</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t217" href="#t217">217</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'out'</span><span class="op">]</span><span class="op">[</span><span class="str">'output_jpg_path'</span><span class="op">]</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t218" href="#t218">218</a></span><span class="t">            <span class="nam">format</span><span class="op">=</span><span class="str">"jpg"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t219" href="#t219">219</a></span><span class="t">        <span class="nam">plt</span><span class="op">.</span><span class="nam">close</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t220" href="#t220">220</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t221" href="#t221">221</a></span><span class="t">        <span class="com"># Remove temporary file(s)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t222" href="#t222">222</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_files</span><span class="op">.</span><span class="nam">extend</span><span class="op">(</span><span class="op">[</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t223" href="#t223">223</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"unique_dir"</span><span class="op">)</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t224" href="#t224">224</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t225" href="#t225">225</a></span><span class="t">        <span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t226" href="#t226">226</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">remove_tmp_files</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t227" href="#t227">227</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t228" href="#t228">228</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_arguments</span><span class="op">(</span><span class="nam">output_files_created</span><span class="op">=</span><span class="key">True</span><span class="op">,</span> <span class="nam">raise_exception</span><span class="op">=</span><span class="key">False</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t229" href="#t229">229</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t230" href="#t230">230</a></span><span class="t">        <span class="key">return</span> <span class="num">0</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t231" href="#t231">231</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t232" href="#t232">232</a></span><span class="t">    <span class="key">def</span> <span class="nam">get_corr_method</span><span class="op">(</span><span class="nam">self</span><span class="op">,</span> <span class="nam">corrtype1</span><span class="op">,</span> <span class="nam">corrtype2</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t233" href="#t233">233</a></span><span class="t">        <span class="key">if</span> <span class="nam">corrtype1</span> <span class="op">==</span> <span class="str">"circular"</span> <span class="key">and</span> <span class="nam">corrtype2</span> <span class="op">==</span> <span class="str">"linear"</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t234" href="#t234">234</a></span><span class="t">            <span class="nam">method</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">circlineal</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t235" href="#t235">235</a></span><span class="t">        <span class="key">if</span> <span class="nam">corrtype1</span> <span class="op">==</span> <span class="str">"linear"</span> <span class="key">and</span> <span class="nam">corrtype2</span> <span class="op">==</span> <span class="str">"circular"</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t236" href="#t236">236</a></span><span class="t">            <span class="nam">method</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">circlineal</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t237" href="#t237">237</a></span><span class="t">        <span class="key">elif</span> <span class="nam">corrtype1</span> <span class="op">==</span> <span class="str">"circular"</span> <span class="key">and</span> <span class="nam">corrtype2</span> <span class="op">==</span> <span class="str">"circular"</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t238" href="#t238">238</a></span><span class="t">            <span class="nam">method</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">circular</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t239" href="#t239">239</a></span><span class="t">        <span class="key">else</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t240" href="#t240">240</a></span><span class="t">            <span class="nam">method</span> <span class="op">=</span> <span class="str">"pearson"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t241" href="#t241">241</a></span><span class="t">        <span class="key">return</span> <span class="nam">method</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t242" href="#t242">242</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t243" href="#t243">243</a></span><span class="t">    <span class="op">@</span><span class="nam">staticmethod</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t244" href="#t244">244</a></span><span class="t">    <span class="key">def</span> <span class="nam">circular</span><span class="op">(</span><span class="nam">x1</span><span class="op">,</span> <span class="nam">x2</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t245" href="#t245">245</a></span><span class="t">        <span class="nam">x1</span> <span class="op">=</span> <span class="nam">x1</span> <span class="op">*</span> <span class="nam">np</span><span class="op">.</span><span class="nam">pi</span> <span class="op">/</span> <span class="num">180</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t246" href="#t246">246</a></span><span class="t">        <span class="nam">x2</span> <span class="op">=</span> <span class="nam">x2</span> <span class="op">*</span> <span class="nam">np</span><span class="op">.</span><span class="nam">pi</span> <span class="op">/</span> <span class="num">180</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t247" href="#t247">247</a></span><span class="t">        <span class="nam">diff_1</span> <span class="op">=</span> <span class="nam">np</span><span class="op">.</span><span class="nam">sin</span><span class="op">(</span><span class="nam">x1</span> <span class="op">-</span> <span class="nam">x1</span><span class="op">.</span><span class="nam">mean</span><span class="op">(</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t248" href="#t248">248</a></span><span class="t">        <span class="nam">diff_2</span> <span class="op">=</span> <span class="nam">np</span><span class="op">.</span><span class="nam">sin</span><span class="op">(</span><span class="nam">x2</span> <span class="op">-</span> <span class="nam">x2</span><span class="op">.</span><span class="nam">mean</span><span class="op">(</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t249" href="#t249">249</a></span><span class="t">        <span class="nam">num</span> <span class="op">=</span> <span class="op">(</span><span class="nam">diff_1</span> <span class="op">*</span> <span class="nam">diff_2</span><span class="op">)</span><span class="op">.</span><span class="nam">sum</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t250" href="#t250">250</a></span><span class="t">        <span class="nam">den</span> <span class="op">=</span> <span class="nam">np</span><span class="op">.</span><span class="nam">sqrt</span><span class="op">(</span><span class="op">(</span><span class="nam">diff_1</span> <span class="op">**</span> <span class="num">2</span><span class="op">)</span><span class="op">.</span><span class="nam">sum</span><span class="op">(</span><span class="op">)</span> <span class="op">*</span> <span class="op">(</span><span class="nam">diff_2</span> <span class="op">**</span> <span class="num">2</span><span class="op">)</span><span class="op">.</span><span class="nam">sum</span><span class="op">(</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t251" href="#t251">251</a></span><span class="t">        <span class="key">return</span> <span class="nam">num</span> <span class="op">/</span> <span class="nam">den</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t252" href="#t252">252</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t253" href="#t253">253</a></span><span class="t">    <span class="op">@</span><span class="nam">staticmethod</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t254" href="#t254">254</a></span><span class="t">    <span class="key">def</span> <span class="nam">circlineal</span><span class="op">(</span><span class="nam">x1</span><span class="op">,</span> <span class="nam">x2</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t255" href="#t255">255</a></span><span class="t">        <span class="nam">x2</span> <span class="op">=</span> <span class="nam">x2</span> <span class="op">*</span> <span class="nam">np</span><span class="op">.</span><span class="nam">pi</span> <span class="op">/</span> <span class="num">180</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t256" href="#t256">256</a></span><span class="t">        <span class="nam">rc</span> <span class="op">=</span> <span class="nam">np</span><span class="op">.</span><span class="nam">corrcoef</span><span class="op">(</span><span class="nam">x1</span><span class="op">,</span> <span class="nam">np</span><span class="op">.</span><span class="nam">cos</span><span class="op">(</span><span class="nam">x2</span><span class="op">)</span><span class="op">)</span><span class="op">[</span><span class="num">1</span><span class="op">,</span> <span class="num">0</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t257" href="#t257">257</a></span><span class="t">        <span class="nam">rs</span> <span class="op">=</span> <span class="nam">np</span><span class="op">.</span><span class="nam">corrcoef</span><span class="op">(</span><span class="nam">x1</span><span class="op">,</span> <span class="nam">np</span><span class="op">.</span><span class="nam">sin</span><span class="op">(</span><span class="nam">x2</span><span class="op">)</span><span class="op">)</span><span class="op">[</span><span class="num">1</span><span class="op">,</span> <span class="num">0</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t258" href="#t258">258</a></span><span class="t">        <span class="nam">rcs</span> <span class="op">=</span> <span class="nam">np</span><span class="op">.</span><span class="nam">corrcoef</span><span class="op">(</span><span class="nam">np</span><span class="op">.</span><span class="nam">sin</span><span class="op">(</span><span class="nam">x2</span><span class="op">)</span><span class="op">,</span> <span class="nam">np</span><span class="op">.</span><span class="nam">cos</span><span class="op">(</span><span class="nam">x2</span><span class="op">)</span><span class="op">)</span><span class="op">[</span><span class="num">1</span><span class="op">,</span> <span class="num">0</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t259" href="#t259">259</a></span><span class="t">        <span class="nam">num</span> <span class="op">=</span> <span class="op">(</span><span class="nam">rc</span> <span class="op">**</span> <span class="num">2</span><span class="op">)</span> <span class="op">+</span> <span class="op">(</span><span class="nam">rs</span> <span class="op">**</span> <span class="num">2</span><span class="op">)</span> <span class="op">-</span> <span class="num">2</span> <span class="op">*</span> <span class="nam">rc</span> <span class="op">*</span> <span class="nam">rs</span> <span class="op">*</span> <span class="nam">rcs</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t260" href="#t260">260</a></span><span class="t">        <span class="nam">den</span> <span class="op">=</span> <span class="num">1</span> <span class="op">-</span> <span class="op">(</span><span class="nam">rcs</span> <span class="op">**</span> <span class="num">2</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t261" href="#t261">261</a></span><span class="t">        <span class="nam">correlation</span> <span class="op">=</span> <span class="nam">np</span><span class="op">.</span><span class="nam">sqrt</span><span class="op">(</span><span class="nam">num</span> <span class="op">/</span> <span class="nam">den</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t262" href="#t262">262</a></span><span class="t">        <span class="key">if</span> <span class="nam">np</span><span class="op">.</span><span class="nam">corrcoef</span><span class="op">(</span><span class="nam">x1</span><span class="op">,</span> <span class="nam">x2</span><span class="op">)</span><span class="op">[</span><span class="num">1</span><span class="op">,</span> <span class="num">0</span><span class="op">]</span> <span class="op">&lt;</span> <span class="num">0</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t263" href="#t263">263</a></span><span class="t">            <span class="nam">correlation</span> <span class="op">*=</span> <span class="op">-</span><span class="num">1</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t264" href="#t264">264</a></span><span class="t">        <span class="key">return</span> <span class="nam">correlation</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t265" href="#t265">265</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t266" href="#t266">266</a></span><span class="t"><span class="key">def</span> <span class="nam">intrahpcorr</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t267" href="#t267">267</a></span><span class="t">        <span class="nam">input_filename_shear</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span> <span class="nam">input_filename_stretch</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t268" href="#t268">268</a></span><span class="t">        <span class="nam">input_filename_stagger</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span> <span class="nam">input_filename_buckle</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t269" href="#t269">269</a></span><span class="t">        <span class="nam">input_filename_propel</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span> <span class="nam">input_filename_opening</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t270" href="#t270">270</a></span><span class="t">        <span class="nam">output_csv_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span> <span class="nam">output_jpg_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t271" href="#t271">271</a></span><span class="t">        <span class="nam">properties</span><span class="op">:</span> <span class="nam">dict</span> <span class="op">=</span> <span class="key">None</span><span class="op">,</span> <span class="op">**</span><span class="nam">kwargs</span><span class="op">)</span> <span class="op">-></span> <span class="nam">int</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t272" href="#t272">272</a></span><span class="t">    <span class="str">"""Create :class:`IntraHelParCorrelation &lt;intrabp_correlations.intrahpcorr.IntraHelParCorrelation>` class and</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t273" href="#t273">273</a></span><span class="t"><span class="str">    execute the :meth:`launch() &lt;intrabp_correlations.intrahpcorr.IntraHelParCorrelation.launch>` method."""</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t274" href="#t274">274</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t275" href="#t275">275</a></span><span class="t">    <span class="key">return</span> <span class="nam">IntraHelParCorrelation</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t276" href="#t276">276</a></span><span class="t">        <span class="nam">input_filename_shear</span><span class="op">=</span><span class="nam">input_filename_shear</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t277" href="#t277">277</a></span><span class="t">        <span class="nam">input_filename_stretch</span><span class="op">=</span><span class="nam">input_filename_stretch</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t278" href="#t278">278</a></span><span class="t">        <span class="nam">input_filename_stagger</span><span class="op">=</span><span class="nam">input_filename_stagger</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t279" href="#t279">279</a></span><span class="t">        <span class="nam">input_filename_buckle</span><span class="op">=</span><span class="nam">input_filename_buckle</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t280" href="#t280">280</a></span><span class="t">        <span class="nam">input_filename_propel</span><span class="op">=</span><span class="nam">input_filename_propel</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t281" href="#t281">281</a></span><span class="t">        <span class="nam">input_filename_opening</span><span class="op">=</span><span class="nam">input_filename_opening</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t282" href="#t282">282</a></span><span class="t">        <span class="nam">output_csv_path</span><span class="op">=</span><span class="nam">output_csv_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t283" href="#t283">283</a></span><span class="t">        <span class="nam">output_jpg_path</span><span class="op">=</span><span class="nam">output_jpg_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t284" href="#t284">284</a></span><span class="t">        <span class="nam">properties</span><span class="op">=</span><span class="nam">properties</span><span class="op">,</span> <span class="op">**</span><span class="nam">kwargs</span><span class="op">)</span><span class="op">.</span><span class="nam">launch</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t285" href="#t285">285</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t266" href="#t266">266</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t267" href="#t267">267</a></span><span class="t"><span class="key">def</span> <span class="nam">intrahpcorr</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t268" href="#t268">268</a></span><span class="t">        <span class="nam">input_filename_shear</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span> <span class="nam">input_filename_stretch</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t269" href="#t269">269</a></span><span class="t">        <span class="nam">input_filename_stagger</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span> <span class="nam">input_filename_buckle</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t270" href="#t270">270</a></span><span class="t">        <span class="nam">input_filename_propel</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span> <span class="nam">input_filename_opening</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t271" href="#t271">271</a></span><span class="t">        <span class="nam">output_csv_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span> <span class="nam">output_jpg_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t272" href="#t272">272</a></span><span class="t">        <span class="nam">properties</span><span class="op">:</span> <span class="nam">dict</span> <span class="op">=</span> <span class="key">None</span><span class="op">,</span> <span class="op">**</span><span class="nam">kwargs</span><span class="op">)</span> <span class="op">-></span> <span class="nam">int</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t273" href="#t273">273</a></span><span class="t">    <span class="str">"""Create :class:`IntraHelParCorrelation &lt;intrabp_correlations.intrahpcorr.IntraHelParCorrelation>` class and</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t274" href="#t274">274</a></span><span class="t"><span class="str">    execute the :meth:`launch() &lt;intrabp_correlations.intrahpcorr.IntraHelParCorrelation.launch>` method."""</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t275" href="#t275">275</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t276" href="#t276">276</a></span><span class="t">    <span class="key">return</span> <span class="nam">IntraHelParCorrelation</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t277" href="#t277">277</a></span><span class="t">        <span class="nam">input_filename_shear</span><span class="op">=</span><span class="nam">input_filename_shear</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t278" href="#t278">278</a></span><span class="t">        <span class="nam">input_filename_stretch</span><span class="op">=</span><span class="nam">input_filename_stretch</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t279" href="#t279">279</a></span><span class="t">        <span class="nam">input_filename_stagger</span><span class="op">=</span><span class="nam">input_filename_stagger</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t280" href="#t280">280</a></span><span class="t">        <span class="nam">input_filename_buckle</span><span class="op">=</span><span class="nam">input_filename_buckle</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t281" href="#t281">281</a></span><span class="t">        <span class="nam">input_filename_propel</span><span class="op">=</span><span class="nam">input_filename_propel</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t282" href="#t282">282</a></span><span class="t">        <span class="nam">input_filename_opening</span><span class="op">=</span><span class="nam">input_filename_opening</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t283" href="#t283">283</a></span><span class="t">        <span class="nam">output_csv_path</span><span class="op">=</span><span class="nam">output_csv_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t284" href="#t284">284</a></span><span class="t">        <span class="nam">output_jpg_path</span><span class="op">=</span><span class="nam">output_jpg_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t285" href="#t285">285</a></span><span class="t">        <span class="nam">properties</span><span class="op">=</span><span class="nam">properties</span><span class="op">,</span> <span class="op">**</span><span class="nam">kwargs</span><span class="op">)</span><span class="op">.</span><span class="nam">launch</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t286" href="#t286">286</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t287" href="#t287">287</a></span><span class="t"><span class="key">def</span> <span class="nam">main</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t288" href="#t288">288</a></span><span class="t">    <span class="str">"""Command line execution of this building block. Please check the command line documentation."""</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t289" href="#t289">289</a></span><span class="t">    <span class="nam">parser</span> <span class="op">=</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">ArgumentParser</span><span class="op">(</span><span class="nam">description</span><span class="op">=</span><span class="str">'Load helical parameter file and save base data individually.'</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t290" href="#t290">290</a></span><span class="t">                                     <span class="nam">formatter_class</span><span class="op">=</span><span class="key">lambda</span> <span class="nam">prog</span><span class="op">:</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">RawTextHelpFormatter</span><span class="op">(</span><span class="nam">prog</span><span class="op">,</span> <span class="nam">width</span><span class="op">=</span><span class="num">99999</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t291" href="#t291">291</a></span><span class="t">    <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--config'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">False</span><span class="op">,</span> <span class="nam">help</span><span class="op">=</span><span class="str">'Configuration file'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t292" href="#t292">292</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t293" href="#t293">293</a></span><span class="t">    <span class="nam">required_args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument_group</span><span class="op">(</span><span class="str">'required arguments'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t294" href="#t294">294</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--input_filename_shear'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t295" href="#t295">295</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Path to csv file with inputs. Accepted formats: csv.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t296" href="#t296">296</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--input_filename_stretch'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t297" href="#t297">297</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Path to csv file with inputs. Accepted formats: csv.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t298" href="#t298">298</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--input_filename_stagger'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t299" href="#t299">299</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Path to csv file with inputs. Accepted formats: csv.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t300" href="#t300">300</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--input_filename_buckle'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t301" href="#t301">301</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Path to csv file with inputs. Accepted formats: csv.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t302" href="#t302">302</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--input_filename_propel'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t303" href="#t303">303</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Path to csv file with inputs. Accepted formats: csv.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t304" href="#t304">304</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--input_filename_opening'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t305" href="#t305">305</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Path to csv file with inputs. Accepted formats: csv.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t306" href="#t306">306</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--output_csv_path'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t307" href="#t307">307</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Path to output file. Accepted formats: csv.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t308" href="#t308">308</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--output_jpg_path'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t309" href="#t309">309</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Path to output file. Accepted formats: csv.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t310" href="#t310">310</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t311" href="#t311">311</a></span><span class="t">    <span class="nam">args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">parse_args</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t312" href="#t312">312</a></span><span class="t">    <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="op">=</span> <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="key">or</span> <span class="str">"{}"</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t313" href="#t313">313</a></span><span class="t">    <span class="nam">properties</span> <span class="op">=</span> <span class="nam">settings</span><span class="op">.</span><span class="nam">ConfReader</span><span class="op">(</span><span class="nam">config</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">config</span><span class="op">)</span><span class="op">.</span><span class="nam">get_prop_dic</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t314" href="#t314">314</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t315" href="#t315">315</a></span><span class="t">    <span class="nam">intrahpcorr</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t316" href="#t316">316</a></span><span class="t">        <span class="nam">input_filename_shear</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_filename_shear</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t317" href="#t317">317</a></span><span class="t">        <span class="nam">input_filename_stretch</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_filename_stretch</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t318" href="#t318">318</a></span><span class="t">        <span class="nam">input_filename_stagger</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_filename_stagger</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t319" href="#t319">319</a></span><span class="t">        <span class="nam">input_filename_buckle</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_filename_buckle</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t320" href="#t320">320</a></span><span class="t">        <span class="nam">input_filename_propel</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_filename_propel</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t321" href="#t321">321</a></span><span class="t">        <span class="nam">input_filename_opening</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_filename_opening</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t322" href="#t322">322</a></span><span class="t">        <span class="nam">output_csv_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">output_csv_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t323" href="#t323">323</a></span><span class="t">        <span class="nam">output_jpg_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">output_jpg_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t324" href="#t324">324</a></span><span class="t">        <span class="nam">properties</span><span class="op">=</span><span class="nam">properties</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t325" href="#t325">325</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t287" href="#t287">287</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t288" href="#t288">288</a></span><span class="t"><span class="key">def</span> <span class="nam">main</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t289" href="#t289">289</a></span><span class="t">    <span class="str">"""Command line execution of this building block. Please check the command line documentation."""</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t290" href="#t290">290</a></span><span class="t">    <span class="nam">parser</span> <span class="op">=</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">ArgumentParser</span><span class="op">(</span><span class="nam">description</span><span class="op">=</span><span class="str">'Load helical parameter file and save base data individually.'</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t291" href="#t291">291</a></span><span class="t">                                     <span class="nam">formatter_class</span><span class="op">=</span><span class="key">lambda</span> <span class="nam">prog</span><span class="op">:</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">RawTextHelpFormatter</span><span class="op">(</span><span class="nam">prog</span><span class="op">,</span> <span class="nam">width</span><span class="op">=</span><span class="num">99999</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t292" href="#t292">292</a></span><span class="t">    <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--config'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">False</span><span class="op">,</span> <span class="nam">help</span><span class="op">=</span><span class="str">'Configuration file'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t293" href="#t293">293</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t294" href="#t294">294</a></span><span class="t">    <span class="nam">required_args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument_group</span><span class="op">(</span><span class="str">'required arguments'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t295" href="#t295">295</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--input_filename_shear'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t296" href="#t296">296</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Path to csv file with inputs. Accepted formats: csv.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t297" href="#t297">297</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--input_filename_stretch'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t298" href="#t298">298</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Path to csv file with inputs. Accepted formats: csv.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t299" href="#t299">299</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--input_filename_stagger'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t300" href="#t300">300</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Path to csv file with inputs. Accepted formats: csv.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t301" href="#t301">301</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--input_filename_buckle'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t302" href="#t302">302</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Path to csv file with inputs. Accepted formats: csv.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t303" href="#t303">303</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--input_filename_propel'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t304" href="#t304">304</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Path to csv file with inputs. Accepted formats: csv.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t305" href="#t305">305</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--input_filename_opening'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t306" href="#t306">306</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Path to csv file with inputs. Accepted formats: csv.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t307" href="#t307">307</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--output_csv_path'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t308" href="#t308">308</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Path to output file. Accepted formats: csv.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t309" href="#t309">309</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--output_jpg_path'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t310" href="#t310">310</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Path to output file. Accepted formats: csv.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t311" href="#t311">311</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t312" href="#t312">312</a></span><span class="t">    <span class="nam">args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">parse_args</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t313" href="#t313">313</a></span><span class="t">    <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="op">=</span> <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="key">or</span> <span class="str">"{}"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t314" href="#t314">314</a></span><span class="t">    <span class="nam">properties</span> <span class="op">=</span> <span class="nam">settings</span><span class="op">.</span><span class="nam">ConfReader</span><span class="op">(</span><span class="nam">config</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">config</span><span class="op">)</span><span class="op">.</span><span class="nam">get_prop_dic</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t315" href="#t315">315</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t316" href="#t316">316</a></span><span class="t">    <span class="nam">intrahpcorr</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t317" href="#t317">317</a></span><span class="t">        <span class="nam">input_filename_shear</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_filename_shear</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t318" href="#t318">318</a></span><span class="t">        <span class="nam">input_filename_stretch</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_filename_stretch</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t319" href="#t319">319</a></span><span class="t">        <span class="nam">input_filename_stagger</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_filename_stagger</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t320" href="#t320">320</a></span><span class="t">        <span class="nam">input_filename_buckle</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_filename_buckle</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t321" href="#t321">321</a></span><span class="t">        <span class="nam">input_filename_propel</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_filename_propel</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t322" href="#t322">322</a></span><span class="t">        <span class="nam">input_filename_opening</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_filename_opening</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t323" href="#t323">323</a></span><span class="t">        <span class="nam">output_csv_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">output_csv_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t324" href="#t324">324</a></span><span class="t">        <span class="nam">output_jpg_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">output_jpg_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t325" href="#t325">325</a></span><span class="t">        <span class="nam">properties</span><span class="op">=</span><span class="nam">properties</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t326" href="#t326">326</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t327" href="#t327">327</a></span><span class="t"><span class="key">if</span> <span class="nam">__name__</span> <span class="op">==</span> <span class="str">'__main__'</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t328" href="#t328">328</a></span><span class="t">    <span class="nam">main</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t327" href="#t327">327</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t328" href="#t328">328</a></span><span class="t"><span class="key">if</span> <span class="nam">__name__</span> <span class="op">==</span> <span class="str">'__main__'</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t329" href="#t329">329</a></span><span class="t">    <span class="nam">main</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
 </main>
 <footer>
     <div class="content">
@@ -417,7 +418,7 @@ <h2>
             <a class="nav" href="z_64e03be4370b7ecc_intraseqcorr_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.5.1">coverage.py v7.5.1</a>,
-            created at 2024-05-07 09:06 +0000
+            created at 2024-05-24 09:29 +0000
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 </footer>
diff --git a/coverage/z_64e03be4370b7ecc_intraseqcorr_py.html b/coverage/z_64e03be4370b7ecc_intraseqcorr_py.html
index 53c60dd3..42c56360 100644
--- a/coverage/z_64e03be4370b7ecc_intraseqcorr_py.html
+++ b/coverage/z_64e03be4370b7ecc_intraseqcorr_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_9de9475b0a6fab52___init___py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.5.1">coverage.py v7.5.1</a>,
-            created at 2024-05-07 09:06 +0000
+            created at 2024-05-24 09:29 +0000
         </p>
         <aside class="hidden">
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@@ -101,221 +101,222 @@ <h2>
     <p class="pln"><span class="n"><a id="t19" href="#t19">19</a></span><span class="t">    <span class="str">"""</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t20" href="#t20">20</a></span><span class="t"><span class="str">    | biobb_dna IntraSequenceCorrelation</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t21" href="#t21">21</a></span><span class="t"><span class="str">    | Calculate correlation between all intra-base pairs of a single sequence and for a single helical parameter.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t22" href="#t22">22</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t23" href="#t23">23</a></span><span class="t"><span class="str">    Args:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t24" href="#t24">24</a></span><span class="t"><span class="str">        input_ser_path (str): Path to .ser file with data for single helical parameter. File type: input. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/correlation/canal_output_buckle.ser>`_. Accepted formats: ser (edam:format_2330).</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t25" href="#t25">25</a></span><span class="t"><span class="str">        output_csv_path (str): Path to directory where output is saved. File type: output. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/reference/correlation/intra_seqcorr_buckle.csv>`_. Accepted formats: csv (edam:format_3752).</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t26" href="#t26">26</a></span><span class="t"><span class="str">        output_jpg_path (str): Path to .jpg file where output is saved. File type: output. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/reference/correlation/intra_seqcorr_buckle.jpg>`_. Accepted formats: jpg (edam:format_3579).</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t27" href="#t27">27</a></span><span class="t"><span class="str">        properties (dict):</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t28" href="#t28">28</a></span><span class="t"><span class="str">            * **sequence** (*str*) - (None) Nucleic acid sequence for the input .ser file. Length of sequence is expected to be the same as the total number of columns in the .ser file, minus the index column (even if later on a subset of columns is selected with the *seqpos* option).</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t29" href="#t29">29</a></span><span class="t"><span class="str">            * **helpar_name** (*str*) - (None) helical parameter name to add to plot title.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t30" href="#t30">30</a></span><span class="t"><span class="str">            * **seqpos** (*list*) - (None) list of sequence positions (columns indices starting by 0) to analyze.  If not specified it will analyse the complete sequence.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t31" href="#t31">31</a></span><span class="t"><span class="str">            * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t32" href="#t32">32</a></span><span class="t"><span class="str">            * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t33" href="#t33">33</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t34" href="#t34">34</a></span><span class="t"><span class="str">    Examples:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t35" href="#t35">35</a></span><span class="t"><span class="str">        This is a use example of how to use the building block from Python::</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t36" href="#t36">36</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t37" href="#t37">37</a></span><span class="t"><span class="str">            from biobb_dna.intrabp_correlations.intraseqcorr import intraseqcorr</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t38" href="#t38">38</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t39" href="#t39">39</a></span><span class="t"><span class="str">            intraseqcorr(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t40" href="#t40">40</a></span><span class="t"><span class="str">                input_ser_path='path/to/input/file.ser',</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t41" href="#t41">41</a></span><span class="t"><span class="str">                output_csv_path='path/to/output/file.csv',</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t42" href="#t42">42</a></span><span class="t"><span class="str">                output_jpg_path='path/to/output/plot.jpg',</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t43" href="#t43">43</a></span><span class="t"><span class="str">                properties=prop)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t44" href="#t44">44</a></span><span class="t"><span class="str">    Info:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t45" href="#t45">45</a></span><span class="t"><span class="str">        * wrapped_software:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t46" href="#t46">46</a></span><span class="t"><span class="str">            * name: In house</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t47" href="#t47">47</a></span><span class="t"><span class="str">            * license: Apache-2.0</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t48" href="#t48">48</a></span><span class="t"><span class="str">        * ontology:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t49" href="#t49">49</a></span><span class="t"><span class="str">            * name: EDAM</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t50" href="#t50">50</a></span><span class="t"><span class="str">            * schema: http://edamontology.org/EDAM.owl</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t51" href="#t51">51</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t52" href="#t52">52</a></span><span class="t"><span class="str">    """</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t53" href="#t53">53</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t54" href="#t54">54</a></span><span class="t">    <span class="key">def</span> <span class="nam">__init__</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t55" href="#t55">55</a></span><span class="t">            <span class="nam">self</span><span class="op">,</span> <span class="nam">input_ser_path</span><span class="op">,</span> <span class="nam">output_csv_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t56" href="#t56">56</a></span><span class="t">            <span class="nam">output_jpg_path</span><span class="op">,</span> <span class="nam">properties</span><span class="op">=</span><span class="key">None</span><span class="op">,</span> <span class="op">**</span><span class="nam">kwargs</span><span class="op">)</span> <span class="op">-></span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t57" href="#t57">57</a></span><span class="t">        <span class="nam">properties</span> <span class="op">=</span> <span class="nam">properties</span> <span class="key">or</span> <span class="op">{</span><span class="op">}</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t58" href="#t58">58</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t59" href="#t59">59</a></span><span class="t">        <span class="com"># Call parent class constructor</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t60" href="#t60">60</a></span><span class="t">        <span class="nam">super</span><span class="op">(</span><span class="op">)</span><span class="op">.</span><span class="nam">__init__</span><span class="op">(</span><span class="nam">properties</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t61" href="#t61">61</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">locals_var_dict</span> <span class="op">=</span> <span class="nam">locals</span><span class="op">(</span><span class="op">)</span><span class="op">.</span><span class="nam">copy</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t62" href="#t62">62</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t63" href="#t63">63</a></span><span class="t">        <span class="com"># Input/Output files</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t64" href="#t64">64</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span> <span class="op">=</span> <span class="op">{</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t65" href="#t65">65</a></span><span class="t">            <span class="str">'in'</span><span class="op">:</span> <span class="op">{</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t66" href="#t66">66</a></span><span class="t">                <span class="str">'input_ser_path'</span><span class="op">:</span> <span class="nam">input_ser_path</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t67" href="#t67">67</a></span><span class="t">            <span class="op">}</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t68" href="#t68">68</a></span><span class="t">            <span class="str">'out'</span><span class="op">:</span> <span class="op">{</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t69" href="#t69">69</a></span><span class="t">                <span class="str">'output_csv_path'</span><span class="op">:</span> <span class="nam">output_csv_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t70" href="#t70">70</a></span><span class="t">                <span class="str">'output_jpg_path'</span><span class="op">:</span> <span class="nam">output_jpg_path</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t71" href="#t71">71</a></span><span class="t">            <span class="op">}</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t72" href="#t72">72</a></span><span class="t">        <span class="op">}</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t73" href="#t73">73</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t74" href="#t74">74</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">properties</span> <span class="op">=</span> <span class="nam">properties</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t75" href="#t75">75</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"sequence"</span><span class="op">,</span> <span class="key">None</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t76" href="#t76">76</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"seqpos"</span><span class="op">,</span> <span class="key">None</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t77" href="#t77">77</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">helpar_name</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"helpar_name"</span><span class="op">,</span> <span class="key">None</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t78" href="#t78">78</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t79" href="#t79">79</a></span><span class="t">        <span class="com"># Check the properties</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t80" href="#t80">80</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_properties</span><span class="op">(</span><span class="nam">properties</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t81" href="#t81">81</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_arguments</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t82" href="#t82">82</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t83" href="#t83">83</a></span><span class="t">    <span class="op">@</span><span class="nam">launchlogger</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t84" href="#t84">84</a></span><span class="t">    <span class="key">def</span> <span class="nam">launch</span><span class="op">(</span><span class="nam">self</span><span class="op">)</span> <span class="op">-></span> <span class="nam">int</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t85" href="#t85">85</a></span><span class="t">        <span class="str">"""Execute the :class:`HelParCorrelation &lt;intrabp_correlations.intraseqcorr.IntraSequenceCorrelation>` object."""</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t86" href="#t86">86</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t87" href="#t87">87</a></span><span class="t">        <span class="com"># Setup Biobb</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t88" href="#t88">88</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">check_restart</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t89" href="#t89">89</a></span><span class="t">            <span class="key">return</span> <span class="num">0</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t90" href="#t90">90</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">stage_files</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t91" href="#t91">91</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t92" href="#t92">92</a></span><span class="t">        <span class="com"># check sequence</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t93" href="#t93">93</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span> <span class="key">is</span> <span class="key">None</span> <span class="key">or</span> <span class="nam">len</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span><span class="op">)</span> <span class="op">&lt;</span> <span class="num">2</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t94" href="#t94">94</a></span><span class="t">            <span class="key">raise</span> <span class="nam">ValueError</span><span class="op">(</span><span class="str">"sequence is null or too short!"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t95" href="#t95">95</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t96" href="#t96">96</a></span><span class="t">        <span class="com"># get helical parameter from filename if not specified</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t97" href="#t97">97</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">helpar_name</span> <span class="key">is</span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t98" href="#t98">98</a></span><span class="t">            <span class="key">for</span> <span class="nam">hp</span> <span class="key">in</span> <span class="nam">constants</span><span class="op">.</span><span class="nam">helical_parameters</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t99" href="#t99">99</a></span><span class="t">                <span class="key">if</span> <span class="nam">hp</span><span class="op">.</span><span class="nam">lower</span><span class="op">(</span><span class="op">)</span> <span class="key">in</span> <span class="nam">Path</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t100" href="#t100">100</a></span><span class="t">                        <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'input_ser_path'</span><span class="op">]</span><span class="op">)</span><span class="op">.</span><span class="nam">name</span><span class="op">.</span><span class="nam">lower</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t101" href="#t101">101</a></span><span class="t">                    <span class="nam">self</span><span class="op">.</span><span class="nam">helpar_name</span> <span class="op">=</span> <span class="nam">hp</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t102" href="#t102">102</a></span><span class="t">            <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">helpar_name</span> <span class="key">is</span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t103" href="#t103">103</a></span><span class="t">                <span class="key">raise</span> <span class="nam">ValueError</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t104" href="#t104">104</a></span><span class="t">                    <span class="str">"Helical parameter name can't be inferred from file, "</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t105" href="#t105">105</a></span><span class="t">                    <span class="str">"so it must be specified!"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t106" href="#t106">106</a></span><span class="t">        <span class="key">else</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t107" href="#t107">107</a></span><span class="t">            <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">helpar_name</span> <span class="key">not</span> <span class="key">in</span> <span class="nam">constants</span><span class="op">.</span><span class="nam">helical_parameters</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t108" href="#t108">108</a></span><span class="t">                <span class="key">raise</span> <span class="nam">ValueError</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t109" href="#t109">109</a></span><span class="t">                    <span class="str">"Helical parameter name is invalid! "</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t110" href="#t110">110</a></span><span class="t">                    <span class="str">f"Options: {constants.helical_parameters}"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t111" href="#t111">111</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t112" href="#t112">112</a></span><span class="t">        <span class="com"># get base length and unit from helical parameter name</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t113" href="#t113">113</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">helpar_name</span> <span class="key">in</span> <span class="nam">constants</span><span class="op">.</span><span class="nam">hp_angular</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t114" href="#t114">114</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">method</span> <span class="op">=</span> <span class="str">"pearson"</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t115" href="#t115">115</a></span><span class="t">        <span class="key">else</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t116" href="#t116">116</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">method</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">circular</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t117" href="#t117">117</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t118" href="#t118">118</a></span><span class="t">        <span class="com"># check seqpos</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t119" href="#t119">119</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span> <span class="key">is</span> <span class="key">not</span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t120" href="#t120">120</a></span><span class="t">            <span class="key">if</span> <span class="key">not</span> <span class="op">(</span><span class="nam">isinstance</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">,</span> <span class="nam">list</span><span class="op">)</span> <span class="key">and</span> <span class="nam">len</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">)</span> <span class="op">></span> <span class="num">1</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t121" href="#t121">121</a></span><span class="t">                <span class="key">raise</span> <span class="nam">ValueError</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t122" href="#t122">122</a></span><span class="t">                    <span class="str">"seqpos must be a list of at least two integers"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t123" href="#t123">123</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t124" href="#t124">124</a></span><span class="t">        <span class="com"># Creating temporary folder</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t125" href="#t125">125</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span> <span class="op">=</span> <span class="nam">fu</span><span class="op">.</span><span class="nam">create_unique_dir</span><span class="op">(</span><span class="nam">prefix</span><span class="op">=</span><span class="str">"bpcorrelation_"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t126" href="#t126">126</a></span><span class="t">        <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="str">'Creating %s temporary folder'</span> <span class="op">%</span> <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t127" href="#t127">127</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t128" href="#t128">128</a></span><span class="t">        <span class="com"># read input .ser file</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t129" href="#t129">129</a></span><span class="t">        <span class="nam">ser_data</span> <span class="op">=</span> <span class="nam">read_series</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t130" href="#t130">130</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'input_ser_path'</span><span class="op">]</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t131" href="#t131">131</a></span><span class="t">            <span class="nam">usecols</span><span class="op">=</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t132" href="#t132">132</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span> <span class="key">is</span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t133" href="#t133">133</a></span><span class="t">            <span class="nam">ser_data</span> <span class="op">=</span> <span class="nam">ser_data</span><span class="op">[</span><span class="nam">ser_data</span><span class="op">.</span><span class="nam">columns</span><span class="op">[</span><span class="num">1</span><span class="op">:</span><span class="op">-</span><span class="num">1</span><span class="op">]</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t134" href="#t134">134</a></span><span class="t">            <span class="com"># discard first and last base(pairs) from strands</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t135" href="#t135">135</a></span><span class="t">            <span class="nam">sequence</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span><span class="op">[</span><span class="num">1</span><span class="op">:</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t136" href="#t136">136</a></span><span class="t">            <span class="nam">labels</span> <span class="op">=</span> <span class="op">[</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t137" href="#t137">137</a></span><span class="t">                <span class="str">f"{i+1}_{sequence[i:i+1]}"</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">range</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">ser_data</span><span class="op">.</span><span class="nam">columns</span><span class="op">)</span><span class="op">)</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t138" href="#t138">138</a></span><span class="t">        <span class="key">else</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t139" href="#t139">139</a></span><span class="t">            <span class="nam">labels</span> <span class="op">=</span> <span class="op">[</span><span class="str">f"{i+1}_{self.sequence[i:i+1]}"</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t140" href="#t140">140</a></span><span class="t">        <span class="nam">ser_data</span><span class="op">.</span><span class="nam">columns</span> <span class="op">=</span> <span class="nam">labels</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t141" href="#t141">141</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t142" href="#t142">142</a></span><span class="t">        <span class="com"># make matrix</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t143" href="#t143">143</a></span><span class="t">        <span class="nam">corr_data</span> <span class="op">=</span> <span class="nam">ser_data</span><span class="op">.</span><span class="nam">corr</span><span class="op">(</span><span class="nam">method</span><span class="op">=</span><span class="nam">self</span><span class="op">.</span><span class="nam">method</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t144" href="#t144">144</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t145" href="#t145">145</a></span><span class="t">        <span class="com"># save csv data</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t146" href="#t146">146</a></span><span class="t">        <span class="nam">corr_data</span><span class="op">.</span><span class="nam">to_csv</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">"out"</span><span class="op">]</span><span class="op">[</span><span class="str">"output_csv_path"</span><span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t147" href="#t147">147</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t148" href="#t148">148</a></span><span class="t">        <span class="com"># create heatmap</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t149" href="#t149">149</a></span><span class="t">        <span class="nam">fig</span><span class="op">,</span> <span class="nam">axs</span> <span class="op">=</span> <span class="nam">plt</span><span class="op">.</span><span class="nam">subplots</span><span class="op">(</span><span class="num">1</span><span class="op">,</span> <span class="num">1</span><span class="op">,</span> <span class="nam">dpi</span><span class="op">=</span><span class="num">300</span><span class="op">,</span> <span class="nam">tight_layout</span><span class="op">=</span><span class="key">True</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t150" href="#t150">150</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">pcolor</span><span class="op">(</span><span class="nam">corr_data</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t151" href="#t151">151</a></span><span class="t">        <span class="com"># Loop over data dimensions and create text annotations.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t152" href="#t152">152</a></span><span class="t">        <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">range</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">corr_data</span><span class="op">)</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t153" href="#t153">153</a></span><span class="t">            <span class="key">for</span> <span class="nam">j</span> <span class="key">in</span> <span class="nam">range</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">corr_data</span><span class="op">)</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t154" href="#t154">154</a></span><span class="t">                <span class="nam">axs</span><span class="op">.</span><span class="nam">text</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t155" href="#t155">155</a></span><span class="t">                    <span class="nam">j</span><span class="op">+</span><span class="num">.5</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t156" href="#t156">156</a></span><span class="t">                    <span class="nam">i</span><span class="op">+</span><span class="num">.5</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t157" href="#t157">157</a></span><span class="t">                    <span class="str">f"{corr_data[corr_data.columns[j]].iloc[i]:.2f}"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t158" href="#t158">158</a></span><span class="t">                    <span class="nam">ha</span><span class="op">=</span><span class="str">"center"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t159" href="#t159">159</a></span><span class="t">                    <span class="nam">va</span><span class="op">=</span><span class="str">"center"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t160" href="#t160">160</a></span><span class="t">                    <span class="nam">color</span><span class="op">=</span><span class="str">"w"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t161" href="#t161">161</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_xticks</span><span class="op">(</span><span class="op">[</span><span class="nam">i</span> <span class="op">+</span> <span class="num">0.5</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">range</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">corr_data</span><span class="op">)</span><span class="op">)</span><span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t162" href="#t162">162</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_xticklabels</span><span class="op">(</span><span class="nam">labels</span><span class="op">,</span> <span class="nam">rotation</span><span class="op">=</span><span class="num">90</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t163" href="#t163">163</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_yticks</span><span class="op">(</span><span class="op">[</span><span class="nam">i</span> <span class="op">+</span> <span class="num">0.5</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">range</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">corr_data</span><span class="op">)</span><span class="op">)</span><span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t164" href="#t164">164</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_yticklabels</span><span class="op">(</span><span class="nam">labels</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t165" href="#t165">165</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_title</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t166" href="#t166">166</a></span><span class="t">            <span class="str">"Base Pair Correlation "</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t167" href="#t167">167</a></span><span class="t">            <span class="str">f"for Helical Parameter \'{self.helpar_name}\'"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t168" href="#t168">168</a></span><span class="t">        <span class="nam">fig</span><span class="op">.</span><span class="nam">tight_layout</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t169" href="#t169">169</a></span><span class="t">        <span class="nam">fig</span><span class="op">.</span><span class="nam">savefig</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t170" href="#t170">170</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'out'</span><span class="op">]</span><span class="op">[</span><span class="str">'output_jpg_path'</span><span class="op">]</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t171" href="#t171">171</a></span><span class="t">            <span class="nam">format</span><span class="op">=</span><span class="str">"jpg"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t172" href="#t172">172</a></span><span class="t">        <span class="nam">plt</span><span class="op">.</span><span class="nam">close</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t173" href="#t173">173</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t174" href="#t174">174</a></span><span class="t">        <span class="com"># Remove temporary file(s)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t175" href="#t175">175</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_files</span><span class="op">.</span><span class="nam">extend</span><span class="op">(</span><span class="op">[</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t176" href="#t176">176</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"unique_dir"</span><span class="op">)</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t177" href="#t177">177</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t178" href="#t178">178</a></span><span class="t">        <span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t179" href="#t179">179</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">remove_tmp_files</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t180" href="#t180">180</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t181" href="#t181">181</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_arguments</span><span class="op">(</span><span class="nam">output_files_created</span><span class="op">=</span><span class="key">True</span><span class="op">,</span> <span class="nam">raise_exception</span><span class="op">=</span><span class="key">False</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t182" href="#t182">182</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t183" href="#t183">183</a></span><span class="t">        <span class="key">return</span> <span class="num">0</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t184" href="#t184">184</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t185" href="#t185">185</a></span><span class="t">    <span class="op">@</span><span class="nam">staticmethod</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t186" href="#t186">186</a></span><span class="t">    <span class="key">def</span> <span class="nam">circular</span><span class="op">(</span><span class="nam">x1</span><span class="op">,</span> <span class="nam">x2</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t187" href="#t187">187</a></span><span class="t">        <span class="nam">x1</span> <span class="op">=</span> <span class="nam">x1</span> <span class="op">*</span> <span class="nam">np</span><span class="op">.</span><span class="nam">pi</span> <span class="op">/</span> <span class="num">180</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t188" href="#t188">188</a></span><span class="t">        <span class="nam">x2</span> <span class="op">=</span> <span class="nam">x2</span> <span class="op">*</span> <span class="nam">np</span><span class="op">.</span><span class="nam">pi</span> <span class="op">/</span> <span class="num">180</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t189" href="#t189">189</a></span><span class="t">        <span class="nam">diff_1</span> <span class="op">=</span> <span class="nam">np</span><span class="op">.</span><span class="nam">sin</span><span class="op">(</span><span class="nam">x1</span> <span class="op">-</span> <span class="nam">x1</span><span class="op">.</span><span class="nam">mean</span><span class="op">(</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t190" href="#t190">190</a></span><span class="t">        <span class="nam">diff_2</span> <span class="op">=</span> <span class="nam">np</span><span class="op">.</span><span class="nam">sin</span><span class="op">(</span><span class="nam">x2</span> <span class="op">-</span> <span class="nam">x2</span><span class="op">.</span><span class="nam">mean</span><span class="op">(</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t191" href="#t191">191</a></span><span class="t">        <span class="nam">num</span> <span class="op">=</span> <span class="op">(</span><span class="nam">diff_1</span> <span class="op">*</span> <span class="nam">diff_2</span><span class="op">)</span><span class="op">.</span><span class="nam">sum</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t192" href="#t192">192</a></span><span class="t">        <span class="nam">den</span> <span class="op">=</span> <span class="nam">np</span><span class="op">.</span><span class="nam">sqrt</span><span class="op">(</span><span class="op">(</span><span class="nam">diff_1</span> <span class="op">**</span> <span class="num">2</span><span class="op">)</span><span class="op">.</span><span class="nam">sum</span><span class="op">(</span><span class="op">)</span> <span class="op">*</span> <span class="op">(</span><span class="nam">diff_2</span> <span class="op">**</span> <span class="num">2</span><span class="op">)</span><span class="op">.</span><span class="nam">sum</span><span class="op">(</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t193" href="#t193">193</a></span><span class="t">        <span class="key">return</span> <span class="nam">num</span> <span class="op">/</span> <span class="nam">den</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t194" href="#t194">194</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t22" href="#t22">22</a></span><span class="t"><span class="str">    | Calculate correlation between all intra-base pairs of a single sequence and for a single helical parameter.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t23" href="#t23">23</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t24" href="#t24">24</a></span><span class="t"><span class="str">    Args:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t25" href="#t25">25</a></span><span class="t"><span class="str">        input_ser_path (str): Path to .ser file with data for single helical parameter. File type: input. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/correlation/canal_output_buckle.ser>`_. Accepted formats: ser (edam:format_2330).</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t26" href="#t26">26</a></span><span class="t"><span class="str">        output_csv_path (str): Path to directory where output is saved. File type: output. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/reference/correlation/intra_seqcorr_buckle.csv>`_. Accepted formats: csv (edam:format_3752).</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t27" href="#t27">27</a></span><span class="t"><span class="str">        output_jpg_path (str): Path to .jpg file where output is saved. File type: output. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/reference/correlation/intra_seqcorr_buckle.jpg>`_. Accepted formats: jpg (edam:format_3579).</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t28" href="#t28">28</a></span><span class="t"><span class="str">        properties (dict):</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t29" href="#t29">29</a></span><span class="t"><span class="str">            * **sequence** (*str*) - (None) Nucleic acid sequence for the input .ser file. Length of sequence is expected to be the same as the total number of columns in the .ser file, minus the index column (even if later on a subset of columns is selected with the *seqpos* option).</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t30" href="#t30">30</a></span><span class="t"><span class="str">            * **helpar_name** (*str*) - (None) helical parameter name to add to plot title.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t31" href="#t31">31</a></span><span class="t"><span class="str">            * **seqpos** (*list*) - (None) list of sequence positions (columns indices starting by 0) to analyze.  If not specified it will analyse the complete sequence.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t32" href="#t32">32</a></span><span class="t"><span class="str">            * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t33" href="#t33">33</a></span><span class="t"><span class="str">            * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t34" href="#t34">34</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t35" href="#t35">35</a></span><span class="t"><span class="str">    Examples:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t36" href="#t36">36</a></span><span class="t"><span class="str">        This is a use example of how to use the building block from Python::</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t37" href="#t37">37</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t38" href="#t38">38</a></span><span class="t"><span class="str">            from biobb_dna.intrabp_correlations.intraseqcorr import intraseqcorr</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t39" href="#t39">39</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t40" href="#t40">40</a></span><span class="t"><span class="str">            intraseqcorr(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t41" href="#t41">41</a></span><span class="t"><span class="str">                input_ser_path='path/to/input/file.ser',</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t42" href="#t42">42</a></span><span class="t"><span class="str">                output_csv_path='path/to/output/file.csv',</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t43" href="#t43">43</a></span><span class="t"><span class="str">                output_jpg_path='path/to/output/plot.jpg',</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t44" href="#t44">44</a></span><span class="t"><span class="str">                properties=prop)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t45" href="#t45">45</a></span><span class="t"><span class="str">    Info:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t46" href="#t46">46</a></span><span class="t"><span class="str">        * wrapped_software:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t47" href="#t47">47</a></span><span class="t"><span class="str">            * name: In house</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t48" href="#t48">48</a></span><span class="t"><span class="str">            * license: Apache-2.0</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t49" href="#t49">49</a></span><span class="t"><span class="str">        * ontology:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t50" href="#t50">50</a></span><span class="t"><span class="str">            * name: EDAM</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t51" href="#t51">51</a></span><span class="t"><span class="str">            * schema: http://edamontology.org/EDAM.owl</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t52" href="#t52">52</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t53" href="#t53">53</a></span><span class="t"><span class="str">    """</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t54" href="#t54">54</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t55" href="#t55">55</a></span><span class="t">    <span class="key">def</span> <span class="nam">__init__</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t56" href="#t56">56</a></span><span class="t">            <span class="nam">self</span><span class="op">,</span> <span class="nam">input_ser_path</span><span class="op">,</span> <span class="nam">output_csv_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t57" href="#t57">57</a></span><span class="t">            <span class="nam">output_jpg_path</span><span class="op">,</span> <span class="nam">properties</span><span class="op">=</span><span class="key">None</span><span class="op">,</span> <span class="op">**</span><span class="nam">kwargs</span><span class="op">)</span> <span class="op">-></span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t58" href="#t58">58</a></span><span class="t">        <span class="nam">properties</span> <span class="op">=</span> <span class="nam">properties</span> <span class="key">or</span> <span class="op">{</span><span class="op">}</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t59" href="#t59">59</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t60" href="#t60">60</a></span><span class="t">        <span class="com"># Call parent class constructor</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t61" href="#t61">61</a></span><span class="t">        <span class="nam">super</span><span class="op">(</span><span class="op">)</span><span class="op">.</span><span class="nam">__init__</span><span class="op">(</span><span class="nam">properties</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t62" href="#t62">62</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">locals_var_dict</span> <span class="op">=</span> <span class="nam">locals</span><span class="op">(</span><span class="op">)</span><span class="op">.</span><span class="nam">copy</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t63" href="#t63">63</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t64" href="#t64">64</a></span><span class="t">        <span class="com"># Input/Output files</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t65" href="#t65">65</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span> <span class="op">=</span> <span class="op">{</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t66" href="#t66">66</a></span><span class="t">            <span class="str">'in'</span><span class="op">:</span> <span class="op">{</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t67" href="#t67">67</a></span><span class="t">                <span class="str">'input_ser_path'</span><span class="op">:</span> <span class="nam">input_ser_path</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t68" href="#t68">68</a></span><span class="t">            <span class="op">}</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t69" href="#t69">69</a></span><span class="t">            <span class="str">'out'</span><span class="op">:</span> <span class="op">{</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t70" href="#t70">70</a></span><span class="t">                <span class="str">'output_csv_path'</span><span class="op">:</span> <span class="nam">output_csv_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t71" href="#t71">71</a></span><span class="t">                <span class="str">'output_jpg_path'</span><span class="op">:</span> <span class="nam">output_jpg_path</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t72" href="#t72">72</a></span><span class="t">            <span class="op">}</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t73" href="#t73">73</a></span><span class="t">        <span class="op">}</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t74" href="#t74">74</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t75" href="#t75">75</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">properties</span> <span class="op">=</span> <span class="nam">properties</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t76" href="#t76">76</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"sequence"</span><span class="op">,</span> <span class="key">None</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t77" href="#t77">77</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"seqpos"</span><span class="op">,</span> <span class="key">None</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t78" href="#t78">78</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">helpar_name</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"helpar_name"</span><span class="op">,</span> <span class="key">None</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t79" href="#t79">79</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t80" href="#t80">80</a></span><span class="t">        <span class="com"># Check the properties</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t81" href="#t81">81</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_properties</span><span class="op">(</span><span class="nam">properties</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t82" href="#t82">82</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_arguments</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t83" href="#t83">83</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t84" href="#t84">84</a></span><span class="t">    <span class="op">@</span><span class="nam">launchlogger</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t85" href="#t85">85</a></span><span class="t">    <span class="key">def</span> <span class="nam">launch</span><span class="op">(</span><span class="nam">self</span><span class="op">)</span> <span class="op">-></span> <span class="nam">int</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t86" href="#t86">86</a></span><span class="t">        <span class="str">"""Execute the :class:`HelParCorrelation &lt;intrabp_correlations.intraseqcorr.IntraSequenceCorrelation>` object."""</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t87" href="#t87">87</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t88" href="#t88">88</a></span><span class="t">        <span class="com"># Setup Biobb</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t89" href="#t89">89</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">check_restart</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t90" href="#t90">90</a></span><span class="t">            <span class="key">return</span> <span class="num">0</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t91" href="#t91">91</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">stage_files</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t92" href="#t92">92</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t93" href="#t93">93</a></span><span class="t">        <span class="com"># check sequence</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t94" href="#t94">94</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span> <span class="key">is</span> <span class="key">None</span> <span class="key">or</span> <span class="nam">len</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span><span class="op">)</span> <span class="op">&lt;</span> <span class="num">2</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t95" href="#t95">95</a></span><span class="t">            <span class="key">raise</span> <span class="nam">ValueError</span><span class="op">(</span><span class="str">"sequence is null or too short!"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t96" href="#t96">96</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t97" href="#t97">97</a></span><span class="t">        <span class="com"># get helical parameter from filename if not specified</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t98" href="#t98">98</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">helpar_name</span> <span class="key">is</span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t99" href="#t99">99</a></span><span class="t">            <span class="key">for</span> <span class="nam">hp</span> <span class="key">in</span> <span class="nam">constants</span><span class="op">.</span><span class="nam">helical_parameters</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t100" href="#t100">100</a></span><span class="t">                <span class="key">if</span> <span class="nam">hp</span><span class="op">.</span><span class="nam">lower</span><span class="op">(</span><span class="op">)</span> <span class="key">in</span> <span class="nam">Path</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t101" href="#t101">101</a></span><span class="t">                        <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'input_ser_path'</span><span class="op">]</span><span class="op">)</span><span class="op">.</span><span class="nam">name</span><span class="op">.</span><span class="nam">lower</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t102" href="#t102">102</a></span><span class="t">                    <span class="nam">self</span><span class="op">.</span><span class="nam">helpar_name</span> <span class="op">=</span> <span class="nam">hp</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t103" href="#t103">103</a></span><span class="t">            <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">helpar_name</span> <span class="key">is</span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t104" href="#t104">104</a></span><span class="t">                <span class="key">raise</span> <span class="nam">ValueError</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t105" href="#t105">105</a></span><span class="t">                    <span class="str">"Helical parameter name can't be inferred from file, "</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t106" href="#t106">106</a></span><span class="t">                    <span class="str">"so it must be specified!"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t107" href="#t107">107</a></span><span class="t">        <span class="key">else</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t108" href="#t108">108</a></span><span class="t">            <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">helpar_name</span> <span class="key">not</span> <span class="key">in</span> <span class="nam">constants</span><span class="op">.</span><span class="nam">helical_parameters</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t109" href="#t109">109</a></span><span class="t">                <span class="key">raise</span> <span class="nam">ValueError</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t110" href="#t110">110</a></span><span class="t">                    <span class="str">"Helical parameter name is invalid! "</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t111" href="#t111">111</a></span><span class="t">                    <span class="str">f"Options: {constants.helical_parameters}"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t112" href="#t112">112</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t113" href="#t113">113</a></span><span class="t">        <span class="com"># get base length and unit from helical parameter name</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t114" href="#t114">114</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">helpar_name</span> <span class="key">in</span> <span class="nam">constants</span><span class="op">.</span><span class="nam">hp_angular</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t115" href="#t115">115</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">method</span> <span class="op">=</span> <span class="str">"pearson"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t116" href="#t116">116</a></span><span class="t">        <span class="key">else</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t117" href="#t117">117</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">method</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">circular</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t118" href="#t118">118</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t119" href="#t119">119</a></span><span class="t">        <span class="com"># check seqpos</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t120" href="#t120">120</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span> <span class="key">is</span> <span class="key">not</span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t121" href="#t121">121</a></span><span class="t">            <span class="key">if</span> <span class="key">not</span> <span class="op">(</span><span class="nam">isinstance</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">,</span> <span class="nam">list</span><span class="op">)</span> <span class="key">and</span> <span class="nam">len</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">)</span> <span class="op">></span> <span class="num">1</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t122" href="#t122">122</a></span><span class="t">                <span class="key">raise</span> <span class="nam">ValueError</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t123" href="#t123">123</a></span><span class="t">                    <span class="str">"seqpos must be a list of at least two integers"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t124" href="#t124">124</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t125" href="#t125">125</a></span><span class="t">        <span class="com"># Creating temporary folder</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t126" href="#t126">126</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span> <span class="op">=</span> <span class="nam">fu</span><span class="op">.</span><span class="nam">create_unique_dir</span><span class="op">(</span><span class="nam">prefix</span><span class="op">=</span><span class="str">"bpcorrelation_"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t127" href="#t127">127</a></span><span class="t">        <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="str">'Creating %s temporary folder'</span> <span class="op">%</span> <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t128" href="#t128">128</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t129" href="#t129">129</a></span><span class="t">        <span class="com"># read input .ser file</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t130" href="#t130">130</a></span><span class="t">        <span class="nam">ser_data</span> <span class="op">=</span> <span class="nam">read_series</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t131" href="#t131">131</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'input_ser_path'</span><span class="op">]</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t132" href="#t132">132</a></span><span class="t">            <span class="nam">usecols</span><span class="op">=</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t133" href="#t133">133</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span> <span class="key">is</span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t134" href="#t134">134</a></span><span class="t">            <span class="nam">ser_data</span> <span class="op">=</span> <span class="nam">ser_data</span><span class="op">[</span><span class="nam">ser_data</span><span class="op">.</span><span class="nam">columns</span><span class="op">[</span><span class="num">1</span><span class="op">:</span><span class="op">-</span><span class="num">1</span><span class="op">]</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t135" href="#t135">135</a></span><span class="t">            <span class="com"># discard first and last base(pairs) from strands</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t136" href="#t136">136</a></span><span class="t">            <span class="nam">sequence</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span><span class="op">[</span><span class="num">1</span><span class="op">:</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t137" href="#t137">137</a></span><span class="t">            <span class="nam">labels</span> <span class="op">=</span> <span class="op">[</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t138" href="#t138">138</a></span><span class="t">                <span class="str">f"{i+1}_{sequence[i:i+1]}"</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">range</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">ser_data</span><span class="op">.</span><span class="nam">columns</span><span class="op">)</span><span class="op">)</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t139" href="#t139">139</a></span><span class="t">        <span class="key">else</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t140" href="#t140">140</a></span><span class="t">            <span class="nam">labels</span> <span class="op">=</span> <span class="op">[</span><span class="str">f"{i+1}_{self.sequence[i:i+1]}"</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t141" href="#t141">141</a></span><span class="t">        <span class="nam">ser_data</span><span class="op">.</span><span class="nam">columns</span> <span class="op">=</span> <span class="nam">labels</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t142" href="#t142">142</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t143" href="#t143">143</a></span><span class="t">        <span class="com"># make matrix</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t144" href="#t144">144</a></span><span class="t">        <span class="nam">corr_data</span> <span class="op">=</span> <span class="nam">ser_data</span><span class="op">.</span><span class="nam">corr</span><span class="op">(</span><span class="nam">method</span><span class="op">=</span><span class="nam">self</span><span class="op">.</span><span class="nam">method</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t145" href="#t145">145</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t146" href="#t146">146</a></span><span class="t">        <span class="com"># save csv data</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t147" href="#t147">147</a></span><span class="t">        <span class="nam">corr_data</span><span class="op">.</span><span class="nam">to_csv</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">"out"</span><span class="op">]</span><span class="op">[</span><span class="str">"output_csv_path"</span><span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t148" href="#t148">148</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t149" href="#t149">149</a></span><span class="t">        <span class="com"># create heatmap</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t150" href="#t150">150</a></span><span class="t">        <span class="nam">fig</span><span class="op">,</span> <span class="nam">axs</span> <span class="op">=</span> <span class="nam">plt</span><span class="op">.</span><span class="nam">subplots</span><span class="op">(</span><span class="num">1</span><span class="op">,</span> <span class="num">1</span><span class="op">,</span> <span class="nam">dpi</span><span class="op">=</span><span class="num">300</span><span class="op">,</span> <span class="nam">tight_layout</span><span class="op">=</span><span class="key">True</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t151" href="#t151">151</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">pcolor</span><span class="op">(</span><span class="nam">corr_data</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t152" href="#t152">152</a></span><span class="t">        <span class="com"># Loop over data dimensions and create text annotations.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t153" href="#t153">153</a></span><span class="t">        <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">range</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">corr_data</span><span class="op">)</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t154" href="#t154">154</a></span><span class="t">            <span class="key">for</span> <span class="nam">j</span> <span class="key">in</span> <span class="nam">range</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">corr_data</span><span class="op">)</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t155" href="#t155">155</a></span><span class="t">                <span class="nam">axs</span><span class="op">.</span><span class="nam">text</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t156" href="#t156">156</a></span><span class="t">                    <span class="nam">j</span><span class="op">+</span><span class="num">.5</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t157" href="#t157">157</a></span><span class="t">                    <span class="nam">i</span><span class="op">+</span><span class="num">.5</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t158" href="#t158">158</a></span><span class="t">                    <span class="str">f"{corr_data[corr_data.columns[j]].iloc[i]:.2f}"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t159" href="#t159">159</a></span><span class="t">                    <span class="nam">ha</span><span class="op">=</span><span class="str">"center"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t160" href="#t160">160</a></span><span class="t">                    <span class="nam">va</span><span class="op">=</span><span class="str">"center"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t161" href="#t161">161</a></span><span class="t">                    <span class="nam">color</span><span class="op">=</span><span class="str">"w"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t162" href="#t162">162</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_xticks</span><span class="op">(</span><span class="op">[</span><span class="nam">i</span> <span class="op">+</span> <span class="num">0.5</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">range</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">corr_data</span><span class="op">)</span><span class="op">)</span><span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t163" href="#t163">163</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_xticklabels</span><span class="op">(</span><span class="nam">labels</span><span class="op">,</span> <span class="nam">rotation</span><span class="op">=</span><span class="num">90</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t164" href="#t164">164</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_yticks</span><span class="op">(</span><span class="op">[</span><span class="nam">i</span> <span class="op">+</span> <span class="num">0.5</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">range</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">corr_data</span><span class="op">)</span><span class="op">)</span><span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t165" href="#t165">165</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_yticklabels</span><span class="op">(</span><span class="nam">labels</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t166" href="#t166">166</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_title</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t167" href="#t167">167</a></span><span class="t">            <span class="str">"Base Pair Correlation "</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t168" href="#t168">168</a></span><span class="t">            <span class="str">f"for Helical Parameter \'{self.helpar_name}\'"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t169" href="#t169">169</a></span><span class="t">        <span class="nam">fig</span><span class="op">.</span><span class="nam">tight_layout</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t170" href="#t170">170</a></span><span class="t">        <span class="nam">fig</span><span class="op">.</span><span class="nam">savefig</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t171" href="#t171">171</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'out'</span><span class="op">]</span><span class="op">[</span><span class="str">'output_jpg_path'</span><span class="op">]</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t172" href="#t172">172</a></span><span class="t">            <span class="nam">format</span><span class="op">=</span><span class="str">"jpg"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t173" href="#t173">173</a></span><span class="t">        <span class="nam">plt</span><span class="op">.</span><span class="nam">close</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t174" href="#t174">174</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t175" href="#t175">175</a></span><span class="t">        <span class="com"># Remove temporary file(s)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t176" href="#t176">176</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_files</span><span class="op">.</span><span class="nam">extend</span><span class="op">(</span><span class="op">[</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t177" href="#t177">177</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"unique_dir"</span><span class="op">)</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t178" href="#t178">178</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t179" href="#t179">179</a></span><span class="t">        <span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t180" href="#t180">180</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">remove_tmp_files</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t181" href="#t181">181</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t182" href="#t182">182</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_arguments</span><span class="op">(</span><span class="nam">output_files_created</span><span class="op">=</span><span class="key">True</span><span class="op">,</span> <span class="nam">raise_exception</span><span class="op">=</span><span class="key">False</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t183" href="#t183">183</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t184" href="#t184">184</a></span><span class="t">        <span class="key">return</span> <span class="num">0</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t185" href="#t185">185</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t186" href="#t186">186</a></span><span class="t">    <span class="op">@</span><span class="nam">staticmethod</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t187" href="#t187">187</a></span><span class="t">    <span class="key">def</span> <span class="nam">circular</span><span class="op">(</span><span class="nam">x1</span><span class="op">,</span> <span class="nam">x2</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t188" href="#t188">188</a></span><span class="t">        <span class="nam">x1</span> <span class="op">=</span> <span class="nam">x1</span> <span class="op">*</span> <span class="nam">np</span><span class="op">.</span><span class="nam">pi</span> <span class="op">/</span> <span class="num">180</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t189" href="#t189">189</a></span><span class="t">        <span class="nam">x2</span> <span class="op">=</span> <span class="nam">x2</span> <span class="op">*</span> <span class="nam">np</span><span class="op">.</span><span class="nam">pi</span> <span class="op">/</span> <span class="num">180</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t190" href="#t190">190</a></span><span class="t">        <span class="nam">diff_1</span> <span class="op">=</span> <span class="nam">np</span><span class="op">.</span><span class="nam">sin</span><span class="op">(</span><span class="nam">x1</span> <span class="op">-</span> <span class="nam">x1</span><span class="op">.</span><span class="nam">mean</span><span class="op">(</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t191" href="#t191">191</a></span><span class="t">        <span class="nam">diff_2</span> <span class="op">=</span> <span class="nam">np</span><span class="op">.</span><span class="nam">sin</span><span class="op">(</span><span class="nam">x2</span> <span class="op">-</span> <span class="nam">x2</span><span class="op">.</span><span class="nam">mean</span><span class="op">(</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t192" href="#t192">192</a></span><span class="t">        <span class="nam">num</span> <span class="op">=</span> <span class="op">(</span><span class="nam">diff_1</span> <span class="op">*</span> <span class="nam">diff_2</span><span class="op">)</span><span class="op">.</span><span class="nam">sum</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t193" href="#t193">193</a></span><span class="t">        <span class="nam">den</span> <span class="op">=</span> <span class="nam">np</span><span class="op">.</span><span class="nam">sqrt</span><span class="op">(</span><span class="op">(</span><span class="nam">diff_1</span> <span class="op">**</span> <span class="num">2</span><span class="op">)</span><span class="op">.</span><span class="nam">sum</span><span class="op">(</span><span class="op">)</span> <span class="op">*</span> <span class="op">(</span><span class="nam">diff_2</span> <span class="op">**</span> <span class="num">2</span><span class="op">)</span><span class="op">.</span><span class="nam">sum</span><span class="op">(</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t194" href="#t194">194</a></span><span class="t">        <span class="key">return</span> <span class="nam">num</span> <span class="op">/</span> <span class="nam">den</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t195" href="#t195">195</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t196" href="#t196">196</a></span><span class="t"><span class="key">def</span> <span class="nam">intraseqcorr</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t197" href="#t197">197</a></span><span class="t">        <span class="nam">input_ser_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t198" href="#t198">198</a></span><span class="t">        <span class="nam">output_csv_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span> <span class="nam">output_jpg_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t199" href="#t199">199</a></span><span class="t">        <span class="nam">properties</span><span class="op">:</span> <span class="nam">dict</span> <span class="op">=</span> <span class="key">None</span><span class="op">,</span> <span class="op">**</span><span class="nam">kwargs</span><span class="op">)</span> <span class="op">-></span> <span class="nam">int</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t200" href="#t200">200</a></span><span class="t">    <span class="str">"""Create :class:`HelParCorrelation &lt;intrabp_correlations.intraseqcorr.IntraSequenceCorrelation>` class and</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t201" href="#t201">201</a></span><span class="t"><span class="str">    execute the :meth:`launch() &lt;intrabp_correlations.intraseqcorr.IntraSequenceCorrelation.launch>` method."""</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t202" href="#t202">202</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t203" href="#t203">203</a></span><span class="t">    <span class="key">return</span> <span class="nam">IntraSequenceCorrelation</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t204" href="#t204">204</a></span><span class="t">        <span class="nam">input_ser_path</span><span class="op">=</span><span class="nam">input_ser_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t205" href="#t205">205</a></span><span class="t">        <span class="nam">output_csv_path</span><span class="op">=</span><span class="nam">output_csv_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t206" href="#t206">206</a></span><span class="t">        <span class="nam">output_jpg_path</span><span class="op">=</span><span class="nam">output_jpg_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t207" href="#t207">207</a></span><span class="t">        <span class="nam">properties</span><span class="op">=</span><span class="nam">properties</span><span class="op">,</span> <span class="op">**</span><span class="nam">kwargs</span><span class="op">)</span><span class="op">.</span><span class="nam">launch</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t208" href="#t208">208</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t196" href="#t196">196</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t197" href="#t197">197</a></span><span class="t"><span class="key">def</span> <span class="nam">intraseqcorr</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t198" href="#t198">198</a></span><span class="t">        <span class="nam">input_ser_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t199" href="#t199">199</a></span><span class="t">        <span class="nam">output_csv_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span> <span class="nam">output_jpg_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t200" href="#t200">200</a></span><span class="t">        <span class="nam">properties</span><span class="op">:</span> <span class="nam">dict</span> <span class="op">=</span> <span class="key">None</span><span class="op">,</span> <span class="op">**</span><span class="nam">kwargs</span><span class="op">)</span> <span class="op">-></span> <span class="nam">int</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t201" href="#t201">201</a></span><span class="t">    <span class="str">"""Create :class:`HelParCorrelation &lt;intrabp_correlations.intraseqcorr.IntraSequenceCorrelation>` class and</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t202" href="#t202">202</a></span><span class="t"><span class="str">    execute the :meth:`launch() &lt;intrabp_correlations.intraseqcorr.IntraSequenceCorrelation.launch>` method."""</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t203" href="#t203">203</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t204" href="#t204">204</a></span><span class="t">    <span class="key">return</span> <span class="nam">IntraSequenceCorrelation</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t205" href="#t205">205</a></span><span class="t">        <span class="nam">input_ser_path</span><span class="op">=</span><span class="nam">input_ser_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t206" href="#t206">206</a></span><span class="t">        <span class="nam">output_csv_path</span><span class="op">=</span><span class="nam">output_csv_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t207" href="#t207">207</a></span><span class="t">        <span class="nam">output_jpg_path</span><span class="op">=</span><span class="nam">output_jpg_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t208" href="#t208">208</a></span><span class="t">        <span class="nam">properties</span><span class="op">=</span><span class="nam">properties</span><span class="op">,</span> <span class="op">**</span><span class="nam">kwargs</span><span class="op">)</span><span class="op">.</span><span class="nam">launch</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t209" href="#t209">209</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t210" href="#t210">210</a></span><span class="t"><span class="key">def</span> <span class="nam">main</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t211" href="#t211">211</a></span><span class="t">    <span class="str">"""Command line execution of this building block. Please check the command line documentation."""</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t212" href="#t212">212</a></span><span class="t">    <span class="nam">parser</span> <span class="op">=</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">ArgumentParser</span><span class="op">(</span><span class="nam">description</span><span class="op">=</span><span class="str">'Load .ser file from Canal output and calculate correlation between base pairs of the corresponding sequence.'</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t213" href="#t213">213</a></span><span class="t">                                     <span class="nam">formatter_class</span><span class="op">=</span><span class="key">lambda</span> <span class="nam">prog</span><span class="op">:</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">RawTextHelpFormatter</span><span class="op">(</span><span class="nam">prog</span><span class="op">,</span> <span class="nam">width</span><span class="op">=</span><span class="num">99999</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t214" href="#t214">214</a></span><span class="t">    <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--config'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">False</span><span class="op">,</span> <span class="nam">help</span><span class="op">=</span><span class="str">'Configuration file'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t215" href="#t215">215</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t216" href="#t216">216</a></span><span class="t">    <span class="nam">required_args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument_group</span><span class="op">(</span><span class="str">'required arguments'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t217" href="#t217">217</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--input_ser_path'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t218" href="#t218">218</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Path to ser file with inputs. Accepted formats: ser.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t219" href="#t219">219</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--output_csv_path'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t220" href="#t220">220</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Path to output file. Accepted formats: csv.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t221" href="#t221">221</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--output_jpg_path'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t222" href="#t222">222</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Path to output plot. Accepted formats: jpg.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t223" href="#t223">223</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t224" href="#t224">224</a></span><span class="t">    <span class="nam">args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">parse_args</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t225" href="#t225">225</a></span><span class="t">    <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="op">=</span> <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="key">or</span> <span class="str">"{}"</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t226" href="#t226">226</a></span><span class="t">    <span class="nam">properties</span> <span class="op">=</span> <span class="nam">settings</span><span class="op">.</span><span class="nam">ConfReader</span><span class="op">(</span><span class="nam">config</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">config</span><span class="op">)</span><span class="op">.</span><span class="nam">get_prop_dic</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t227" href="#t227">227</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t228" href="#t228">228</a></span><span class="t">    <span class="nam">intraseqcorr</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t229" href="#t229">229</a></span><span class="t">        <span class="nam">input_ser_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_ser_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t230" href="#t230">230</a></span><span class="t">        <span class="nam">output_csv_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">output_csv_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t231" href="#t231">231</a></span><span class="t">        <span class="nam">output_jpg_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">output_jpg_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t232" href="#t232">232</a></span><span class="t">        <span class="nam">properties</span><span class="op">=</span><span class="nam">properties</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t233" href="#t233">233</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t210" href="#t210">210</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t211" href="#t211">211</a></span><span class="t"><span class="key">def</span> <span class="nam">main</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t212" href="#t212">212</a></span><span class="t">    <span class="str">"""Command line execution of this building block. Please check the command line documentation."""</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t213" href="#t213">213</a></span><span class="t">    <span class="nam">parser</span> <span class="op">=</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">ArgumentParser</span><span class="op">(</span><span class="nam">description</span><span class="op">=</span><span class="str">'Load .ser file from Canal output and calculate correlation between base pairs of the corresponding sequence.'</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t214" href="#t214">214</a></span><span class="t">                                     <span class="nam">formatter_class</span><span class="op">=</span><span class="key">lambda</span> <span class="nam">prog</span><span class="op">:</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">RawTextHelpFormatter</span><span class="op">(</span><span class="nam">prog</span><span class="op">,</span> <span class="nam">width</span><span class="op">=</span><span class="num">99999</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t215" href="#t215">215</a></span><span class="t">    <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--config'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">False</span><span class="op">,</span> <span class="nam">help</span><span class="op">=</span><span class="str">'Configuration file'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t216" href="#t216">216</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t217" href="#t217">217</a></span><span class="t">    <span class="nam">required_args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument_group</span><span class="op">(</span><span class="str">'required arguments'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t218" href="#t218">218</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--input_ser_path'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t219" href="#t219">219</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Path to ser file with inputs. Accepted formats: ser.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t220" href="#t220">220</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--output_csv_path'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t221" href="#t221">221</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Path to output file. Accepted formats: csv.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t222" href="#t222">222</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--output_jpg_path'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t223" href="#t223">223</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Path to output plot. Accepted formats: jpg.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t224" href="#t224">224</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t225" href="#t225">225</a></span><span class="t">    <span class="nam">args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">parse_args</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t226" href="#t226">226</a></span><span class="t">    <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="op">=</span> <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="key">or</span> <span class="str">"{}"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t227" href="#t227">227</a></span><span class="t">    <span class="nam">properties</span> <span class="op">=</span> <span class="nam">settings</span><span class="op">.</span><span class="nam">ConfReader</span><span class="op">(</span><span class="nam">config</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">config</span><span class="op">)</span><span class="op">.</span><span class="nam">get_prop_dic</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t228" href="#t228">228</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t229" href="#t229">229</a></span><span class="t">    <span class="nam">intraseqcorr</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t230" href="#t230">230</a></span><span class="t">        <span class="nam">input_ser_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_ser_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t231" href="#t231">231</a></span><span class="t">        <span class="nam">output_csv_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">output_csv_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t232" href="#t232">232</a></span><span class="t">        <span class="nam">output_jpg_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">output_jpg_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t233" href="#t233">233</a></span><span class="t">        <span class="nam">properties</span><span class="op">=</span><span class="nam">properties</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t234" href="#t234">234</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t235" href="#t235">235</a></span><span class="t"><span class="key">if</span> <span class="nam">__name__</span> <span class="op">==</span> <span class="str">'__main__'</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t236" href="#t236">236</a></span><span class="t">    <span class="nam">main</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t235" href="#t235">235</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t236" href="#t236">236</a></span><span class="t"><span class="key">if</span> <span class="nam">__name__</span> <span class="op">==</span> <span class="str">'__main__'</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t237" href="#t237">237</a></span><span class="t">    <span class="nam">main</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
 </main>
 <footer>
     <div class="content">
@@ -325,7 +326,7 @@ <h2>
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-            created at 2024-05-07 09:06 +0000
+            created at 2024-05-24 09:29 +0000
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diff --git a/coverage/z_74fa14c6d0e940a4___init___py.html b/coverage/z_74fa14c6d0e940a4___init___py.html
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+++ b/coverage/z_74fa14c6d0e940a4___init___py.html
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@@ -99,233 +99,234 @@ <h2>
     <p class="pln"><span class="n"><a id="t17" href="#t17">17</a></span><span class="t">    <span class="str">"""</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t18" href="#t18">18</a></span><span class="t"><span class="str">    | biobb_dna Canal</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t19" href="#t19">19</a></span><span class="t"><span class="str">    | Wrapper for the Canal executable that is part of the Curves+ software suite.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t20" href="#t20">20</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t21" href="#t21">21</a></span><span class="t"><span class="str">    Args:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t22" href="#t22">22</a></span><span class="t"><span class="str">        input_cda_file (str): Input cda file, from Cur+ output. File type: input. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/curvesplus/curves_output.cda>`_. Accepted formats: cda (edam:format_2330).</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t23" href="#t23">23</a></span><span class="t"><span class="str">        input_lis_file (str) (Optional): Input lis file, from Cur+ output. File type: input. Accepted formats: lis (edam:format_2330).</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t24" href="#t24">24</a></span><span class="t"><span class="str">        output_zip_path (str): zip filename for output files. File type: output. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/reference/curvesplus/canal_output.zip>`_. Accepted formats: zip (edam:format_3987).</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t25" href="#t25">25</a></span><span class="t"><span class="str">        properties (dic):</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t26" href="#t26">26</a></span><span class="t"><span class="str">            * **bases** (*str*) - (None) sequence of bases to be searched for in the I/P data (default is blank, meaning no specified sequence).</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t27" href="#t27">27</a></span><span class="t"><span class="str">            * **itst** (*int*) - (0) Iteration start index.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t28" href="#t28">28</a></span><span class="t"><span class="str">            * **itnd** (*int*) - (0) Iteration end index.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t29" href="#t29">29</a></span><span class="t"><span class="str">            * **itdel** (*int*) - (1) Iteration delimiter.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t30" href="#t30">30</a></span><span class="t"><span class="str">            * **lev1** (*int*) - (0) Lower base level limit (i.e. base pairs) used for analysis.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t31" href="#t31">31</a></span><span class="t"><span class="str">            * **lev2** (*int*) - (0) Upper base level limit used for analysis. If lev1 > 0 and lev2 = 0, lev2 is set to lev1 (i.e. analyze lev1 only). If lev1=lev2=0, lev1 is set to 1 and lev2 is set to the length of the oligmer (i.e. analyze all levels).</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t32" href="#t32">32</a></span><span class="t"><span class="str">            * **nastr** (*str*) - ('NA') character string used to indicate missing data in .ser files.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t33" href="#t33">33</a></span><span class="t"><span class="str">            * **cormin** (*float*) - (0.6) minimal absolute value for printing linear correlation coefficients between pairs of analyzed variables.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t34" href="#t34">34</a></span><span class="t"><span class="str">            * **series** (*str*) - (False) if True then output spatial or time series data. Only possible for the analysis of single structures or single trajectories.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t35" href="#t35">35</a></span><span class="t"><span class="str">            * **histo** (*str*) - (False) if True then output histogram data.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t36" href="#t36">36</a></span><span class="t"><span class="str">            * **corr** (*str*) - (False) if True than output linear correlation coefficients between all variables.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t37" href="#t37">37</a></span><span class="t"><span class="str">            * **sequence** (*str*) - (Optional) sequence of the first strand of the corresponding DNA fragment, for each .cda file. If not given it will be parsed from .lis file.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t38" href="#t38">38</a></span><span class="t"><span class="str">            * **binary_path** (*str*) - ('Canal') Path to Canal executable, otherwise the program wil look for Canal executable in the binaries folder.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t39" href="#t39">39</a></span><span class="t"><span class="str">            * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t40" href="#t40">40</a></span><span class="t"><span class="str">            * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t41" href="#t41">41</a></span><span class="t"><span class="str">    Examples:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t42" href="#t42">42</a></span><span class="t"><span class="str">        This is a use example of how to use the building block from Python::</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t43" href="#t43">43</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t44" href="#t44">44</a></span><span class="t"><span class="str">            from biobb_dna.curvesplus.biobb_canal import biobb_canal</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t45" href="#t45">45</a></span><span class="t"><span class="str">            prop = {</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t46" href="#t46">46</a></span><span class="t"><span class="str">                'series': '.t.',</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t47" href="#t47">47</a></span><span class="t"><span class="str">                'histo': '.t.',</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t48" href="#t48">48</a></span><span class="t"><span class="str">                'sequence': 'CGCGAATTCGCG'</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t49" href="#t49">49</a></span><span class="t"><span class="str">            }</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t50" href="#t50">50</a></span><span class="t"><span class="str">            biobb_canal(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t51" href="#t51">51</a></span><span class="t"><span class="str">                input_cda_file='/path/to/curves/output.cda',</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t52" href="#t52">52</a></span><span class="t"><span class="str">                output_zip_path='/path/to/output.zip',</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t53" href="#t53">53</a></span><span class="t"><span class="str">                properties=prop)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t54" href="#t54">54</a></span><span class="t"><span class="str">    Info:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t55" href="#t55">55</a></span><span class="t"><span class="str">        * wrapped_software:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t56" href="#t56">56</a></span><span class="t"><span class="str">            * name: Canal</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t57" href="#t57">57</a></span><span class="t"><span class="str">            * version: >=2.6</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t58" href="#t58">58</a></span><span class="t"><span class="str">            * license: BSD 3-Clause</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t59" href="#t59">59</a></span><span class="t"><span class="str">        * ontology:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t60" href="#t60">60</a></span><span class="t"><span class="str">            * name: EDAM</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t61" href="#t61">61</a></span><span class="t"><span class="str">            * schema: http://edamontology.org/EDAM.owl</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t62" href="#t62">62</a></span><span class="t"><span class="str">    """</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t63" href="#t63">63</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t64" href="#t64">64</a></span><span class="t">    <span class="key">def</span> <span class="nam">__init__</span><span class="op">(</span><span class="nam">self</span><span class="op">,</span> <span class="nam">input_cda_file</span><span class="op">,</span> <span class="nam">input_lis_file</span><span class="op">=</span><span class="key">None</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t65" href="#t65">65</a></span><span class="t">                 <span class="nam">output_zip_path</span><span class="op">=</span><span class="key">None</span><span class="op">,</span> <span class="nam">properties</span><span class="op">=</span><span class="key">None</span><span class="op">,</span> <span class="op">**</span><span class="nam">kwargs</span><span class="op">)</span> <span class="op">-></span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t66" href="#t66">66</a></span><span class="t">        <span class="nam">properties</span> <span class="op">=</span> <span class="nam">properties</span> <span class="key">or</span> <span class="op">{</span><span class="op">}</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t67" href="#t67">67</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t68" href="#t68">68</a></span><span class="t">        <span class="com"># Call parent class constructor</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t69" href="#t69">69</a></span><span class="t">        <span class="nam">super</span><span class="op">(</span><span class="op">)</span><span class="op">.</span><span class="nam">__init__</span><span class="op">(</span><span class="nam">properties</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t70" href="#t70">70</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">locals_var_dict</span> <span class="op">=</span> <span class="nam">locals</span><span class="op">(</span><span class="op">)</span><span class="op">.</span><span class="nam">copy</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t71" href="#t71">71</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t72" href="#t72">72</a></span><span class="t">        <span class="com"># Input/Output files</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t73" href="#t73">73</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span> <span class="op">=</span> <span class="op">{</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t74" href="#t74">74</a></span><span class="t">            <span class="str">'in'</span><span class="op">:</span> <span class="op">{</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t75" href="#t75">75</a></span><span class="t">                <span class="str">'input_cda_file'</span><span class="op">:</span> <span class="nam">input_cda_file</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t76" href="#t76">76</a></span><span class="t">                <span class="str">'input_lis_file'</span><span class="op">:</span> <span class="nam">input_lis_file</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t77" href="#t77">77</a></span><span class="t">            <span class="op">}</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t78" href="#t78">78</a></span><span class="t">            <span class="str">'out'</span><span class="op">:</span> <span class="op">{</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t79" href="#t79">79</a></span><span class="t">                <span class="str">'output_zip_path'</span><span class="op">:</span> <span class="nam">output_zip_path</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t80" href="#t80">80</a></span><span class="t">            <span class="op">}</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t81" href="#t81">81</a></span><span class="t">        <span class="op">}</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t82" href="#t82">82</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t83" href="#t83">83</a></span><span class="t">        <span class="com"># Properties specific for BB</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t84" href="#t84">84</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">bases</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'bases'</span><span class="op">,</span> <span class="key">None</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t85" href="#t85">85</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">nastr</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'nastr'</span><span class="op">,</span> <span class="key">None</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t86" href="#t86">86</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">cormin</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'cormin'</span><span class="op">,</span> <span class="num">0.6</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t87" href="#t87">87</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">lev1</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'lev1'</span><span class="op">,</span> <span class="num">0</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t88" href="#t88">88</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">lev2</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'lev2'</span><span class="op">,</span> <span class="num">0</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t89" href="#t89">89</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">itst</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'itst'</span><span class="op">,</span> <span class="num">0</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t90" href="#t90">90</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">itnd</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'itnd'</span><span class="op">,</span> <span class="num">0</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t91" href="#t91">91</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">itdel</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'itdel'</span><span class="op">,</span> <span class="num">1</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t92" href="#t92">92</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">series</span> <span class="op">=</span> <span class="str">".t."</span> <span class="key">if</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'series'</span><span class="op">,</span> <span class="key">False</span><span class="op">)</span> <span class="key">else</span> <span class="str">".f."</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t93" href="#t93">93</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">histo</span> <span class="op">=</span> <span class="str">".t."</span> <span class="key">if</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'histo'</span><span class="op">,</span> <span class="key">False</span><span class="op">)</span> <span class="key">else</span> <span class="str">".f."</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t94" href="#t94">94</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">corr</span> <span class="op">=</span> <span class="str">".t."</span> <span class="key">if</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'corr'</span><span class="op">,</span> <span class="key">False</span><span class="op">)</span> <span class="key">else</span> <span class="str">".f."</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t95" href="#t95">95</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'sequence'</span><span class="op">,</span> <span class="key">None</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t96" href="#t96">96</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">binary_path</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'binary_path'</span><span class="op">,</span> <span class="str">'Canal'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t97" href="#t97">97</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">properties</span> <span class="op">=</span> <span class="nam">properties</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t98" href="#t98">98</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t99" href="#t99">99</a></span><span class="t">        <span class="com"># Check the properties</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t100" href="#t100">100</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_properties</span><span class="op">(</span><span class="nam">properties</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t101" href="#t101">101</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_arguments</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t102" href="#t102">102</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t103" href="#t103">103</a></span><span class="t">    <span class="op">@</span><span class="nam">launchlogger</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t104" href="#t104">104</a></span><span class="t">    <span class="key">def</span> <span class="nam">launch</span><span class="op">(</span><span class="nam">self</span><span class="op">)</span> <span class="op">-></span> <span class="nam">int</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t105" href="#t105">105</a></span><span class="t">        <span class="str">"""Execute the :class:`Canal &lt;biobb_dna.curvesplus.biobb_canal.Canal>` object."""</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t106" href="#t106">106</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t107" href="#t107">107</a></span><span class="t">        <span class="com"># Setup Biobb</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t108" href="#t108">108</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">check_restart</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t109" href="#t109">109</a></span><span class="t">            <span class="key">return</span> <span class="num">0</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t110" href="#t110">110</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">stage_files</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t111" href="#t111">111</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t112" href="#t112">112</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span> <span class="key">is</span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t113" href="#t113">113</a></span><span class="t">            <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'input_lis_file'</span><span class="op">]</span> <span class="key">is</span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t114" href="#t114">114</a></span><span class="t">                <span class="key">raise</span> <span class="nam">RuntimeError</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t115" href="#t115">115</a></span><span class="t">                    <span class="str">"if no sequence is passed in the configuration, "</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t116" href="#t116">116</a></span><span class="t">                    <span class="str">"you must at least specify `input_lis_file` "</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t117" href="#t117">117</a></span><span class="t">                    <span class="str">"so sequence can be parsed from there"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t118" href="#t118">118</a></span><span class="t">            <span class="nam">lis_lines</span> <span class="op">=</span> <span class="nam">Path</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t119" href="#t119">119</a></span><span class="t">                <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'input_lis_file'</span><span class="op">]</span><span class="op">)</span><span class="op">.</span><span class="nam">read_text</span><span class="op">(</span><span class="op">)</span><span class="op">.</span><span class="nam">splitlines</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t120" href="#t120">120</a></span><span class="t">            <span class="key">for</span> <span class="nam">line</span> <span class="key">in</span> <span class="nam">lis_lines</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t121" href="#t121">121</a></span><span class="t">                <span class="key">if</span> <span class="nam">line</span><span class="op">.</span><span class="nam">strip</span><span class="op">(</span><span class="op">)</span><span class="op">.</span><span class="nam">startswith</span><span class="op">(</span><span class="str">"Strand  1"</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t122" href="#t122">122</a></span><span class="t">                    <span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span> <span class="op">=</span> <span class="nam">line</span><span class="op">.</span><span class="nam">split</span><span class="op">(</span><span class="str">" "</span><span class="op">)</span><span class="op">[</span><span class="op">-</span><span class="num">1</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t123" href="#t123">123</a></span><span class="t">                    <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t124" href="#t124">124</a></span><span class="t">                        <span class="str">f"using sequence {self.sequence} "</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t125" href="#t125">125</a></span><span class="t">                        <span class="str">f"from {self.io_dict['in']['input_lis_file']}"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t126" href="#t126">126</a></span><span class="t">                        <span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t127" href="#t127">127</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t128" href="#t128">128</a></span><span class="t">        <span class="com"># Creating temporary folder</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t129" href="#t129">129</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span> <span class="op">=</span> <span class="nam">fu</span><span class="op">.</span><span class="nam">create_unique_dir</span><span class="op">(</span><span class="nam">prefix</span><span class="op">=</span><span class="str">"canal_"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t130" href="#t130">130</a></span><span class="t">        <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="str">'Creating %s temporary folder'</span> <span class="op">%</span> <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t131" href="#t131">131</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t132" href="#t132">132</a></span><span class="t">        <span class="com"># copy input files to temporary folder</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t133" href="#t133">133</a></span><span class="t">        <span class="nam">shutil</span><span class="op">.</span><span class="nam">copy</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t134" href="#t134">134</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'input_cda_file'</span><span class="op">]</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t135" href="#t135">135</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t136" href="#t136">136</a></span><span class="t">        <span class="nam">tmp_cda_path</span> <span class="op">=</span> <span class="nam">Path</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'input_cda_file'</span><span class="op">]</span><span class="op">)</span><span class="op">.</span><span class="nam">name</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t137" href="#t137">137</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'input_lis_file'</span><span class="op">]</span> <span class="key">is</span> <span class="key">not</span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t138" href="#t138">138</a></span><span class="t">            <span class="nam">shutil</span><span class="op">.</span><span class="nam">copy</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t139" href="#t139">139</a></span><span class="t">                <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'input_lis_file'</span><span class="op">]</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t140" href="#t140">140</a></span><span class="t">                <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t141" href="#t141">141</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t142" href="#t142">142</a></span><span class="t">        <span class="com"># change directory to temporary folder</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t143" href="#t143">143</a></span><span class="t">        <span class="nam">original_directory</span> <span class="op">=</span> <span class="nam">os</span><span class="op">.</span><span class="nam">getcwd</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t144" href="#t144">144</a></span><span class="t">        <span class="nam">os</span><span class="op">.</span><span class="nam">chdir</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t145" href="#t145">145</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t146" href="#t146">146</a></span><span class="t">        <span class="com"># create intructions</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t147" href="#t147">147</a></span><span class="t">        <span class="nam">instructions</span> <span class="op">=</span> <span class="op">[</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t148" href="#t148">148</a></span><span class="t">            <span class="str">f"{self.binary_path} &lt;&lt;! "</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t149" href="#t149">149</a></span><span class="t">            <span class="str">"&amp;inp"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t150" href="#t150">150</a></span><span class="t">            <span class="str">"  lis=canal_output,"</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t151" href="#t151">151</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">bases</span> <span class="key">is</span> <span class="key">not</span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t152" href="#t152">152</a></span><span class="t">            <span class="com"># add topology file if needed</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t153" href="#t153">153</a></span><span class="t">            <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="str">'Appending sequence of bases to be searched to command'</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t154" href="#t154">154</a></span><span class="t">                   <span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">global_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t155" href="#t155">155</a></span><span class="t">            <span class="nam">instructions</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="str">f"  seq={self.bases},"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t156" href="#t156">156</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">nastr</span> <span class="key">is</span> <span class="key">not</span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t157" href="#t157">157</a></span><span class="t">            <span class="com"># add topology file if needed</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t158" href="#t158">158</a></span><span class="t">            <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="str">'Adding null values string specification to command'</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t159" href="#t159">159</a></span><span class="t">                   <span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">global_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t160" href="#t160">160</a></span><span class="t">            <span class="nam">instructions</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="str">f"  nastr={self.nastr},"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t161" href="#t161">161</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t162" href="#t162">162</a></span><span class="t">        <span class="nam">instructions</span> <span class="op">=</span> <span class="nam">instructions</span> <span class="op">+</span> <span class="op">[</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t163" href="#t163">163</a></span><span class="t">            <span class="str">f"  cormin={self.cormin},"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t164" href="#t164">164</a></span><span class="t">            <span class="str">f"  lev1={self.lev1},lev2={self.lev2},"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t165" href="#t165">165</a></span><span class="t">            <span class="str">f"  itst={self.itst},itnd={self.itnd},itdel={self.itdel},"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t166" href="#t166">166</a></span><span class="t">            <span class="str">f"  histo={self.histo},"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t167" href="#t167">167</a></span><span class="t">            <span class="str">f"  series={self.series},"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t168" href="#t168">168</a></span><span class="t">            <span class="str">f"  corr={self.corr},"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t169" href="#t169">169</a></span><span class="t">            <span class="str">"&amp;end"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t170" href="#t170">170</a></span><span class="t">            <span class="str">f"{tmp_cda_path} {self.sequence}"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t171" href="#t171">171</a></span><span class="t">            <span class="str">"!"</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t172" href="#t172">172</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t173" href="#t173">173</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">cmd</span> <span class="op">=</span> <span class="op">[</span><span class="str">"\n"</span><span class="op">.</span><span class="nam">join</span><span class="op">(</span><span class="nam">instructions</span><span class="op">)</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t174" href="#t174">174</a></span><span class="t">        <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="str">'Creating command line with instructions and required arguments'</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t175" href="#t175">175</a></span><span class="t">               <span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">global_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t176" href="#t176">176</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t177" href="#t177">177</a></span><span class="t">        <span class="com"># Run Biobb block</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t178" href="#t178">178</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">run_biobb</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t179" href="#t179">179</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t180" href="#t180">180</a></span><span class="t">        <span class="com"># change back to original directory</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t181" href="#t181">181</a></span><span class="t">        <span class="nam">os</span><span class="op">.</span><span class="nam">chdir</span><span class="op">(</span><span class="nam">original_directory</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t182" href="#t182">182</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t183" href="#t183">183</a></span><span class="t">        <span class="com"># create zipfile and write output inside</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t184" href="#t184">184</a></span><span class="t">        <span class="nam">zf</span> <span class="op">=</span> <span class="nam">zipfile</span><span class="op">.</span><span class="nam">ZipFile</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t185" href="#t185">185</a></span><span class="t">            <span class="nam">Path</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">"out"</span><span class="op">]</span><span class="op">[</span><span class="str">"output_zip_path"</span><span class="op">]</span><span class="op">)</span><span class="op">,</span> <span class="str">"w"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t186" href="#t186">186</a></span><span class="t">        <span class="key">for</span> <span class="nam">canal_outfile</span> <span class="key">in</span> <span class="nam">Path</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span><span class="op">)</span><span class="op">.</span><span class="nam">glob</span><span class="op">(</span><span class="str">"canal_output*"</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t187" href="#t187">187</a></span><span class="t">            <span class="nam">zf</span><span class="op">.</span><span class="nam">write</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t188" href="#t188">188</a></span><span class="t">                <span class="nam">canal_outfile</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t189" href="#t189">189</a></span><span class="t">                <span class="nam">arcname</span><span class="op">=</span><span class="nam">canal_outfile</span><span class="op">.</span><span class="nam">name</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t190" href="#t190">190</a></span><span class="t">        <span class="nam">zf</span><span class="op">.</span><span class="nam">close</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t191" href="#t191">191</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t192" href="#t192">192</a></span><span class="t">        <span class="com"># Remove temporary file(s)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t193" href="#t193">193</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_files</span><span class="op">.</span><span class="nam">extend</span><span class="op">(</span><span class="op">[</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t194" href="#t194">194</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"unique_dir"</span><span class="op">)</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t195" href="#t195">195</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t196" href="#t196">196</a></span><span class="t">        <span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t197" href="#t197">197</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">remove_tmp_files</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t198" href="#t198">198</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t199" href="#t199">199</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_arguments</span><span class="op">(</span><span class="nam">output_files_created</span><span class="op">=</span><span class="key">True</span><span class="op">,</span> <span class="nam">raise_exception</span><span class="op">=</span><span class="key">False</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t200" href="#t200">200</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t201" href="#t201">201</a></span><span class="t">        <span class="key">return</span> <span class="nam">self</span><span class="op">.</span><span class="nam">return_code</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t202" href="#t202">202</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t20" href="#t20">20</a></span><span class="t"><span class="str">    | The Canal program is used to analyze the curvature of DNA structures.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t21" href="#t21">21</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t22" href="#t22">22</a></span><span class="t"><span class="str">    Args:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t23" href="#t23">23</a></span><span class="t"><span class="str">        input_cda_file (str): Input cda file, from Cur+ output. File type: input. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/curvesplus/curves_output.cda>`_. Accepted formats: cda (edam:format_2330).</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t24" href="#t24">24</a></span><span class="t"><span class="str">        input_lis_file (str) (Optional): Input lis file, from Cur+ output. File type: input. Accepted formats: lis (edam:format_2330).</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t25" href="#t25">25</a></span><span class="t"><span class="str">        output_zip_path (str): zip filename for output files. File type: output. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/reference/curvesplus/canal_output.zip>`_. Accepted formats: zip (edam:format_3987).</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t26" href="#t26">26</a></span><span class="t"><span class="str">        properties (dic):</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t27" href="#t27">27</a></span><span class="t"><span class="str">            * **bases** (*str*) - (None) sequence of bases to be searched for in the I/P data (default is blank, meaning no specified sequence).</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t28" href="#t28">28</a></span><span class="t"><span class="str">            * **itst** (*int*) - (0) Iteration start index.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t29" href="#t29">29</a></span><span class="t"><span class="str">            * **itnd** (*int*) - (0) Iteration end index.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t30" href="#t30">30</a></span><span class="t"><span class="str">            * **itdel** (*int*) - (1) Iteration delimiter.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t31" href="#t31">31</a></span><span class="t"><span class="str">            * **lev1** (*int*) - (0) Lower base level limit (i.e. base pairs) used for analysis.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t32" href="#t32">32</a></span><span class="t"><span class="str">            * **lev2** (*int*) - (0) Upper base level limit used for analysis. If lev1 > 0 and lev2 = 0, lev2 is set to lev1 (i.e. analyze lev1 only). If lev1=lev2=0, lev1 is set to 1 and lev2 is set to the length of the oligmer (i.e. analyze all levels).</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t33" href="#t33">33</a></span><span class="t"><span class="str">            * **nastr** (*str*) - ('NA') character string used to indicate missing data in .ser files.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t34" href="#t34">34</a></span><span class="t"><span class="str">            * **cormin** (*float*) - (0.6) minimal absolute value for printing linear correlation coefficients between pairs of analyzed variables.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t35" href="#t35">35</a></span><span class="t"><span class="str">            * **series** (*str*) - (False) if True then output spatial or time series data. Only possible for the analysis of single structures or single trajectories.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t36" href="#t36">36</a></span><span class="t"><span class="str">            * **histo** (*str*) - (False) if True then output histogram data.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t37" href="#t37">37</a></span><span class="t"><span class="str">            * **corr** (*str*) - (False) if True than output linear correlation coefficients between all variables.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t38" href="#t38">38</a></span><span class="t"><span class="str">            * **sequence** (*str*) - (Optional) sequence of the first strand of the corresponding DNA fragment, for each .cda file. If not given it will be parsed from .lis file.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t39" href="#t39">39</a></span><span class="t"><span class="str">            * **binary_path** (*str*) - ('Canal') Path to Canal executable, otherwise the program wil look for Canal executable in the binaries folder.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t40" href="#t40">40</a></span><span class="t"><span class="str">            * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t41" href="#t41">41</a></span><span class="t"><span class="str">            * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t42" href="#t42">42</a></span><span class="t"><span class="str">    Examples:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t43" href="#t43">43</a></span><span class="t"><span class="str">        This is a use example of how to use the building block from Python::</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t44" href="#t44">44</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t45" href="#t45">45</a></span><span class="t"><span class="str">            from biobb_dna.curvesplus.biobb_canal import biobb_canal</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t46" href="#t46">46</a></span><span class="t"><span class="str">            prop = {</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t47" href="#t47">47</a></span><span class="t"><span class="str">                'series': '.t.',</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t48" href="#t48">48</a></span><span class="t"><span class="str">                'histo': '.t.',</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t49" href="#t49">49</a></span><span class="t"><span class="str">                'sequence': 'CGCGAATTCGCG'</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t50" href="#t50">50</a></span><span class="t"><span class="str">            }</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t51" href="#t51">51</a></span><span class="t"><span class="str">            biobb_canal(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t52" href="#t52">52</a></span><span class="t"><span class="str">                input_cda_file='/path/to/curves/output.cda',</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t53" href="#t53">53</a></span><span class="t"><span class="str">                output_zip_path='/path/to/output.zip',</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t54" href="#t54">54</a></span><span class="t"><span class="str">                properties=prop)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t55" href="#t55">55</a></span><span class="t"><span class="str">    Info:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t56" href="#t56">56</a></span><span class="t"><span class="str">        * wrapped_software:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t57" href="#t57">57</a></span><span class="t"><span class="str">            * name: Canal</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t58" href="#t58">58</a></span><span class="t"><span class="str">            * version: >=2.6</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t59" href="#t59">59</a></span><span class="t"><span class="str">            * license: BSD 3-Clause</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t60" href="#t60">60</a></span><span class="t"><span class="str">        * ontology:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t61" href="#t61">61</a></span><span class="t"><span class="str">            * name: EDAM</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t62" href="#t62">62</a></span><span class="t"><span class="str">            * schema: http://edamontology.org/EDAM.owl</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t63" href="#t63">63</a></span><span class="t"><span class="str">    """</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t64" href="#t64">64</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t65" href="#t65">65</a></span><span class="t">    <span class="key">def</span> <span class="nam">__init__</span><span class="op">(</span><span class="nam">self</span><span class="op">,</span> <span class="nam">input_cda_file</span><span class="op">,</span> <span class="nam">input_lis_file</span><span class="op">=</span><span class="key">None</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t66" href="#t66">66</a></span><span class="t">                 <span class="nam">output_zip_path</span><span class="op">=</span><span class="key">None</span><span class="op">,</span> <span class="nam">properties</span><span class="op">=</span><span class="key">None</span><span class="op">,</span> <span class="op">**</span><span class="nam">kwargs</span><span class="op">)</span> <span class="op">-></span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t67" href="#t67">67</a></span><span class="t">        <span class="nam">properties</span> <span class="op">=</span> <span class="nam">properties</span> <span class="key">or</span> <span class="op">{</span><span class="op">}</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t68" href="#t68">68</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t69" href="#t69">69</a></span><span class="t">        <span class="com"># Call parent class constructor</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t70" href="#t70">70</a></span><span class="t">        <span class="nam">super</span><span class="op">(</span><span class="op">)</span><span class="op">.</span><span class="nam">__init__</span><span class="op">(</span><span class="nam">properties</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t71" href="#t71">71</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">locals_var_dict</span> <span class="op">=</span> <span class="nam">locals</span><span class="op">(</span><span class="op">)</span><span class="op">.</span><span class="nam">copy</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t72" href="#t72">72</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t73" href="#t73">73</a></span><span class="t">        <span class="com"># Input/Output files</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t74" href="#t74">74</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span> <span class="op">=</span> <span class="op">{</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t75" href="#t75">75</a></span><span class="t">            <span class="str">'in'</span><span class="op">:</span> <span class="op">{</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t76" href="#t76">76</a></span><span class="t">                <span class="str">'input_cda_file'</span><span class="op">:</span> <span class="nam">input_cda_file</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t77" href="#t77">77</a></span><span class="t">                <span class="str">'input_lis_file'</span><span class="op">:</span> <span class="nam">input_lis_file</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t78" href="#t78">78</a></span><span class="t">            <span class="op">}</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t79" href="#t79">79</a></span><span class="t">            <span class="str">'out'</span><span class="op">:</span> <span class="op">{</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t80" href="#t80">80</a></span><span class="t">                <span class="str">'output_zip_path'</span><span class="op">:</span> <span class="nam">output_zip_path</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t81" href="#t81">81</a></span><span class="t">            <span class="op">}</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t82" href="#t82">82</a></span><span class="t">        <span class="op">}</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t83" href="#t83">83</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t84" href="#t84">84</a></span><span class="t">        <span class="com"># Properties specific for BB</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t85" href="#t85">85</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">bases</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'bases'</span><span class="op">,</span> <span class="key">None</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t86" href="#t86">86</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">nastr</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'nastr'</span><span class="op">,</span> <span class="key">None</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t87" href="#t87">87</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">cormin</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'cormin'</span><span class="op">,</span> <span class="num">0.6</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t88" href="#t88">88</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">lev1</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'lev1'</span><span class="op">,</span> <span class="num">0</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t89" href="#t89">89</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">lev2</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'lev2'</span><span class="op">,</span> <span class="num">0</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t90" href="#t90">90</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">itst</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'itst'</span><span class="op">,</span> <span class="num">0</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t91" href="#t91">91</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">itnd</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'itnd'</span><span class="op">,</span> <span class="num">0</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t92" href="#t92">92</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">itdel</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'itdel'</span><span class="op">,</span> <span class="num">1</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t93" href="#t93">93</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">series</span> <span class="op">=</span> <span class="str">".t."</span> <span class="key">if</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'series'</span><span class="op">,</span> <span class="key">False</span><span class="op">)</span> <span class="key">else</span> <span class="str">".f."</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t94" href="#t94">94</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">histo</span> <span class="op">=</span> <span class="str">".t."</span> <span class="key">if</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'histo'</span><span class="op">,</span> <span class="key">False</span><span class="op">)</span> <span class="key">else</span> <span class="str">".f."</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t95" href="#t95">95</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">corr</span> <span class="op">=</span> <span class="str">".t."</span> <span class="key">if</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'corr'</span><span class="op">,</span> <span class="key">False</span><span class="op">)</span> <span class="key">else</span> <span class="str">".f."</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t96" href="#t96">96</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'sequence'</span><span class="op">,</span> <span class="key">None</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t97" href="#t97">97</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">binary_path</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'binary_path'</span><span class="op">,</span> <span class="str">'Canal'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t98" href="#t98">98</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">properties</span> <span class="op">=</span> <span class="nam">properties</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t99" href="#t99">99</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t100" href="#t100">100</a></span><span class="t">        <span class="com"># Check the properties</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t101" href="#t101">101</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_properties</span><span class="op">(</span><span class="nam">properties</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t102" href="#t102">102</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_arguments</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t103" href="#t103">103</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t104" href="#t104">104</a></span><span class="t">    <span class="op">@</span><span class="nam">launchlogger</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t105" href="#t105">105</a></span><span class="t">    <span class="key">def</span> <span class="nam">launch</span><span class="op">(</span><span class="nam">self</span><span class="op">)</span> <span class="op">-></span> <span class="nam">int</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t106" href="#t106">106</a></span><span class="t">        <span class="str">"""Execute the :class:`Canal &lt;biobb_dna.curvesplus.biobb_canal.Canal>` object."""</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t107" href="#t107">107</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t108" href="#t108">108</a></span><span class="t">        <span class="com"># Setup Biobb</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t109" href="#t109">109</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">check_restart</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t110" href="#t110">110</a></span><span class="t">            <span class="key">return</span> <span class="num">0</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t111" href="#t111">111</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">stage_files</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t112" href="#t112">112</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t113" href="#t113">113</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span> <span class="key">is</span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t114" href="#t114">114</a></span><span class="t">            <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'input_lis_file'</span><span class="op">]</span> <span class="key">is</span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t115" href="#t115">115</a></span><span class="t">                <span class="key">raise</span> <span class="nam">RuntimeError</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t116" href="#t116">116</a></span><span class="t">                    <span class="str">"if no sequence is passed in the configuration, "</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t117" href="#t117">117</a></span><span class="t">                    <span class="str">"you must at least specify `input_lis_file` "</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t118" href="#t118">118</a></span><span class="t">                    <span class="str">"so sequence can be parsed from there"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t119" href="#t119">119</a></span><span class="t">            <span class="nam">lis_lines</span> <span class="op">=</span> <span class="nam">Path</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t120" href="#t120">120</a></span><span class="t">                <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'input_lis_file'</span><span class="op">]</span><span class="op">)</span><span class="op">.</span><span class="nam">read_text</span><span class="op">(</span><span class="op">)</span><span class="op">.</span><span class="nam">splitlines</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t121" href="#t121">121</a></span><span class="t">            <span class="key">for</span> <span class="nam">line</span> <span class="key">in</span> <span class="nam">lis_lines</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t122" href="#t122">122</a></span><span class="t">                <span class="key">if</span> <span class="nam">line</span><span class="op">.</span><span class="nam">strip</span><span class="op">(</span><span class="op">)</span><span class="op">.</span><span class="nam">startswith</span><span class="op">(</span><span class="str">"Strand  1"</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t123" href="#t123">123</a></span><span class="t">                    <span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span> <span class="op">=</span> <span class="nam">line</span><span class="op">.</span><span class="nam">split</span><span class="op">(</span><span class="str">" "</span><span class="op">)</span><span class="op">[</span><span class="op">-</span><span class="num">1</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t124" href="#t124">124</a></span><span class="t">                    <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t125" href="#t125">125</a></span><span class="t">                        <span class="str">f"using sequence {self.sequence} "</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t126" href="#t126">126</a></span><span class="t">                        <span class="str">f"from {self.io_dict['in']['input_lis_file']}"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t127" href="#t127">127</a></span><span class="t">                        <span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t128" href="#t128">128</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t129" href="#t129">129</a></span><span class="t">        <span class="com"># Creating temporary folder</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t130" href="#t130">130</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span> <span class="op">=</span> <span class="nam">fu</span><span class="op">.</span><span class="nam">create_unique_dir</span><span class="op">(</span><span class="nam">prefix</span><span class="op">=</span><span class="str">"canal_"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t131" href="#t131">131</a></span><span class="t">        <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="str">'Creating %s temporary folder'</span> <span class="op">%</span> <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t132" href="#t132">132</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t133" href="#t133">133</a></span><span class="t">        <span class="com"># copy input files to temporary folder</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t134" href="#t134">134</a></span><span class="t">        <span class="nam">shutil</span><span class="op">.</span><span class="nam">copy</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t135" href="#t135">135</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'input_cda_file'</span><span class="op">]</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t136" href="#t136">136</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t137" href="#t137">137</a></span><span class="t">        <span class="nam">tmp_cda_path</span> <span class="op">=</span> <span class="nam">Path</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'input_cda_file'</span><span class="op">]</span><span class="op">)</span><span class="op">.</span><span class="nam">name</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t138" href="#t138">138</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'input_lis_file'</span><span class="op">]</span> <span class="key">is</span> <span class="key">not</span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t139" href="#t139">139</a></span><span class="t">            <span class="nam">shutil</span><span class="op">.</span><span class="nam">copy</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t140" href="#t140">140</a></span><span class="t">                <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'input_lis_file'</span><span class="op">]</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t141" href="#t141">141</a></span><span class="t">                <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t142" href="#t142">142</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t143" href="#t143">143</a></span><span class="t">        <span class="com"># change directory to temporary folder</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t144" href="#t144">144</a></span><span class="t">        <span class="nam">original_directory</span> <span class="op">=</span> <span class="nam">os</span><span class="op">.</span><span class="nam">getcwd</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t145" href="#t145">145</a></span><span class="t">        <span class="nam">os</span><span class="op">.</span><span class="nam">chdir</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t146" href="#t146">146</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t147" href="#t147">147</a></span><span class="t">        <span class="com"># create intructions</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t148" href="#t148">148</a></span><span class="t">        <span class="nam">instructions</span> <span class="op">=</span> <span class="op">[</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t149" href="#t149">149</a></span><span class="t">            <span class="str">f"{self.binary_path} &lt;&lt;! "</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t150" href="#t150">150</a></span><span class="t">            <span class="str">"&amp;inp"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t151" href="#t151">151</a></span><span class="t">            <span class="str">"  lis=canal_output,"</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t152" href="#t152">152</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">bases</span> <span class="key">is</span> <span class="key">not</span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t153" href="#t153">153</a></span><span class="t">            <span class="com"># add topology file if needed</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t154" href="#t154">154</a></span><span class="t">            <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="str">'Appending sequence of bases to be searched to command'</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t155" href="#t155">155</a></span><span class="t">                   <span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">global_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t156" href="#t156">156</a></span><span class="t">            <span class="nam">instructions</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="str">f"  seq={self.bases},"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t157" href="#t157">157</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">nastr</span> <span class="key">is</span> <span class="key">not</span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t158" href="#t158">158</a></span><span class="t">            <span class="com"># add topology file if needed</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t159" href="#t159">159</a></span><span class="t">            <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="str">'Adding null values string specification to command'</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t160" href="#t160">160</a></span><span class="t">                   <span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">global_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t161" href="#t161">161</a></span><span class="t">            <span class="nam">instructions</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="str">f"  nastr={self.nastr},"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t162" href="#t162">162</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t163" href="#t163">163</a></span><span class="t">        <span class="nam">instructions</span> <span class="op">=</span> <span class="nam">instructions</span> <span class="op">+</span> <span class="op">[</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t164" href="#t164">164</a></span><span class="t">            <span class="str">f"  cormin={self.cormin},"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t165" href="#t165">165</a></span><span class="t">            <span class="str">f"  lev1={self.lev1},lev2={self.lev2},"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t166" href="#t166">166</a></span><span class="t">            <span class="str">f"  itst={self.itst},itnd={self.itnd},itdel={self.itdel},"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t167" href="#t167">167</a></span><span class="t">            <span class="str">f"  histo={self.histo},"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t168" href="#t168">168</a></span><span class="t">            <span class="str">f"  series={self.series},"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t169" href="#t169">169</a></span><span class="t">            <span class="str">f"  corr={self.corr},"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t170" href="#t170">170</a></span><span class="t">            <span class="str">"&amp;end"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t171" href="#t171">171</a></span><span class="t">            <span class="str">f"{tmp_cda_path} {self.sequence}"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t172" href="#t172">172</a></span><span class="t">            <span class="str">"!"</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t173" href="#t173">173</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t174" href="#t174">174</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">cmd</span> <span class="op">=</span> <span class="op">[</span><span class="str">"\n"</span><span class="op">.</span><span class="nam">join</span><span class="op">(</span><span class="nam">instructions</span><span class="op">)</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t175" href="#t175">175</a></span><span class="t">        <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="str">'Creating command line with instructions and required arguments'</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t176" href="#t176">176</a></span><span class="t">               <span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">global_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t177" href="#t177">177</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t178" href="#t178">178</a></span><span class="t">        <span class="com"># Run Biobb block</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t179" href="#t179">179</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">run_biobb</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t180" href="#t180">180</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t181" href="#t181">181</a></span><span class="t">        <span class="com"># change back to original directory</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t182" href="#t182">182</a></span><span class="t">        <span class="nam">os</span><span class="op">.</span><span class="nam">chdir</span><span class="op">(</span><span class="nam">original_directory</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t183" href="#t183">183</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t184" href="#t184">184</a></span><span class="t">        <span class="com"># create zipfile and write output inside</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t185" href="#t185">185</a></span><span class="t">        <span class="nam">zf</span> <span class="op">=</span> <span class="nam">zipfile</span><span class="op">.</span><span class="nam">ZipFile</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t186" href="#t186">186</a></span><span class="t">            <span class="nam">Path</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">"out"</span><span class="op">]</span><span class="op">[</span><span class="str">"output_zip_path"</span><span class="op">]</span><span class="op">)</span><span class="op">,</span> <span class="str">"w"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t187" href="#t187">187</a></span><span class="t">        <span class="key">for</span> <span class="nam">canal_outfile</span> <span class="key">in</span> <span class="nam">Path</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span><span class="op">)</span><span class="op">.</span><span class="nam">glob</span><span class="op">(</span><span class="str">"canal_output*"</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t188" href="#t188">188</a></span><span class="t">            <span class="nam">zf</span><span class="op">.</span><span class="nam">write</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t189" href="#t189">189</a></span><span class="t">                <span class="nam">canal_outfile</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t190" href="#t190">190</a></span><span class="t">                <span class="nam">arcname</span><span class="op">=</span><span class="nam">canal_outfile</span><span class="op">.</span><span class="nam">name</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t191" href="#t191">191</a></span><span class="t">        <span class="nam">zf</span><span class="op">.</span><span class="nam">close</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t192" href="#t192">192</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t193" href="#t193">193</a></span><span class="t">        <span class="com"># Remove temporary file(s)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t194" href="#t194">194</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_files</span><span class="op">.</span><span class="nam">extend</span><span class="op">(</span><span class="op">[</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t195" href="#t195">195</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"unique_dir"</span><span class="op">)</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t196" href="#t196">196</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t197" href="#t197">197</a></span><span class="t">        <span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t198" href="#t198">198</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">remove_tmp_files</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t199" href="#t199">199</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t200" href="#t200">200</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_arguments</span><span class="op">(</span><span class="nam">output_files_created</span><span class="op">=</span><span class="key">True</span><span class="op">,</span> <span class="nam">raise_exception</span><span class="op">=</span><span class="key">False</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t201" href="#t201">201</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t202" href="#t202">202</a></span><span class="t">        <span class="key">return</span> <span class="nam">self</span><span class="op">.</span><span class="nam">return_code</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t203" href="#t203">203</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t204" href="#t204">204</a></span><span class="t"><span class="key">def</span> <span class="nam">biobb_canal</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t205" href="#t205">205</a></span><span class="t">        <span class="nam">input_cda_file</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t206" href="#t206">206</a></span><span class="t">        <span class="nam">output_zip_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t207" href="#t207">207</a></span><span class="t">        <span class="nam">input_lis_file</span><span class="op">:</span> <span class="nam">str</span> <span class="op">=</span> <span class="key">None</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t208" href="#t208">208</a></span><span class="t">        <span class="nam">properties</span><span class="op">:</span> <span class="nam">dict</span> <span class="op">=</span> <span class="key">None</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t209" href="#t209">209</a></span><span class="t">        <span class="op">**</span><span class="nam">kwargs</span><span class="op">)</span> <span class="op">-></span> <span class="nam">int</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t210" href="#t210">210</a></span><span class="t">    <span class="str">"""Create :class:`Canal &lt;biobb_dna.curvesplus.biobb_canal.Canal>` class and</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t211" href="#t211">211</a></span><span class="t"><span class="str">    execute the :meth:`launch() &lt;biobb_dna.curvesplus.biobb_canal.Canal.launch>` method."""</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t212" href="#t212">212</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t213" href="#t213">213</a></span><span class="t">    <span class="key">return</span> <span class="nam">Canal</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t214" href="#t214">214</a></span><span class="t">        <span class="nam">input_cda_file</span><span class="op">=</span><span class="nam">input_cda_file</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t215" href="#t215">215</a></span><span class="t">        <span class="nam">input_lis_file</span><span class="op">=</span><span class="nam">input_lis_file</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t216" href="#t216">216</a></span><span class="t">        <span class="nam">output_zip_path</span><span class="op">=</span><span class="nam">output_zip_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t217" href="#t217">217</a></span><span class="t">        <span class="nam">properties</span><span class="op">=</span><span class="nam">properties</span><span class="op">,</span> <span class="op">**</span><span class="nam">kwargs</span><span class="op">)</span><span class="op">.</span><span class="nam">launch</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t218" href="#t218">218</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t204" href="#t204">204</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t205" href="#t205">205</a></span><span class="t"><span class="key">def</span> <span class="nam">biobb_canal</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t206" href="#t206">206</a></span><span class="t">        <span class="nam">input_cda_file</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t207" href="#t207">207</a></span><span class="t">        <span class="nam">output_zip_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t208" href="#t208">208</a></span><span class="t">        <span class="nam">input_lis_file</span><span class="op">:</span> <span class="nam">str</span> <span class="op">=</span> <span class="key">None</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t209" href="#t209">209</a></span><span class="t">        <span class="nam">properties</span><span class="op">:</span> <span class="nam">dict</span> <span class="op">=</span> <span class="key">None</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t210" href="#t210">210</a></span><span class="t">        <span class="op">**</span><span class="nam">kwargs</span><span class="op">)</span> <span class="op">-></span> <span class="nam">int</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t211" href="#t211">211</a></span><span class="t">    <span class="str">"""Create :class:`Canal &lt;biobb_dna.curvesplus.biobb_canal.Canal>` class and</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t212" href="#t212">212</a></span><span class="t"><span class="str">    execute the :meth:`launch() &lt;biobb_dna.curvesplus.biobb_canal.Canal.launch>` method."""</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t213" href="#t213">213</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t214" href="#t214">214</a></span><span class="t">    <span class="key">return</span> <span class="nam">Canal</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t215" href="#t215">215</a></span><span class="t">        <span class="nam">input_cda_file</span><span class="op">=</span><span class="nam">input_cda_file</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t216" href="#t216">216</a></span><span class="t">        <span class="nam">input_lis_file</span><span class="op">=</span><span class="nam">input_lis_file</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t217" href="#t217">217</a></span><span class="t">        <span class="nam">output_zip_path</span><span class="op">=</span><span class="nam">output_zip_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t218" href="#t218">218</a></span><span class="t">        <span class="nam">properties</span><span class="op">=</span><span class="nam">properties</span><span class="op">,</span> <span class="op">**</span><span class="nam">kwargs</span><span class="op">)</span><span class="op">.</span><span class="nam">launch</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t219" href="#t219">219</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t220" href="#t220">220</a></span><span class="t"><span class="key">def</span> <span class="nam">main</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t221" href="#t221">221</a></span><span class="t">    <span class="str">"""Command line execution of this building block. Please check the command line documentation."""</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t222" href="#t222">222</a></span><span class="t">    <span class="nam">parser</span> <span class="op">=</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">ArgumentParser</span><span class="op">(</span><span class="nam">description</span><span class="op">=</span><span class="str">'Execute Canal from the Curves+ software suite.'</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t223" href="#t223">223</a></span><span class="t">                                     <span class="nam">formatter_class</span><span class="op">=</span><span class="key">lambda</span> <span class="nam">prog</span><span class="op">:</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">RawTextHelpFormatter</span><span class="op">(</span><span class="nam">prog</span><span class="op">,</span> <span class="nam">width</span><span class="op">=</span><span class="num">99999</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t224" href="#t224">224</a></span><span class="t">    <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--config'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">False</span><span class="op">,</span> <span class="nam">help</span><span class="op">=</span><span class="str">'Configuration file'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t225" href="#t225">225</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t226" href="#t226">226</a></span><span class="t">    <span class="nam">required_args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument_group</span><span class="op">(</span><span class="str">'required arguments'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t227" href="#t227">227</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--input_cda_file'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t228" href="#t228">228</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'cda input file from Curves+ output. Accepted formats: cda.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t229" href="#t229">229</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--output_zip_path'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t230" href="#t230">230</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Filename for .zip file with Canal output. Accepted formats: zip.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t231" href="#t231">231</a></span><span class="t">    <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--input_lis_file'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">False</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t232" href="#t232">232</a></span><span class="t">                        <span class="nam">help</span><span class="op">=</span><span class="str">'lis input file from Curves+ output. Accepted formats: lis.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t233" href="#t233">233</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t234" href="#t234">234</a></span><span class="t">    <span class="nam">args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">parse_args</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t235" href="#t235">235</a></span><span class="t">    <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="op">=</span> <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="key">or</span> <span class="str">"{}"</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t236" href="#t236">236</a></span><span class="t">    <span class="nam">properties</span> <span class="op">=</span> <span class="nam">settings</span><span class="op">.</span><span class="nam">ConfReader</span><span class="op">(</span><span class="nam">config</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">config</span><span class="op">)</span><span class="op">.</span><span class="nam">get_prop_dic</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t237" href="#t237">237</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t238" href="#t238">238</a></span><span class="t">    <span class="nam">biobb_canal</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t239" href="#t239">239</a></span><span class="t">        <span class="nam">input_cda_file</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_cda_file</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t240" href="#t240">240</a></span><span class="t">        <span class="nam">input_lis_file</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_lis_file</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t241" href="#t241">241</a></span><span class="t">        <span class="nam">output_zip_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">output_zip_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t242" href="#t242">242</a></span><span class="t">        <span class="nam">properties</span><span class="op">=</span><span class="nam">properties</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t243" href="#t243">243</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t220" href="#t220">220</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t221" href="#t221">221</a></span><span class="t"><span class="key">def</span> <span class="nam">main</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t222" href="#t222">222</a></span><span class="t">    <span class="str">"""Command line execution of this building block. Please check the command line documentation."""</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t223" href="#t223">223</a></span><span class="t">    <span class="nam">parser</span> <span class="op">=</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">ArgumentParser</span><span class="op">(</span><span class="nam">description</span><span class="op">=</span><span class="str">'Execute Canal from the Curves+ software suite.'</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t224" href="#t224">224</a></span><span class="t">                                     <span class="nam">formatter_class</span><span class="op">=</span><span class="key">lambda</span> <span class="nam">prog</span><span class="op">:</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">RawTextHelpFormatter</span><span class="op">(</span><span class="nam">prog</span><span class="op">,</span> <span class="nam">width</span><span class="op">=</span><span class="num">99999</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t225" href="#t225">225</a></span><span class="t">    <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--config'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">False</span><span class="op">,</span> <span class="nam">help</span><span class="op">=</span><span class="str">'Configuration file'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t226" href="#t226">226</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t227" href="#t227">227</a></span><span class="t">    <span class="nam">required_args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument_group</span><span class="op">(</span><span class="str">'required arguments'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t228" href="#t228">228</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--input_cda_file'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t229" href="#t229">229</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'cda input file from Curves+ output. Accepted formats: cda.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t230" href="#t230">230</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--output_zip_path'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t231" href="#t231">231</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Filename for .zip file with Canal output. Accepted formats: zip.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t232" href="#t232">232</a></span><span class="t">    <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--input_lis_file'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">False</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t233" href="#t233">233</a></span><span class="t">                        <span class="nam">help</span><span class="op">=</span><span class="str">'lis input file from Curves+ output. Accepted formats: lis.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t234" href="#t234">234</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t235" href="#t235">235</a></span><span class="t">    <span class="nam">args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">parse_args</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t236" href="#t236">236</a></span><span class="t">    <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="op">=</span> <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="key">or</span> <span class="str">"{}"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t237" href="#t237">237</a></span><span class="t">    <span class="nam">properties</span> <span class="op">=</span> <span class="nam">settings</span><span class="op">.</span><span class="nam">ConfReader</span><span class="op">(</span><span class="nam">config</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">config</span><span class="op">)</span><span class="op">.</span><span class="nam">get_prop_dic</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t238" href="#t238">238</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t239" href="#t239">239</a></span><span class="t">    <span class="nam">biobb_canal</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t240" href="#t240">240</a></span><span class="t">        <span class="nam">input_cda_file</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_cda_file</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t241" href="#t241">241</a></span><span class="t">        <span class="nam">input_lis_file</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_lis_file</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t242" href="#t242">242</a></span><span class="t">        <span class="nam">output_zip_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">output_zip_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t243" href="#t243">243</a></span><span class="t">        <span class="nam">properties</span><span class="op">=</span><span class="nam">properties</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t244" href="#t244">244</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t245" href="#t245">245</a></span><span class="t"><span class="key">if</span> <span class="nam">__name__</span> <span class="op">==</span> <span class="str">'__main__'</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t246" href="#t246">246</a></span><span class="t">    <span class="nam">main</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t245" href="#t245">245</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t246" href="#t246">246</a></span><span class="t"><span class="key">if</span> <span class="nam">__name__</span> <span class="op">==</span> <span class="str">'__main__'</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t247" href="#t247">247</a></span><span class="t">    <span class="nam">main</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
 </main>
 <footer>
     <div class="content">
@@ -335,7 +336,7 @@ <h2>
             <a class="nav" href="z_74fa14c6d0e940a4_biobb_canion_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.5.1">coverage.py v7.5.1</a>,
-            created at 2024-05-07 09:06 +0000
+            created at 2024-05-24 09:29 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_74fa14c6d0e940a4_biobb_canion_py.html b/coverage/z_74fa14c6d0e940a4_biobb_canion_py.html
index b5b5756a..1f3725b3 100644
--- a/coverage/z_74fa14c6d0e940a4_biobb_canion_py.html
+++ b/coverage/z_74fa14c6d0e940a4_biobb_canion_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_74fa14c6d0e940a4_biobb_curves_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.5.1">coverage.py v7.5.1</a>,
-            created at 2024-05-07 09:06 +0000
+            created at 2024-05-24 09:29 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -98,238 +98,239 @@ <h2>
     <p class="pln"><span class="n"><a id="t16" href="#t16">16</a></span><span class="t">    <span class="str">"""</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t17" href="#t17">17</a></span><span class="t"><span class="str">    | biobb_dna Canion</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t18" href="#t18">18</a></span><span class="t"><span class="str">    | Wrapper for the Canion executable  that is part of the Curves+ software suite.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t19" href="#t19">19</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t20" href="#t20">20</a></span><span class="t"><span class="str">    Args:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t21" href="#t21">21</a></span><span class="t"><span class="str">        input_cdi_path (str): Trajectory input file. File type: input. `Sample file &lt;https://mmb.irbbarcelona.org/biobb-dev/biobb-api/public/samples/THGA_K.cdi>`_. Accepted formats: cdi (edam:format_2330).</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t22" href="#t22">22</a></span><span class="t"><span class="str">        input_afr_path (str): Helical axis frames corresponding to the input conformation to be analyzed. File type: input. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/curvesplus/THGA.afr>`_. Accepted formats: afr (edam:format_2330).</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t23" href="#t23">23</a></span><span class="t"><span class="str">        input_avg_struc_path (str): Average DNA conformation. File type: input. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/curvesplus/THGA_avg.pdb>`_. Accepted formats: pdb (edam:format_1476).</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t24" href="#t24">24</a></span><span class="t"><span class="str">        output_zip_path (str) (Optional): Filename for .zip files containing Canion output files. File type: output. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/reference/curvesplus/canion_output.zip>`_. Accepted formats: zip (edam:format_3987).</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t25" href="#t25">25</a></span><span class="t"><span class="str">        properties (dict):</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t26" href="#t26">26</a></span><span class="t"><span class="str">            * **bases** (*str*) - (None) Sequence of bases to be analyzed (default is blank, meaning no specified sequence).</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t27" href="#t27">27</a></span><span class="t"><span class="str">            * **type** (*str*) - ('*') Ions (or atoms) to be analyzed. Options are 'Na+', 'K', 'K+', 'Cl', 'Cl-', 'CL', 'P', 'C1*', 'NH1', 'NH2', 'NZ', '1' for all cations, '-1' for all anions, '0' for neutral species or '*' for all available data.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t28" href="#t28">28</a></span><span class="t"><span class="str">            * **dlow** (*float*) - (0) Select starting segment of the oglimer to analyze. If both dhig and dlow are 0, entire oglimer is analyzed.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t29" href="#t29">29</a></span><span class="t"><span class="str">            * **dhig** (*float*) - (0) Select ending segment of the oglimer to analyze, being the maximum value the total number of base pairs in the oligomer. If both dhig and dlow are 0, entire oglimer is analyzed.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t30" href="#t30">30</a></span><span class="t"><span class="str">            * **rlow** (*float*) - (0) Minimal distances from the helical axis taken into account in the analysis.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t31" href="#t31">31</a></span><span class="t"><span class="str">            * **rhig** (*float*) - (0) Maximal distances from the helical axis taken into account in the analysis.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t32" href="#t32">32</a></span><span class="t"><span class="str">            * **alow** (*float*) - (0) Minimal angle range to analyze.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t33" href="#t33">33</a></span><span class="t"><span class="str">            * **ahig** (*float*) - (360) Maximal angle range to analyze.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t34" href="#t34">34</a></span><span class="t"><span class="str">            * **itst** (*int*) - (None) Number of first snapshot to be analyzed.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t35" href="#t35">35</a></span><span class="t"><span class="str">            * **itnd** (*int*) - (None) Number of last snapshot to be analyzed.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t36" href="#t36">36</a></span><span class="t"><span class="str">            * **itdel** (*int*) - (None) Spacing between analyzed snapshots.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t37" href="#t37">37</a></span><span class="t"><span class="str">            * **rmsf** (*bool*) - (False) If set to True uses the combination of the helical ion parameters and an average helical axis to map the ions into Cartesian space and then calculates their average position (pdb output) and their root mean square fluctuation values (rmsf output). A single pass rmsf algorithm to make this calculation possible with a single read of the trajectory file. This option is generally used for solute atoms and not for solvent molecules or ions.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t38" href="#t38">38</a></span><span class="t"><span class="str">            * **circ** (*bool*) - (False) If set to True, minicircles are analyzed.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t39" href="#t39">39</a></span><span class="t"><span class="str">            * **binary_path** (*str*) - (Canion) Path to Canion executable, otherwise the program wil look for Canion executable in the binaries folder.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t40" href="#t40">40</a></span><span class="t"><span class="str">            * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t41" href="#t41">41</a></span><span class="t"><span class="str">            * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t42" href="#t42">42</a></span><span class="t"><span class="str">    Examples:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t43" href="#t43">43</a></span><span class="t"><span class="str">        This is a use example of how to use the building block from Python::</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t44" href="#t44">44</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t45" href="#t45">45</a></span><span class="t"><span class="str">            from biobb_dna.curvesplus.biobb_canion import biobb_canion</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t46" href="#t46">46</a></span><span class="t"><span class="str">            prop = {</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t47" href="#t47">47</a></span><span class="t"><span class="str">                'type': 'K+',</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t48" href="#t48">48</a></span><span class="t"><span class="str">                'bases': 'G'</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t49" href="#t49">49</a></span><span class="t"><span class="str">            }</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t50" href="#t50">50</a></span><span class="t"><span class="str">            biobb_canion(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t51" href="#t51">51</a></span><span class="t"><span class="str">                input_cdi_path='/path/to/input.cdi',</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t52" href="#t52">52</a></span><span class="t"><span class="str">                input_afr_path='/path/to/input.afr',</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t53" href="#t53">53</a></span><span class="t"><span class="str">                input_avg_struc_path='/path/to/input.pdb',</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t54" href="#t54">54</a></span><span class="t"><span class="str">                output_zip_path='/path/to/output.zip',</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t55" href="#t55">55</a></span><span class="t"><span class="str">                properties=prop)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t56" href="#t56">56</a></span><span class="t"><span class="str">    Info:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t57" href="#t57">57</a></span><span class="t"><span class="str">        * wrapped_software:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t58" href="#t58">58</a></span><span class="t"><span class="str">            * name: Canion</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t59" href="#t59">59</a></span><span class="t"><span class="str">            * version: >=2.6</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t60" href="#t60">60</a></span><span class="t"><span class="str">            * license: BSD 3-Clause</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t61" href="#t61">61</a></span><span class="t"><span class="str">        * ontology:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t62" href="#t62">62</a></span><span class="t"><span class="str">            * name: EDAM</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t63" href="#t63">63</a></span><span class="t"><span class="str">            * schema: http://edamontology.org/EDAM.owl</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t64" href="#t64">64</a></span><span class="t"><span class="str">    """</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t65" href="#t65">65</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t66" href="#t66">66</a></span><span class="t">    <span class="key">def</span> <span class="nam">__init__</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t67" href="#t67">67</a></span><span class="t">            <span class="nam">self</span><span class="op">,</span> <span class="nam">input_cdi_path</span><span class="op">,</span> <span class="nam">input_afr_path</span><span class="op">,</span> <span class="nam">input_avg_struc_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t68" href="#t68">68</a></span><span class="t">            <span class="nam">output_zip_path</span><span class="op">=</span><span class="key">None</span><span class="op">,</span> <span class="nam">properties</span><span class="op">=</span><span class="key">None</span><span class="op">,</span> <span class="op">**</span><span class="nam">kwargs</span><span class="op">)</span> <span class="op">-></span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t69" href="#t69">69</a></span><span class="t">        <span class="nam">properties</span> <span class="op">=</span> <span class="nam">properties</span> <span class="key">or</span> <span class="op">{</span><span class="op">}</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t70" href="#t70">70</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t71" href="#t71">71</a></span><span class="t">        <span class="com"># Call parent class constructor</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t72" href="#t72">72</a></span><span class="t">        <span class="nam">super</span><span class="op">(</span><span class="op">)</span><span class="op">.</span><span class="nam">__init__</span><span class="op">(</span><span class="nam">properties</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t73" href="#t73">73</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">locals_var_dict</span> <span class="op">=</span> <span class="nam">locals</span><span class="op">(</span><span class="op">)</span><span class="op">.</span><span class="nam">copy</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t74" href="#t74">74</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t75" href="#t75">75</a></span><span class="t">        <span class="com"># Input/Output files</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t76" href="#t76">76</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span> <span class="op">=</span> <span class="op">{</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t77" href="#t77">77</a></span><span class="t">            <span class="str">'in'</span><span class="op">:</span> <span class="op">{</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t78" href="#t78">78</a></span><span class="t">                <span class="str">'input_cdi_path'</span><span class="op">:</span> <span class="nam">input_cdi_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t79" href="#t79">79</a></span><span class="t">                <span class="str">'input_afr_path'</span><span class="op">:</span> <span class="nam">input_afr_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t80" href="#t80">80</a></span><span class="t">                <span class="str">'input_avg_struc_path'</span><span class="op">:</span> <span class="nam">input_avg_struc_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t81" href="#t81">81</a></span><span class="t">            <span class="op">}</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t82" href="#t82">82</a></span><span class="t">            <span class="str">'out'</span><span class="op">:</span> <span class="op">{</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t83" href="#t83">83</a></span><span class="t">                <span class="str">'output_zip_path'</span><span class="op">:</span> <span class="nam">output_zip_path</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t84" href="#t84">84</a></span><span class="t">            <span class="op">}</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t85" href="#t85">85</a></span><span class="t">        <span class="op">}</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t86" href="#t86">86</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t87" href="#t87">87</a></span><span class="t">        <span class="com"># Properties specific for BB</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t88" href="#t88">88</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">binary_path</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'binary_path'</span><span class="op">,</span> <span class="str">'Canion'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t89" href="#t89">89</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">bases</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'bases'</span><span class="op">,</span> <span class="key">None</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t90" href="#t90">90</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">type</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'type'</span><span class="op">,</span> <span class="str">'*'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t91" href="#t91">91</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">dlow</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'dlow'</span><span class="op">,</span> <span class="num">0</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t92" href="#t92">92</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">dhig</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'dhig'</span><span class="op">,</span> <span class="num">0</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t93" href="#t93">93</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">rlow</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'rlow'</span><span class="op">,</span> <span class="num">0</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t94" href="#t94">94</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">rhig</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'rhig'</span><span class="op">,</span> <span class="num">0</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t95" href="#t95">95</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">alow</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'alow'</span><span class="op">,</span> <span class="num">0</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t96" href="#t96">96</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">ahig</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'ahig'</span><span class="op">,</span> <span class="num">360</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t97" href="#t97">97</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">itst</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'itst'</span><span class="op">,</span> <span class="key">None</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t98" href="#t98">98</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">itnd</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'itnd'</span><span class="op">,</span> <span class="key">None</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t99" href="#t99">99</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">itdel</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'itdel'</span><span class="op">,</span> <span class="key">None</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t100" href="#t100">100</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">rmsf</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'rmsf'</span><span class="op">,</span> <span class="str">'.f.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t101" href="#t101">101</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">circ</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'circ'</span><span class="op">,</span> <span class="str">'.f.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t102" href="#t102">102</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">properties</span> <span class="op">=</span> <span class="nam">properties</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t103" href="#t103">103</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t104" href="#t104">104</a></span><span class="t">        <span class="com"># Check the properties</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t105" href="#t105">105</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_properties</span><span class="op">(</span><span class="nam">properties</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t106" href="#t106">106</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_arguments</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t107" href="#t107">107</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t108" href="#t108">108</a></span><span class="t">    <span class="op">@</span><span class="nam">launchlogger</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t109" href="#t109">109</a></span><span class="t">    <span class="key">def</span> <span class="nam">launch</span><span class="op">(</span><span class="nam">self</span><span class="op">)</span> <span class="op">-></span> <span class="nam">int</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t110" href="#t110">110</a></span><span class="t">        <span class="str">"""Execute the :class:`Canion &lt;biobb_dna.curvesplus.biobb_canion.Canion>` object."""</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t111" href="#t111">111</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t112" href="#t112">112</a></span><span class="t">        <span class="com"># Setup Biobb</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t113" href="#t113">113</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">check_restart</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t114" href="#t114">114</a></span><span class="t">            <span class="key">return</span> <span class="num">0</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t115" href="#t115">115</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">stage_files</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t116" href="#t116">116</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t117" href="#t117">117</a></span><span class="t">        <span class="nam">ion_type_options</span> <span class="op">=</span> <span class="op">[</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t118" href="#t118">118</a></span><span class="t">            <span class="str">'Na+'</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t119" href="#t119">119</a></span><span class="t">            <span class="str">'K'</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t120" href="#t120">120</a></span><span class="t">            <span class="str">'K+'</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t121" href="#t121">121</a></span><span class="t">            <span class="str">'Cl'</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t122" href="#t122">122</a></span><span class="t">            <span class="str">'Cl-'</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t123" href="#t123">123</a></span><span class="t">            <span class="str">'CL'</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t124" href="#t124">124</a></span><span class="t">            <span class="str">'P'</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t125" href="#t125">125</a></span><span class="t">            <span class="str">'C1*'</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t126" href="#t126">126</a></span><span class="t">            <span class="str">'NH1'</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t127" href="#t127">127</a></span><span class="t">            <span class="str">'NH2'</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t128" href="#t128">128</a></span><span class="t">            <span class="str">'NZ'</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t129" href="#t129">129</a></span><span class="t">            <span class="str">'1'</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t130" href="#t130">130</a></span><span class="t">            <span class="str">'-1'</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t131" href="#t131">131</a></span><span class="t">            <span class="str">'0'</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t132" href="#t132">132</a></span><span class="t">            <span class="str">'*'</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t133" href="#t133">133</a></span><span class="t">        <span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t134" href="#t134">134</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">type</span> <span class="key">not</span> <span class="key">in</span> <span class="nam">ion_type_options</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t135" href="#t135">135</a></span><span class="t">            <span class="key">raise</span> <span class="nam">ValueError</span><span class="op">(</span><span class="op">(</span><span class="str">"Invalid value for property type! "</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t136" href="#t136">136</a></span><span class="t">                              <span class="str">f"Option include: {ion_type_options}"</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t137" href="#t137">137</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t138" href="#t138">138</a></span><span class="t">        <span class="com"># Creating temporary folder</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t139" href="#t139">139</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span> <span class="op">=</span> <span class="nam">fu</span><span class="op">.</span><span class="nam">create_unique_dir</span><span class="op">(</span><span class="nam">prefix</span><span class="op">=</span><span class="str">"canion_"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t140" href="#t140">140</a></span><span class="t">        <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="str">'Creating %s temporary folder'</span> <span class="op">%</span> <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t141" href="#t141">141</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t142" href="#t142">142</a></span><span class="t">        <span class="com"># copy input files to temporary folder</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t143" href="#t143">143</a></span><span class="t">        <span class="nam">shutil</span><span class="op">.</span><span class="nam">copy</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'input_cdi_path'</span><span class="op">]</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t144" href="#t144">144</a></span><span class="t">        <span class="nam">shutil</span><span class="op">.</span><span class="nam">copy</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'input_afr_path'</span><span class="op">]</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t145" href="#t145">145</a></span><span class="t">        <span class="nam">shutil</span><span class="op">.</span><span class="nam">copy</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t146" href="#t146">146</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'input_avg_struc_path'</span><span class="op">]</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t147" href="#t147">147</a></span><span class="t">        <span class="nam">input_cdi_file</span> <span class="op">=</span> <span class="nam">Path</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'input_cdi_path'</span><span class="op">]</span><span class="op">)</span><span class="op">.</span><span class="nam">name</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t148" href="#t148">148</a></span><span class="t">        <span class="nam">input_afr_file</span> <span class="op">=</span> <span class="nam">Path</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'input_afr_path'</span><span class="op">]</span><span class="op">)</span><span class="op">.</span><span class="nam">name</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t149" href="#t149">149</a></span><span class="t">        <span class="nam">input_avg_struc</span> <span class="op">=</span> <span class="nam">Path</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'input_avg_struc_path'</span><span class="op">]</span><span class="op">)</span><span class="op">.</span><span class="nam">name</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t150" href="#t150">150</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t151" href="#t151">151</a></span><span class="t">        <span class="com"># change directory to temporary folder</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t152" href="#t152">152</a></span><span class="t">        <span class="nam">original_directory</span> <span class="op">=</span> <span class="nam">os</span><span class="op">.</span><span class="nam">getcwd</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t153" href="#t153">153</a></span><span class="t">        <span class="nam">os</span><span class="op">.</span><span class="nam">chdir</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t154" href="#t154">154</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t155" href="#t155">155</a></span><span class="t">        <span class="com"># create intructions</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t156" href="#t156">156</a></span><span class="t">        <span class="nam">instructions</span> <span class="op">=</span> <span class="op">[</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t157" href="#t157">157</a></span><span class="t">            <span class="str">f"{self.binary_path} &lt;&lt;! "</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t158" href="#t158">158</a></span><span class="t">            <span class="str">"&amp;inp"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t159" href="#t159">159</a></span><span class="t">            <span class="str">"  lis=canion_output,"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t160" href="#t160">160</a></span><span class="t">            <span class="str">f"  dat={input_cdi_file[:-4]},"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t161" href="#t161">161</a></span><span class="t">            <span class="str">f"  axfrm={input_afr_file[:-4]},"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t162" href="#t162">162</a></span><span class="t">            <span class="str">f"  solute={input_avg_struc[:-4]},"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t163" href="#t163">163</a></span><span class="t">            <span class="str">f"  type={self.type},"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t164" href="#t164">164</a></span><span class="t">            <span class="str">f"  dlow={self.dlow},"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t165" href="#t165">165</a></span><span class="t">            <span class="str">f"  dhig={self.dhig},"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t166" href="#t166">166</a></span><span class="t">            <span class="str">f"  rlow={self.rlow},"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t167" href="#t167">167</a></span><span class="t">            <span class="str">f"  rhig={self.rhig},"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t168" href="#t168">168</a></span><span class="t">            <span class="str">f"  alow={self.alow},"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t169" href="#t169">169</a></span><span class="t">            <span class="str">f"  ahig={self.ahig},"</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t170" href="#t170">170</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">bases</span> <span class="key">is</span> <span class="key">not</span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t171" href="#t171">171</a></span><span class="t">            <span class="com"># add topology file if needed</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t172" href="#t172">172</a></span><span class="t">            <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="str">'Appending sequence of bases to be searched to command'</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t173" href="#t173">173</a></span><span class="t">                   <span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">global_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t174" href="#t174">174</a></span><span class="t">            <span class="nam">instructions</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="str">f"  seq={self.bases},"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t175" href="#t175">175</a></span><span class="t">        <span class="nam">instructions</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="str">"&amp;end"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t176" href="#t176">176</a></span><span class="t">        <span class="nam">instructions</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="str">"!"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t177" href="#t177">177</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">cmd</span> <span class="op">=</span> <span class="op">[</span><span class="str">"\n"</span><span class="op">.</span><span class="nam">join</span><span class="op">(</span><span class="nam">instructions</span><span class="op">)</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t178" href="#t178">178</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t179" href="#t179">179</a></span><span class="t">        <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="str">'Creating command line with instructions and required arguments'</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t180" href="#t180">180</a></span><span class="t">               <span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">global_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t181" href="#t181">181</a></span><span class="t">        <span class="com"># Run Biobb block</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t182" href="#t182">182</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">run_biobb</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t183" href="#t183">183</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t184" href="#t184">184</a></span><span class="t">        <span class="com"># change back to original directory</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t185" href="#t185">185</a></span><span class="t">        <span class="nam">os</span><span class="op">.</span><span class="nam">chdir</span><span class="op">(</span><span class="nam">original_directory</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t186" href="#t186">186</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t187" href="#t187">187</a></span><span class="t">        <span class="com"># create zipfile and write output inside</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t188" href="#t188">188</a></span><span class="t">        <span class="nam">zf</span> <span class="op">=</span> <span class="nam">zipfile</span><span class="op">.</span><span class="nam">ZipFile</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t189" href="#t189">189</a></span><span class="t">            <span class="nam">Path</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">"out"</span><span class="op">]</span><span class="op">[</span><span class="str">"output_zip_path"</span><span class="op">]</span><span class="op">)</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t190" href="#t190">190</a></span><span class="t">            <span class="str">"w"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t191" href="#t191">191</a></span><span class="t">        <span class="key">for</span> <span class="nam">curves_outfile</span> <span class="key">in</span> <span class="nam">Path</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span><span class="op">)</span><span class="op">.</span><span class="nam">glob</span><span class="op">(</span><span class="str">"canion_output*"</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t192" href="#t192">192</a></span><span class="t">            <span class="nam">zf</span><span class="op">.</span><span class="nam">write</span><span class="op">(</span><span class="nam">curves_outfile</span><span class="op">,</span> <span class="nam">arcname</span><span class="op">=</span><span class="nam">curves_outfile</span><span class="op">.</span><span class="nam">name</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t193" href="#t193">193</a></span><span class="t">        <span class="nam">zf</span><span class="op">.</span><span class="nam">close</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t194" href="#t194">194</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t195" href="#t195">195</a></span><span class="t">        <span class="com"># Remove temporary file(s)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t196" href="#t196">196</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_files</span><span class="op">.</span><span class="nam">extend</span><span class="op">(</span><span class="op">[</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t197" href="#t197">197</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"unique_dir"</span><span class="op">)</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t198" href="#t198">198</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t199" href="#t199">199</a></span><span class="t">        <span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t200" href="#t200">200</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">remove_tmp_files</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t201" href="#t201">201</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t202" href="#t202">202</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_arguments</span><span class="op">(</span><span class="nam">output_files_created</span><span class="op">=</span><span class="key">True</span><span class="op">,</span> <span class="nam">raise_exception</span><span class="op">=</span><span class="key">False</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t203" href="#t203">203</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t204" href="#t204">204</a></span><span class="t">        <span class="key">return</span> <span class="nam">self</span><span class="op">.</span><span class="nam">return_code</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t205" href="#t205">205</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t19" href="#t19">19</a></span><span class="t"><span class="str">    | Analyzes the trajectory of ions around a DNA molecule.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t20" href="#t20">20</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t21" href="#t21">21</a></span><span class="t"><span class="str">    Args:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t22" href="#t22">22</a></span><span class="t"><span class="str">        input_cdi_path (str): Trajectory input file. File type: input. `Sample file &lt;https://mmb.irbbarcelona.org/biobb-dev/biobb-api/public/samples/THGA_K.cdi>`_. Accepted formats: cdi (edam:format_2330).</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t23" href="#t23">23</a></span><span class="t"><span class="str">        input_afr_path (str): Helical axis frames corresponding to the input conformation to be analyzed. File type: input. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/curvesplus/THGA.afr>`_. Accepted formats: afr (edam:format_2330).</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t24" href="#t24">24</a></span><span class="t"><span class="str">        input_avg_struc_path (str): Average DNA conformation. File type: input. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/curvesplus/THGA_avg.pdb>`_. Accepted formats: pdb (edam:format_1476).</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t25" href="#t25">25</a></span><span class="t"><span class="str">        output_zip_path (str) (Optional): Filename for .zip files containing Canion output files. File type: output. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/reference/curvesplus/canion_output.zip>`_. Accepted formats: zip (edam:format_3987).</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t26" href="#t26">26</a></span><span class="t"><span class="str">        properties (dict):</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t27" href="#t27">27</a></span><span class="t"><span class="str">            * **bases** (*str*) - (None) Sequence of bases to be analyzed (default is blank, meaning no specified sequence).</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t28" href="#t28">28</a></span><span class="t"><span class="str">            * **type** (*str*) - ('*') Ions (or atoms) to be analyzed. Options are 'Na+', 'K', 'K+', 'Cl', 'Cl-', 'CL', 'P', 'C1*', 'NH1', 'NH2', 'NZ', '1' for all cations, '-1' for all anions, '0' for neutral species or '*' for all available data.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t29" href="#t29">29</a></span><span class="t"><span class="str">            * **dlow** (*float*) - (0) Select starting segment of the oglimer to analyze. If both dhig and dlow are 0, entire oglimer is analyzed.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t30" href="#t30">30</a></span><span class="t"><span class="str">            * **dhig** (*float*) - (0) Select ending segment of the oglimer to analyze, being the maximum value the total number of base pairs in the oligomer. If both dhig and dlow are 0, entire oglimer is analyzed.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t31" href="#t31">31</a></span><span class="t"><span class="str">            * **rlow** (*float*) - (0) Minimal distances from the helical axis taken into account in the analysis.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t32" href="#t32">32</a></span><span class="t"><span class="str">            * **rhig** (*float*) - (0) Maximal distances from the helical axis taken into account in the analysis.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t33" href="#t33">33</a></span><span class="t"><span class="str">            * **alow** (*float*) - (0) Minimal angle range to analyze.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t34" href="#t34">34</a></span><span class="t"><span class="str">            * **ahig** (*float*) - (360) Maximal angle range to analyze.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t35" href="#t35">35</a></span><span class="t"><span class="str">            * **itst** (*int*) - (None) Number of first snapshot to be analyzed.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t36" href="#t36">36</a></span><span class="t"><span class="str">            * **itnd** (*int*) - (None) Number of last snapshot to be analyzed.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t37" href="#t37">37</a></span><span class="t"><span class="str">            * **itdel** (*int*) - (None) Spacing between analyzed snapshots.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t38" href="#t38">38</a></span><span class="t"><span class="str">            * **rmsf** (*bool*) - (False) If set to True uses the combination of the helical ion parameters and an average helical axis to map the ions into Cartesian space and then calculates their average position (pdb output) and their root mean square fluctuation values (rmsf output). A single pass rmsf algorithm to make this calculation possible with a single read of the trajectory file. This option is generally used for solute atoms and not for solvent molecules or ions.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t39" href="#t39">39</a></span><span class="t"><span class="str">            * **circ** (*bool*) - (False) If set to True, minicircles are analyzed.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t40" href="#t40">40</a></span><span class="t"><span class="str">            * **binary_path** (*str*) - (Canion) Path to Canion executable, otherwise the program wil look for Canion executable in the binaries folder.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t41" href="#t41">41</a></span><span class="t"><span class="str">            * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t42" href="#t42">42</a></span><span class="t"><span class="str">            * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t43" href="#t43">43</a></span><span class="t"><span class="str">    Examples:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t44" href="#t44">44</a></span><span class="t"><span class="str">        This is a use example of how to use the building block from Python::</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t45" href="#t45">45</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t46" href="#t46">46</a></span><span class="t"><span class="str">            from biobb_dna.curvesplus.biobb_canion import biobb_canion</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t47" href="#t47">47</a></span><span class="t"><span class="str">            prop = {</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t48" href="#t48">48</a></span><span class="t"><span class="str">                'type': 'K+',</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t49" href="#t49">49</a></span><span class="t"><span class="str">                'bases': 'G'</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t50" href="#t50">50</a></span><span class="t"><span class="str">            }</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t51" href="#t51">51</a></span><span class="t"><span class="str">            biobb_canion(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t52" href="#t52">52</a></span><span class="t"><span class="str">                input_cdi_path='/path/to/input.cdi',</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t53" href="#t53">53</a></span><span class="t"><span class="str">                input_afr_path='/path/to/input.afr',</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t54" href="#t54">54</a></span><span class="t"><span class="str">                input_avg_struc_path='/path/to/input.pdb',</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t55" href="#t55">55</a></span><span class="t"><span class="str">                output_zip_path='/path/to/output.zip',</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t56" href="#t56">56</a></span><span class="t"><span class="str">                properties=prop)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t57" href="#t57">57</a></span><span class="t"><span class="str">    Info:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t58" href="#t58">58</a></span><span class="t"><span class="str">        * wrapped_software:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t59" href="#t59">59</a></span><span class="t"><span class="str">            * name: Canion</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t60" href="#t60">60</a></span><span class="t"><span class="str">            * version: >=2.6</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t61" href="#t61">61</a></span><span class="t"><span class="str">            * license: BSD 3-Clause</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t62" href="#t62">62</a></span><span class="t"><span class="str">        * ontology:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t63" href="#t63">63</a></span><span class="t"><span class="str">            * name: EDAM</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t64" href="#t64">64</a></span><span class="t"><span class="str">            * schema: http://edamontology.org/EDAM.owl</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t65" href="#t65">65</a></span><span class="t"><span class="str">    """</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t66" href="#t66">66</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t67" href="#t67">67</a></span><span class="t">    <span class="key">def</span> <span class="nam">__init__</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t68" href="#t68">68</a></span><span class="t">            <span class="nam">self</span><span class="op">,</span> <span class="nam">input_cdi_path</span><span class="op">,</span> <span class="nam">input_afr_path</span><span class="op">,</span> <span class="nam">input_avg_struc_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t69" href="#t69">69</a></span><span class="t">            <span class="nam">output_zip_path</span><span class="op">=</span><span class="key">None</span><span class="op">,</span> <span class="nam">properties</span><span class="op">=</span><span class="key">None</span><span class="op">,</span> <span class="op">**</span><span class="nam">kwargs</span><span class="op">)</span> <span class="op">-></span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t70" href="#t70">70</a></span><span class="t">        <span class="nam">properties</span> <span class="op">=</span> <span class="nam">properties</span> <span class="key">or</span> <span class="op">{</span><span class="op">}</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t71" href="#t71">71</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t72" href="#t72">72</a></span><span class="t">        <span class="com"># Call parent class constructor</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t73" href="#t73">73</a></span><span class="t">        <span class="nam">super</span><span class="op">(</span><span class="op">)</span><span class="op">.</span><span class="nam">__init__</span><span class="op">(</span><span class="nam">properties</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t74" href="#t74">74</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">locals_var_dict</span> <span class="op">=</span> <span class="nam">locals</span><span class="op">(</span><span class="op">)</span><span class="op">.</span><span class="nam">copy</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t75" href="#t75">75</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t76" href="#t76">76</a></span><span class="t">        <span class="com"># Input/Output files</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t77" href="#t77">77</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span> <span class="op">=</span> <span class="op">{</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t78" href="#t78">78</a></span><span class="t">            <span class="str">'in'</span><span class="op">:</span> <span class="op">{</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t79" href="#t79">79</a></span><span class="t">                <span class="str">'input_cdi_path'</span><span class="op">:</span> <span class="nam">input_cdi_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t80" href="#t80">80</a></span><span class="t">                <span class="str">'input_afr_path'</span><span class="op">:</span> <span class="nam">input_afr_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t81" href="#t81">81</a></span><span class="t">                <span class="str">'input_avg_struc_path'</span><span class="op">:</span> <span class="nam">input_avg_struc_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t82" href="#t82">82</a></span><span class="t">            <span class="op">}</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t83" href="#t83">83</a></span><span class="t">            <span class="str">'out'</span><span class="op">:</span> <span class="op">{</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t84" href="#t84">84</a></span><span class="t">                <span class="str">'output_zip_path'</span><span class="op">:</span> <span class="nam">output_zip_path</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t85" href="#t85">85</a></span><span class="t">            <span class="op">}</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t86" href="#t86">86</a></span><span class="t">        <span class="op">}</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t87" href="#t87">87</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t88" href="#t88">88</a></span><span class="t">        <span class="com"># Properties specific for BB</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t89" href="#t89">89</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">binary_path</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'binary_path'</span><span class="op">,</span> <span class="str">'Canion'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t90" href="#t90">90</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">bases</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'bases'</span><span class="op">,</span> <span class="key">None</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t91" href="#t91">91</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">type</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'type'</span><span class="op">,</span> <span class="str">'*'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t92" href="#t92">92</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">dlow</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'dlow'</span><span class="op">,</span> <span class="num">0</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t93" href="#t93">93</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">dhig</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'dhig'</span><span class="op">,</span> <span class="num">0</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t94" href="#t94">94</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">rlow</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'rlow'</span><span class="op">,</span> <span class="num">0</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t95" href="#t95">95</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">rhig</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'rhig'</span><span class="op">,</span> <span class="num">0</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t96" href="#t96">96</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">alow</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'alow'</span><span class="op">,</span> <span class="num">0</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t97" href="#t97">97</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">ahig</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'ahig'</span><span class="op">,</span> <span class="num">360</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t98" href="#t98">98</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">itst</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'itst'</span><span class="op">,</span> <span class="key">None</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t99" href="#t99">99</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">itnd</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'itnd'</span><span class="op">,</span> <span class="key">None</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t100" href="#t100">100</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">itdel</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'itdel'</span><span class="op">,</span> <span class="key">None</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t101" href="#t101">101</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">rmsf</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'rmsf'</span><span class="op">,</span> <span class="str">'.f.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t102" href="#t102">102</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">circ</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'circ'</span><span class="op">,</span> <span class="str">'.f.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t103" href="#t103">103</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">properties</span> <span class="op">=</span> <span class="nam">properties</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t104" href="#t104">104</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t105" href="#t105">105</a></span><span class="t">        <span class="com"># Check the properties</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t106" href="#t106">106</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_properties</span><span class="op">(</span><span class="nam">properties</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t107" href="#t107">107</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_arguments</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t108" href="#t108">108</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t109" href="#t109">109</a></span><span class="t">    <span class="op">@</span><span class="nam">launchlogger</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t110" href="#t110">110</a></span><span class="t">    <span class="key">def</span> <span class="nam">launch</span><span class="op">(</span><span class="nam">self</span><span class="op">)</span> <span class="op">-></span> <span class="nam">int</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t111" href="#t111">111</a></span><span class="t">        <span class="str">"""Execute the :class:`Canion &lt;biobb_dna.curvesplus.biobb_canion.Canion>` object."""</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t112" href="#t112">112</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t113" href="#t113">113</a></span><span class="t">        <span class="com"># Setup Biobb</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t114" href="#t114">114</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">check_restart</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t115" href="#t115">115</a></span><span class="t">            <span class="key">return</span> <span class="num">0</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t116" href="#t116">116</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">stage_files</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t117" href="#t117">117</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t118" href="#t118">118</a></span><span class="t">        <span class="nam">ion_type_options</span> <span class="op">=</span> <span class="op">[</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t119" href="#t119">119</a></span><span class="t">            <span class="str">'Na+'</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t120" href="#t120">120</a></span><span class="t">            <span class="str">'K'</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t121" href="#t121">121</a></span><span class="t">            <span class="str">'K+'</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t122" href="#t122">122</a></span><span class="t">            <span class="str">'Cl'</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t123" href="#t123">123</a></span><span class="t">            <span class="str">'Cl-'</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t124" href="#t124">124</a></span><span class="t">            <span class="str">'CL'</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t125" href="#t125">125</a></span><span class="t">            <span class="str">'P'</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t126" href="#t126">126</a></span><span class="t">            <span class="str">'C1*'</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t127" href="#t127">127</a></span><span class="t">            <span class="str">'NH1'</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t128" href="#t128">128</a></span><span class="t">            <span class="str">'NH2'</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t129" href="#t129">129</a></span><span class="t">            <span class="str">'NZ'</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t130" href="#t130">130</a></span><span class="t">            <span class="str">'1'</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t131" href="#t131">131</a></span><span class="t">            <span class="str">'-1'</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t132" href="#t132">132</a></span><span class="t">            <span class="str">'0'</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t133" href="#t133">133</a></span><span class="t">            <span class="str">'*'</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t134" href="#t134">134</a></span><span class="t">        <span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t135" href="#t135">135</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">type</span> <span class="key">not</span> <span class="key">in</span> <span class="nam">ion_type_options</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t136" href="#t136">136</a></span><span class="t">            <span class="key">raise</span> <span class="nam">ValueError</span><span class="op">(</span><span class="op">(</span><span class="str">"Invalid value for property type! "</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t137" href="#t137">137</a></span><span class="t">                              <span class="str">f"Option include: {ion_type_options}"</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t138" href="#t138">138</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t139" href="#t139">139</a></span><span class="t">        <span class="com"># Creating temporary folder</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t140" href="#t140">140</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span> <span class="op">=</span> <span class="nam">fu</span><span class="op">.</span><span class="nam">create_unique_dir</span><span class="op">(</span><span class="nam">prefix</span><span class="op">=</span><span class="str">"canion_"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t141" href="#t141">141</a></span><span class="t">        <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="str">'Creating %s temporary folder'</span> <span class="op">%</span> <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t142" href="#t142">142</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t143" href="#t143">143</a></span><span class="t">        <span class="com"># copy input files to temporary folder</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t144" href="#t144">144</a></span><span class="t">        <span class="nam">shutil</span><span class="op">.</span><span class="nam">copy</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'input_cdi_path'</span><span class="op">]</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t145" href="#t145">145</a></span><span class="t">        <span class="nam">shutil</span><span class="op">.</span><span class="nam">copy</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'input_afr_path'</span><span class="op">]</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t146" href="#t146">146</a></span><span class="t">        <span class="nam">shutil</span><span class="op">.</span><span class="nam">copy</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t147" href="#t147">147</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'input_avg_struc_path'</span><span class="op">]</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t148" href="#t148">148</a></span><span class="t">        <span class="nam">input_cdi_file</span> <span class="op">=</span> <span class="nam">Path</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'input_cdi_path'</span><span class="op">]</span><span class="op">)</span><span class="op">.</span><span class="nam">name</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t149" href="#t149">149</a></span><span class="t">        <span class="nam">input_afr_file</span> <span class="op">=</span> <span class="nam">Path</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'input_afr_path'</span><span class="op">]</span><span class="op">)</span><span class="op">.</span><span class="nam">name</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t150" href="#t150">150</a></span><span class="t">        <span class="nam">input_avg_struc</span> <span class="op">=</span> <span class="nam">Path</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'input_avg_struc_path'</span><span class="op">]</span><span class="op">)</span><span class="op">.</span><span class="nam">name</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t151" href="#t151">151</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t152" href="#t152">152</a></span><span class="t">        <span class="com"># change directory to temporary folder</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t153" href="#t153">153</a></span><span class="t">        <span class="nam">original_directory</span> <span class="op">=</span> <span class="nam">os</span><span class="op">.</span><span class="nam">getcwd</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t154" href="#t154">154</a></span><span class="t">        <span class="nam">os</span><span class="op">.</span><span class="nam">chdir</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t155" href="#t155">155</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t156" href="#t156">156</a></span><span class="t">        <span class="com"># create intructions</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t157" href="#t157">157</a></span><span class="t">        <span class="nam">instructions</span> <span class="op">=</span> <span class="op">[</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t158" href="#t158">158</a></span><span class="t">            <span class="str">f"{self.binary_path} &lt;&lt;! "</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t159" href="#t159">159</a></span><span class="t">            <span class="str">"&amp;inp"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t160" href="#t160">160</a></span><span class="t">            <span class="str">"  lis=canion_output,"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t161" href="#t161">161</a></span><span class="t">            <span class="str">f"  dat={input_cdi_file[:-4]},"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t162" href="#t162">162</a></span><span class="t">            <span class="str">f"  axfrm={input_afr_file[:-4]},"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t163" href="#t163">163</a></span><span class="t">            <span class="str">f"  solute={input_avg_struc[:-4]},"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t164" href="#t164">164</a></span><span class="t">            <span class="str">f"  type={self.type},"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t165" href="#t165">165</a></span><span class="t">            <span class="str">f"  dlow={self.dlow},"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t166" href="#t166">166</a></span><span class="t">            <span class="str">f"  dhig={self.dhig},"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t167" href="#t167">167</a></span><span class="t">            <span class="str">f"  rlow={self.rlow},"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t168" href="#t168">168</a></span><span class="t">            <span class="str">f"  rhig={self.rhig},"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t169" href="#t169">169</a></span><span class="t">            <span class="str">f"  alow={self.alow},"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t170" href="#t170">170</a></span><span class="t">            <span class="str">f"  ahig={self.ahig},"</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t171" href="#t171">171</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">bases</span> <span class="key">is</span> <span class="key">not</span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t172" href="#t172">172</a></span><span class="t">            <span class="com"># add topology file if needed</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t173" href="#t173">173</a></span><span class="t">            <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="str">'Appending sequence of bases to be searched to command'</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t174" href="#t174">174</a></span><span class="t">                   <span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">global_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t175" href="#t175">175</a></span><span class="t">            <span class="nam">instructions</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="str">f"  seq={self.bases},"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t176" href="#t176">176</a></span><span class="t">        <span class="nam">instructions</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="str">"&amp;end"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t177" href="#t177">177</a></span><span class="t">        <span class="nam">instructions</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="str">"!"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t178" href="#t178">178</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">cmd</span> <span class="op">=</span> <span class="op">[</span><span class="str">"\n"</span><span class="op">.</span><span class="nam">join</span><span class="op">(</span><span class="nam">instructions</span><span class="op">)</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t179" href="#t179">179</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t180" href="#t180">180</a></span><span class="t">        <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="str">'Creating command line with instructions and required arguments'</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t181" href="#t181">181</a></span><span class="t">               <span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">global_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t182" href="#t182">182</a></span><span class="t">        <span class="com"># Run Biobb block</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t183" href="#t183">183</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">run_biobb</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t184" href="#t184">184</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t185" href="#t185">185</a></span><span class="t">        <span class="com"># change back to original directory</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t186" href="#t186">186</a></span><span class="t">        <span class="nam">os</span><span class="op">.</span><span class="nam">chdir</span><span class="op">(</span><span class="nam">original_directory</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t187" href="#t187">187</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t188" href="#t188">188</a></span><span class="t">        <span class="com"># create zipfile and write output inside</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t189" href="#t189">189</a></span><span class="t">        <span class="nam">zf</span> <span class="op">=</span> <span class="nam">zipfile</span><span class="op">.</span><span class="nam">ZipFile</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t190" href="#t190">190</a></span><span class="t">            <span class="nam">Path</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">"out"</span><span class="op">]</span><span class="op">[</span><span class="str">"output_zip_path"</span><span class="op">]</span><span class="op">)</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t191" href="#t191">191</a></span><span class="t">            <span class="str">"w"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t192" href="#t192">192</a></span><span class="t">        <span class="key">for</span> <span class="nam">curves_outfile</span> <span class="key">in</span> <span class="nam">Path</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span><span class="op">)</span><span class="op">.</span><span class="nam">glob</span><span class="op">(</span><span class="str">"canion_output*"</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t193" href="#t193">193</a></span><span class="t">            <span class="nam">zf</span><span class="op">.</span><span class="nam">write</span><span class="op">(</span><span class="nam">curves_outfile</span><span class="op">,</span> <span class="nam">arcname</span><span class="op">=</span><span class="nam">curves_outfile</span><span class="op">.</span><span class="nam">name</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t194" href="#t194">194</a></span><span class="t">        <span class="nam">zf</span><span class="op">.</span><span class="nam">close</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t195" href="#t195">195</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t196" href="#t196">196</a></span><span class="t">        <span class="com"># Remove temporary file(s)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t197" href="#t197">197</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_files</span><span class="op">.</span><span class="nam">extend</span><span class="op">(</span><span class="op">[</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t198" href="#t198">198</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"unique_dir"</span><span class="op">)</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t199" href="#t199">199</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t200" href="#t200">200</a></span><span class="t">        <span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t201" href="#t201">201</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">remove_tmp_files</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t202" href="#t202">202</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t203" href="#t203">203</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_arguments</span><span class="op">(</span><span class="nam">output_files_created</span><span class="op">=</span><span class="key">True</span><span class="op">,</span> <span class="nam">raise_exception</span><span class="op">=</span><span class="key">False</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t204" href="#t204">204</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t205" href="#t205">205</a></span><span class="t">        <span class="key">return</span> <span class="nam">self</span><span class="op">.</span><span class="nam">return_code</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t206" href="#t206">206</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t207" href="#t207">207</a></span><span class="t"><span class="key">def</span> <span class="nam">biobb_canion</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t208" href="#t208">208</a></span><span class="t">        <span class="nam">input_cdi_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span> <span class="nam">input_afr_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span> <span class="nam">input_avg_struc_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t209" href="#t209">209</a></span><span class="t">        <span class="nam">output_zip_path</span><span class="op">:</span> <span class="nam">str</span> <span class="op">=</span> <span class="key">None</span><span class="op">,</span> <span class="nam">properties</span><span class="op">:</span> <span class="nam">dict</span> <span class="op">=</span> <span class="key">None</span><span class="op">,</span> <span class="op">**</span><span class="nam">kwargs</span><span class="op">)</span> <span class="op">-></span> <span class="nam">int</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t210" href="#t210">210</a></span><span class="t">    <span class="str">"""Create :class:`Canion &lt;biobb_dna.curvesplus.biobb_canion.Canion>` class and</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t211" href="#t211">211</a></span><span class="t"><span class="str">    execute the :meth:`launch() &lt;biobb_dna.curvesplus.biobb_canion.Canion.launch>` method."""</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t212" href="#t212">212</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t213" href="#t213">213</a></span><span class="t">    <span class="key">return</span> <span class="nam">Canion</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t214" href="#t214">214</a></span><span class="t">        <span class="nam">input_cdi_path</span><span class="op">=</span><span class="nam">input_cdi_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t215" href="#t215">215</a></span><span class="t">        <span class="nam">input_afr_path</span><span class="op">=</span><span class="nam">input_afr_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t216" href="#t216">216</a></span><span class="t">        <span class="nam">input_avg_struc_path</span><span class="op">=</span><span class="nam">input_avg_struc_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t217" href="#t217">217</a></span><span class="t">        <span class="nam">output_zip_path</span><span class="op">=</span><span class="nam">output_zip_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t218" href="#t218">218</a></span><span class="t">        <span class="nam">properties</span><span class="op">=</span><span class="nam">properties</span><span class="op">,</span> <span class="op">**</span><span class="nam">kwargs</span><span class="op">)</span><span class="op">.</span><span class="nam">launch</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t219" href="#t219">219</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t207" href="#t207">207</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t208" href="#t208">208</a></span><span class="t"><span class="key">def</span> <span class="nam">biobb_canion</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t209" href="#t209">209</a></span><span class="t">        <span class="nam">input_cdi_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span> <span class="nam">input_afr_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span> <span class="nam">input_avg_struc_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t210" href="#t210">210</a></span><span class="t">        <span class="nam">output_zip_path</span><span class="op">:</span> <span class="nam">str</span> <span class="op">=</span> <span class="key">None</span><span class="op">,</span> <span class="nam">properties</span><span class="op">:</span> <span class="nam">dict</span> <span class="op">=</span> <span class="key">None</span><span class="op">,</span> <span class="op">**</span><span class="nam">kwargs</span><span class="op">)</span> <span class="op">-></span> <span class="nam">int</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t211" href="#t211">211</a></span><span class="t">    <span class="str">"""Create :class:`Canion &lt;biobb_dna.curvesplus.biobb_canion.Canion>` class and</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t212" href="#t212">212</a></span><span class="t"><span class="str">    execute the :meth:`launch() &lt;biobb_dna.curvesplus.biobb_canion.Canion.launch>` method."""</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t213" href="#t213">213</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t214" href="#t214">214</a></span><span class="t">    <span class="key">return</span> <span class="nam">Canion</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t215" href="#t215">215</a></span><span class="t">        <span class="nam">input_cdi_path</span><span class="op">=</span><span class="nam">input_cdi_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t216" href="#t216">216</a></span><span class="t">        <span class="nam">input_afr_path</span><span class="op">=</span><span class="nam">input_afr_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t217" href="#t217">217</a></span><span class="t">        <span class="nam">input_avg_struc_path</span><span class="op">=</span><span class="nam">input_avg_struc_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t218" href="#t218">218</a></span><span class="t">        <span class="nam">output_zip_path</span><span class="op">=</span><span class="nam">output_zip_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t219" href="#t219">219</a></span><span class="t">        <span class="nam">properties</span><span class="op">=</span><span class="nam">properties</span><span class="op">,</span> <span class="op">**</span><span class="nam">kwargs</span><span class="op">)</span><span class="op">.</span><span class="nam">launch</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t220" href="#t220">220</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t221" href="#t221">221</a></span><span class="t"><span class="key">def</span> <span class="nam">main</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t222" href="#t222">222</a></span><span class="t">    <span class="str">"""Command line execution of this building block. Please check the command line documentation."""</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t223" href="#t223">223</a></span><span class="t">    <span class="nam">parser</span> <span class="op">=</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">ArgumentParser</span><span class="op">(</span><span class="nam">description</span><span class="op">=</span><span class="str">'Execute Canion form the Curves+ software suite.'</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t224" href="#t224">224</a></span><span class="t">                                     <span class="nam">formatter_class</span><span class="op">=</span><span class="key">lambda</span> <span class="nam">prog</span><span class="op">:</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">RawTextHelpFormatter</span><span class="op">(</span><span class="nam">prog</span><span class="op">,</span> <span class="nam">width</span><span class="op">=</span><span class="num">99999</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t225" href="#t225">225</a></span><span class="t">    <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--config'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">False</span><span class="op">,</span> <span class="nam">help</span><span class="op">=</span><span class="str">'Configuration file'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t226" href="#t226">226</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t227" href="#t227">227</a></span><span class="t">    <span class="nam">required_args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument_group</span><span class="op">(</span><span class="str">'required arguments'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t228" href="#t228">228</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--input_cdi_path'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t229" href="#t229">229</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Ion position data file. Accepted formats: cdi.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t230" href="#t230">230</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--input_afr_path'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t231" href="#t231">231</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Helical axis frames data. Accepted formats: afr.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t232" href="#t232">232</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--input_avg_struc_path'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t233" href="#t233">233</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Average DNA conformation fike file. Accepted formats: pdb.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t234" href="#t234">234</a></span><span class="t">    <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--output_zip_path'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">False</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t235" href="#t235">235</a></span><span class="t">                        <span class="nam">help</span><span class="op">=</span><span class="str">'Filename to give to output files. Accepted formats: zip.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t236" href="#t236">236</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t237" href="#t237">237</a></span><span class="t">    <span class="nam">args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">parse_args</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t238" href="#t238">238</a></span><span class="t">    <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="op">=</span> <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="key">or</span> <span class="str">"{}"</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t239" href="#t239">239</a></span><span class="t">    <span class="nam">properties</span> <span class="op">=</span> <span class="nam">settings</span><span class="op">.</span><span class="nam">ConfReader</span><span class="op">(</span><span class="nam">config</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">config</span><span class="op">)</span><span class="op">.</span><span class="nam">get_prop_dic</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t240" href="#t240">240</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t241" href="#t241">241</a></span><span class="t">    <span class="nam">biobb_canion</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t242" href="#t242">242</a></span><span class="t">        <span class="nam">input_cdi_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_cdi_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t243" href="#t243">243</a></span><span class="t">        <span class="nam">input_afr_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_afr_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t244" href="#t244">244</a></span><span class="t">        <span class="nam">input_avg_struc_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_avg_struc_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t245" href="#t245">245</a></span><span class="t">        <span class="nam">output_zip_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">output_zip_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t246" href="#t246">246</a></span><span class="t">        <span class="nam">properties</span><span class="op">=</span><span class="nam">properties</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t247" href="#t247">247</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t221" href="#t221">221</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t222" href="#t222">222</a></span><span class="t"><span class="key">def</span> <span class="nam">main</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t223" href="#t223">223</a></span><span class="t">    <span class="str">"""Command line execution of this building block. Please check the command line documentation."""</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t224" href="#t224">224</a></span><span class="t">    <span class="nam">parser</span> <span class="op">=</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">ArgumentParser</span><span class="op">(</span><span class="nam">description</span><span class="op">=</span><span class="str">'Execute Canion form the Curves+ software suite.'</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t225" href="#t225">225</a></span><span class="t">                                     <span class="nam">formatter_class</span><span class="op">=</span><span class="key">lambda</span> <span class="nam">prog</span><span class="op">:</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">RawTextHelpFormatter</span><span class="op">(</span><span class="nam">prog</span><span class="op">,</span> <span class="nam">width</span><span class="op">=</span><span class="num">99999</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t226" href="#t226">226</a></span><span class="t">    <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--config'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">False</span><span class="op">,</span> <span class="nam">help</span><span class="op">=</span><span class="str">'Configuration file'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t227" href="#t227">227</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t228" href="#t228">228</a></span><span class="t">    <span class="nam">required_args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument_group</span><span class="op">(</span><span class="str">'required arguments'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t229" href="#t229">229</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--input_cdi_path'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t230" href="#t230">230</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Ion position data file. Accepted formats: cdi.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t231" href="#t231">231</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--input_afr_path'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t232" href="#t232">232</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Helical axis frames data. Accepted formats: afr.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t233" href="#t233">233</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--input_avg_struc_path'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t234" href="#t234">234</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Average DNA conformation fike file. Accepted formats: pdb.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t235" href="#t235">235</a></span><span class="t">    <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--output_zip_path'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">False</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t236" href="#t236">236</a></span><span class="t">                        <span class="nam">help</span><span class="op">=</span><span class="str">'Filename to give to output files. Accepted formats: zip.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t237" href="#t237">237</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t238" href="#t238">238</a></span><span class="t">    <span class="nam">args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">parse_args</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t239" href="#t239">239</a></span><span class="t">    <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="op">=</span> <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="key">or</span> <span class="str">"{}"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t240" href="#t240">240</a></span><span class="t">    <span class="nam">properties</span> <span class="op">=</span> <span class="nam">settings</span><span class="op">.</span><span class="nam">ConfReader</span><span class="op">(</span><span class="nam">config</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">config</span><span class="op">)</span><span class="op">.</span><span class="nam">get_prop_dic</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t241" href="#t241">241</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t242" href="#t242">242</a></span><span class="t">    <span class="nam">biobb_canion</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t243" href="#t243">243</a></span><span class="t">        <span class="nam">input_cdi_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_cdi_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t244" href="#t244">244</a></span><span class="t">        <span class="nam">input_afr_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_afr_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t245" href="#t245">245</a></span><span class="t">        <span class="nam">input_avg_struc_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_avg_struc_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t246" href="#t246">246</a></span><span class="t">        <span class="nam">output_zip_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">output_zip_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t247" href="#t247">247</a></span><span class="t">        <span class="nam">properties</span><span class="op">=</span><span class="nam">properties</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t248" href="#t248">248</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t249" href="#t249">249</a></span><span class="t"><span class="key">if</span> <span class="nam">__name__</span> <span class="op">==</span> <span class="str">'__main__'</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t250" href="#t250">250</a></span><span class="t">    <span class="nam">main</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t249" href="#t249">249</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t250" href="#t250">250</a></span><span class="t"><span class="key">if</span> <span class="nam">__name__</span> <span class="op">==</span> <span class="str">'__main__'</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t251" href="#t251">251</a></span><span class="t">    <span class="nam">main</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
 </main>
 <footer>
     <div class="content">
@@ -339,7 +340,7 @@ <h2>
             <a class="nav" href="z_74fa14c6d0e940a4_biobb_curves_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.5.1">coverage.py v7.5.1</a>,
-            created at 2024-05-07 09:06 +0000
+            created at 2024-05-24 09:29 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_74fa14c6d0e940a4_biobb_curves_py.html b/coverage/z_74fa14c6d0e940a4_biobb_curves_py.html
index 38529d3f..f05c02c2 100644
--- a/coverage/z_74fa14c6d0e940a4_biobb_curves_py.html
+++ b/coverage/z_74fa14c6d0e940a4_biobb_curves_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_3afbcd666ed82c91___init___py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.5.1">coverage.py v7.5.1</a>,
-            created at 2024-05-07 09:06 +0000
+            created at 2024-05-24 09:29 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -98,268 +98,269 @@ <h2>
     <p class="pln"><span class="n"><a id="t16" href="#t16">16</a></span><span class="t">    <span class="str">"""</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t17" href="#t17">17</a></span><span class="t"><span class="str">    | biobb_dna Curves</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t18" href="#t18">18</a></span><span class="t"><span class="str">    | Wrapper for the Cur+ executable  that is part of the Curves+ software suite.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t19" href="#t19">19</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t20" href="#t20">20</a></span><span class="t"><span class="str">    Args:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t21" href="#t21">21</a></span><span class="t"><span class="str">        input_struc_path (str): Trajectory or PDB input file. File type: input. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/curvesplus/structure.stripped.trj>`_. Accepted formats: trj (edam:format_3910), pdb (edam:format_1476), netcdf (edam:format_3650), nc (edam:format_3650).</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t22" href="#t22">22</a></span><span class="t"><span class="str">        input_top_path (str) (Optional): Topology file, needed along with .trj file (optional). File type: input. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/curvesplus/structure.stripped.top>`_. Accepted formats: top (edam:format_3881).</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t23" href="#t23">23</a></span><span class="t"><span class="str">        output_cda_path (str): Filename for Curves+ output .cda file. File type: output. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/reference/curvesplus/curves_trj_output.cda>`_. Accepted formats: cda (edam:format_2330).</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t24" href="#t24">24</a></span><span class="t"><span class="str">        output_lis_path (str): Filename for Curves+ output .lis file. File type: output. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/reference/curvesplus/curves_trj_output.lis>`_. Accepted formats: lis (edam:format_2330).</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t25" href="#t25">25</a></span><span class="t"><span class="str">        output_zip_path (str) (Optional): Filename for .zip files containing Curves+ output that is not .cda or .lis files. File type: output. Accepted formats: zip (edam:format_3987).</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t26" href="#t26">26</a></span><span class="t"><span class="str">        properties (dict):</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t27" href="#t27">27</a></span><span class="t"><span class="str">            * **s1range** (*str*) - (None) Range of first strand. Must be specified in the form "start:end".</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t28" href="#t28">28</a></span><span class="t"><span class="str">            * **s2range** (*str*) - (None) Range of second strand. Must be specified in the form "start:end".</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t29" href="#t29">29</a></span><span class="t"><span class="str">            * **stdlib_path** (*str*) - ('standard') Path to Curves' standard library files for nucleotides. If not specified will look for 'standard' files in current directory.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t30" href="#t30">30</a></span><span class="t"><span class="str">            * **itst** (*int*) - (0) Iteration start index.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t31" href="#t31">31</a></span><span class="t"><span class="str">            * **itnd** (*int*) - (0) Iteration end index.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t32" href="#t32">32</a></span><span class="t"><span class="str">            * **itdel** (*int*) - (1) Iteration delimiter.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t33" href="#t33">33</a></span><span class="t"><span class="str">            * **ions** (*bool*) - (False) If True, helicoidal analysis of ions (or solvent molecules) around solute is carried out.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t34" href="#t34">34</a></span><span class="t"><span class="str">            * **test** (*bool*) - (False) If True, provide addition output in .lis file on fitting and axis generation.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t35" href="#t35">35</a></span><span class="t"><span class="str">            * **line** (*bool*) - (False) if True, find the best linear helical axis.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t36" href="#t36">36</a></span><span class="t"><span class="str">            * **fit** (*bool*) - (True) if True, fit a standard bases to the input coordinates (important for MD snapshots to avoid base distortions leading to noisy helical parameters).</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t37" href="#t37">37</a></span><span class="t"><span class="str">            * **axfrm** (*bool*) - (False) if True, generates closely spaced helical axis frames as input for Canal and Canion.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t38" href="#t38">38</a></span><span class="t"><span class="str">            * **binary_path** (*str*) - (Cur+) Path to Curves+ executable, otherwise the program wil look for Cur+ executable in the binaries folder.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t39" href="#t39">39</a></span><span class="t"><span class="str">            * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t40" href="#t40">40</a></span><span class="t"><span class="str">            * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t41" href="#t41">41</a></span><span class="t"><span class="str">    Examples:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t42" href="#t42">42</a></span><span class="t"><span class="str">        This is a use example of how to use the building block from Python::</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t43" href="#t43">43</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t44" href="#t44">44</a></span><span class="t"><span class="str">            from biobb_dna.curvesplus.biobb_curves import biobb_curves</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t45" href="#t45">45</a></span><span class="t"><span class="str">            prop = {</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t46" href="#t46">46</a></span><span class="t"><span class="str">                's1range': '1:12',</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t47" href="#t47">47</a></span><span class="t"><span class="str">                's2range': '24:13',</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t48" href="#t48">48</a></span><span class="t"><span class="str">            }</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t49" href="#t49">49</a></span><span class="t"><span class="str">            biobb_curves(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t50" href="#t50">50</a></span><span class="t"><span class="str">                input_struc_path='/path/to/structure/file.trj',</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t51" href="#t51">51</a></span><span class="t"><span class="str">                input_top_path='/path/to/topology/file.top',</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t52" href="#t52">52</a></span><span class="t"><span class="str">                output_cda_path='/path/to/output/file.cda',</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t53" href="#t53">53</a></span><span class="t"><span class="str">                output_lis_path='/path/to/output/file.lis',</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t54" href="#t54">54</a></span><span class="t"><span class="str">                properties=prop)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t55" href="#t55">55</a></span><span class="t"><span class="str">    Info:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t56" href="#t56">56</a></span><span class="t"><span class="str">        * wrapped_software:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t57" href="#t57">57</a></span><span class="t"><span class="str">            * name: Curves</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t58" href="#t58">58</a></span><span class="t"><span class="str">            * version: >=2.6</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t59" href="#t59">59</a></span><span class="t"><span class="str">            * license: BSD 3-Clause</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t60" href="#t60">60</a></span><span class="t"><span class="str">        * ontology:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t61" href="#t61">61</a></span><span class="t"><span class="str">            * name: EDAM</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t62" href="#t62">62</a></span><span class="t"><span class="str">            * schema: http://edamontology.org/EDAM.owl</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t63" href="#t63">63</a></span><span class="t"><span class="str">    """</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t64" href="#t64">64</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t65" href="#t65">65</a></span><span class="t">    <span class="key">def</span> <span class="nam">__init__</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t66" href="#t66">66</a></span><span class="t">            <span class="nam">self</span><span class="op">,</span> <span class="nam">input_struc_path</span><span class="op">,</span> <span class="nam">output_lis_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t67" href="#t67">67</a></span><span class="t">            <span class="nam">output_cda_path</span><span class="op">,</span> <span class="nam">output_zip_path</span><span class="op">=</span><span class="key">None</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t68" href="#t68">68</a></span><span class="t">            <span class="nam">input_top_path</span><span class="op">=</span><span class="key">None</span><span class="op">,</span> <span class="nam">properties</span><span class="op">=</span><span class="key">None</span><span class="op">,</span> <span class="op">**</span><span class="nam">kwargs</span><span class="op">)</span> <span class="op">-></span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t69" href="#t69">69</a></span><span class="t">        <span class="nam">properties</span> <span class="op">=</span> <span class="nam">properties</span> <span class="key">or</span> <span class="op">{</span><span class="op">}</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t70" href="#t70">70</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t71" href="#t71">71</a></span><span class="t">        <span class="com"># Call parent class constructor</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t72" href="#t72">72</a></span><span class="t">        <span class="nam">super</span><span class="op">(</span><span class="op">)</span><span class="op">.</span><span class="nam">__init__</span><span class="op">(</span><span class="nam">properties</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t73" href="#t73">73</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">locals_var_dict</span> <span class="op">=</span> <span class="nam">locals</span><span class="op">(</span><span class="op">)</span><span class="op">.</span><span class="nam">copy</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t74" href="#t74">74</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t75" href="#t75">75</a></span><span class="t">        <span class="com"># Input/Output files</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t76" href="#t76">76</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span> <span class="op">=</span> <span class="op">{</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t77" href="#t77">77</a></span><span class="t">            <span class="str">'in'</span><span class="op">:</span> <span class="op">{</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t78" href="#t78">78</a></span><span class="t">                <span class="str">'input_struc_path'</span><span class="op">:</span> <span class="nam">input_struc_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t79" href="#t79">79</a></span><span class="t">                <span class="str">'input_top_path'</span><span class="op">:</span> <span class="nam">input_top_path</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t80" href="#t80">80</a></span><span class="t">            <span class="op">}</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t81" href="#t81">81</a></span><span class="t">            <span class="str">'out'</span><span class="op">:</span> <span class="op">{</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t82" href="#t82">82</a></span><span class="t">                <span class="str">'output_lis_path'</span><span class="op">:</span> <span class="nam">output_lis_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t83" href="#t83">83</a></span><span class="t">                <span class="str">'output_cda_path'</span><span class="op">:</span> <span class="nam">output_cda_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t84" href="#t84">84</a></span><span class="t">                <span class="str">'output_zip_path'</span><span class="op">:</span> <span class="nam">output_zip_path</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t85" href="#t85">85</a></span><span class="t">            <span class="op">}</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t86" href="#t86">86</a></span><span class="t">        <span class="op">}</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t87" href="#t87">87</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t88" href="#t88">88</a></span><span class="t">        <span class="com"># Properties specific for BB</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t89" href="#t89">89</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">s1range</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'s1range'</span><span class="op">,</span> <span class="key">None</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t90" href="#t90">90</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">binary_path</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'binary_path'</span><span class="op">,</span> <span class="str">'Cur+'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t91" href="#t91">91</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">stdlib_path</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'stdlib_path'</span><span class="op">,</span> <span class="key">None</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t92" href="#t92">92</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">s2range</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'s2range'</span><span class="op">,</span> <span class="key">None</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t93" href="#t93">93</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">itst</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'itst'</span><span class="op">,</span> <span class="num">0</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t94" href="#t94">94</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">itnd</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'itnd'</span><span class="op">,</span> <span class="num">0</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t95" href="#t95">95</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">itdel</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'itdel'</span><span class="op">,</span> <span class="num">1</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t96" href="#t96">96</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">ions</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'ions'</span><span class="op">,</span> <span class="str">'.f.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t97" href="#t97">97</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">test</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'test'</span><span class="op">,</span> <span class="str">'.f.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t98" href="#t98">98</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">line</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'line'</span><span class="op">,</span> <span class="str">'.f.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t99" href="#t99">99</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">fit</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'fit'</span><span class="op">,</span> <span class="str">'.t.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t100" href="#t100">100</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">axfrm</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'axfrm'</span><span class="op">,</span> <span class="str">'.f.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t101" href="#t101">101</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">properties</span> <span class="op">=</span> <span class="nam">properties</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t102" href="#t102">102</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t103" href="#t103">103</a></span><span class="t">        <span class="com"># Check the properties</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t104" href="#t104">104</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_properties</span><span class="op">(</span><span class="nam">properties</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t105" href="#t105">105</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_arguments</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t106" href="#t106">106</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t107" href="#t107">107</a></span><span class="t">    <span class="op">@</span><span class="nam">launchlogger</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t108" href="#t108">108</a></span><span class="t">    <span class="key">def</span> <span class="nam">launch</span><span class="op">(</span><span class="nam">self</span><span class="op">)</span> <span class="op">-></span> <span class="nam">int</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t109" href="#t109">109</a></span><span class="t">        <span class="str">"""Execute the :class:`Curves &lt;biobb_dna.curvesplus.biobb_curves.Curves>` object."""</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t110" href="#t110">110</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t111" href="#t111">111</a></span><span class="t">        <span class="com"># Setup Biobb</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t112" href="#t112">112</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">check_restart</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t113" href="#t113">113</a></span><span class="t">            <span class="key">return</span> <span class="num">0</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t114" href="#t114">114</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">stage_files</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t115" href="#t115">115</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t116" href="#t116">116</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">s1range</span> <span class="key">is</span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t117" href="#t117">117</a></span><span class="t">            <span class="key">raise</span> <span class="nam">ValueError</span><span class="op">(</span><span class="str">"property 's1range' must be specified!"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t118" href="#t118">118</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">s2range</span> <span class="key">is</span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t119" href="#t119">119</a></span><span class="t">            <span class="com"># compute s2range if not provided</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t120" href="#t120">120</a></span><span class="t">            <span class="nam">range1_end</span> <span class="op">=</span> <span class="nam">int</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">s1range</span><span class="op">.</span><span class="nam">split</span><span class="op">(</span><span class="str">":"</span><span class="op">)</span><span class="op">[</span><span class="num">1</span><span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t121" href="#t121">121</a></span><span class="t">            <span class="nam">s2start</span> <span class="op">=</span> <span class="nam">range1_end</span> <span class="op">+</span> <span class="num">1</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t122" href="#t122">122</a></span><span class="t">            <span class="nam">s2end</span> <span class="op">=</span> <span class="num">2</span> <span class="op">*</span> <span class="nam">range1_end</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t123" href="#t123">123</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">s2range</span> <span class="op">=</span> <span class="str">f"{s2end}:{s2start}"</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t124" href="#t124">124</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t125" href="#t125">125</a></span><span class="t">        <span class="com"># check standard library files location if not provided</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t126" href="#t126">126</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">stdlib_path</span> <span class="key">is</span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t127" href="#t127">127</a></span><span class="t">            <span class="key">if</span> <span class="nam">os</span><span class="op">.</span><span class="nam">getenv</span><span class="op">(</span><span class="str">"CONDA_PREFIX"</span><span class="op">,</span> <span class="key">False</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t128" href="#t128">128</a></span><span class="t">                <span class="nam">curves_aux_path</span> <span class="op">=</span> <span class="nam">Path</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t129" href="#t129">129</a></span><span class="t">                    <span class="nam">os</span><span class="op">.</span><span class="nam">getenv</span><span class="op">(</span><span class="str">"CONDA_PREFIX"</span><span class="op">)</span><span class="op">)</span> <span class="op">/</span> <span class="str">".curvesplus"</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t130" href="#t130">130</a></span><span class="t">                <span class="com"># check if .curvesplus directory is in $CONDA_PREFIX</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t131" href="#t131">131</a></span><span class="t">                <span class="key">if</span> <span class="nam">curves_aux_path</span><span class="op">.</span><span class="nam">exists</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t132" href="#t132">132</a></span><span class="t">                    <span class="key">if</span> <span class="nam">len</span><span class="op">(</span><span class="nam">list</span><span class="op">(</span><span class="nam">curves_aux_path</span><span class="op">.</span><span class="nam">glob</span><span class="op">(</span><span class="str">"standard_*.lib"</span><span class="op">)</span><span class="op">)</span><span class="op">)</span> <span class="op">!=</span> <span class="num">3</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t133" href="#t133">133</a></span><span class="t">                        <span class="key">raise</span> <span class="nam">FileNotFoundError</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t134" href="#t134">134</a></span><span class="t">                            <span class="str">"One or all standard library files "</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t135" href="#t135">135</a></span><span class="t">                            <span class="str">f"missing from {curves_aux_path}! "</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t136" href="#t136">136</a></span><span class="t">                            <span class="str">"Check files standard_b.lib, "</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t137" href="#t137">137</a></span><span class="t">                            <span class="str">"standard_s.lib and standard_i.lib exist."</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t138" href="#t138">138</a></span><span class="t">                    <span class="nam">self</span><span class="op">.</span><span class="nam">stdlib_path</span> <span class="op">=</span> <span class="nam">curves_aux_path</span> <span class="op">/</span> <span class="str">"standard"</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t139" href="#t139">139</a></span><span class="t">                <span class="key">else</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t140" href="#t140">140</a></span><span class="t">                    <span class="key">raise</span> <span class="nam">FileNotFoundError</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t141" href="#t141">141</a></span><span class="t">                        <span class="str">".curvesplus directory not found in "</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t142" href="#t142">142</a></span><span class="t">                        <span class="str">f"{os.getenv('CONDA_PREFIX')} !"</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t143" href="#t143">143</a></span><span class="t">                        <span class="str">"Please indicate where standard_*.lib files are "</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t144" href="#t144">144</a></span><span class="t">                        <span class="str">"located with the stdlib_path property."</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t145" href="#t145">145</a></span><span class="t">            <span class="key">else</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t146" href="#t146">146</a></span><span class="t">                <span class="com"># CONDA_PREFIX undefined</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t147" href="#t147">147</a></span><span class="t">                <span class="nam">self</span><span class="op">.</span><span class="nam">stdlib_path</span> <span class="op">=</span> <span class="nam">Path</span><span class="op">.</span><span class="nam">cwd</span><span class="op">(</span><span class="op">)</span> <span class="op">/</span> <span class="str">"standard"</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t148" href="#t148">148</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t149" href="#t149">149</a></span><span class="t">        <span class="com"># Creating temporary folder</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t150" href="#t150">150</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span> <span class="op">=</span> <span class="nam">fu</span><span class="op">.</span><span class="nam">create_unique_dir</span><span class="op">(</span><span class="nam">prefix</span><span class="op">=</span><span class="str">"curves_"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t151" href="#t151">151</a></span><span class="t">        <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="str">'Creating %s temporary folder'</span> <span class="op">%</span> <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t152" href="#t152">152</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t153" href="#t153">153</a></span><span class="t">        <span class="com"># copy input files to temporary folder</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t154" href="#t154">154</a></span><span class="t">        <span class="nam">shutil</span><span class="op">.</span><span class="nam">copy</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'input_struc_path'</span><span class="op">]</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t155" href="#t155">155</a></span><span class="t">        <span class="nam">tmp_struc_input</span> <span class="op">=</span> <span class="nam">Path</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'input_struc_path'</span><span class="op">]</span><span class="op">)</span><span class="op">.</span><span class="nam">name</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t156" href="#t156">156</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'input_top_path'</span><span class="op">]</span> <span class="key">is</span> <span class="key">not</span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t157" href="#t157">157</a></span><span class="t">            <span class="nam">shutil</span><span class="op">.</span><span class="nam">copy</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'input_top_path'</span><span class="op">]</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t158" href="#t158">158</a></span><span class="t">            <span class="nam">tmp_top_input</span> <span class="op">=</span> <span class="nam">Path</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'input_top_path'</span><span class="op">]</span><span class="op">)</span><span class="op">.</span><span class="nam">name</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t159" href="#t159">159</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t160" href="#t160">160</a></span><span class="t">        <span class="com"># change directory to temporary folder</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t161" href="#t161">161</a></span><span class="t">        <span class="nam">original_directory</span> <span class="op">=</span> <span class="nam">os</span><span class="op">.</span><span class="nam">getcwd</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t162" href="#t162">162</a></span><span class="t">        <span class="nam">os</span><span class="op">.</span><span class="nam">chdir</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t163" href="#t163">163</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t164" href="#t164">164</a></span><span class="t">        <span class="com"># create intructions</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t165" href="#t165">165</a></span><span class="t">        <span class="nam">instructions</span> <span class="op">=</span> <span class="op">[</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t166" href="#t166">166</a></span><span class="t">            <span class="str">f"{self.binary_path} &lt;&lt;! "</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t167" href="#t167">167</a></span><span class="t">            <span class="str">"&amp;inp"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t168" href="#t168">168</a></span><span class="t">            <span class="str">f"  file={tmp_struc_input},"</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t169" href="#t169">169</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'input_top_path'</span><span class="op">]</span> <span class="key">is</span> <span class="key">not</span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t170" href="#t170">170</a></span><span class="t">            <span class="com"># add topology file if needed</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t171" href="#t171">171</a></span><span class="t">            <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="str">'Appending provided topology to command'</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t172" href="#t172">172</a></span><span class="t">                   <span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">global_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t173" href="#t173">173</a></span><span class="t">            <span class="nam">instructions</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t174" href="#t174">174</a></span><span class="t">                <span class="str">f"  ftop={tmp_top_input},"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t175" href="#t175">175</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t176" href="#t176">176</a></span><span class="t">        <span class="com"># create intructions</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t177" href="#t177">177</a></span><span class="t">        <span class="nam">instructions</span> <span class="op">=</span> <span class="nam">instructions</span> <span class="op">+</span> <span class="op">[</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t178" href="#t178">178</a></span><span class="t">            <span class="str">"  lis='curves_output',"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t179" href="#t179">179</a></span><span class="t">            <span class="str">f"  lib={self.stdlib_path},"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t180" href="#t180">180</a></span><span class="t">            <span class="str">f"  ions={self.ions},"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t181" href="#t181">181</a></span><span class="t">            <span class="str">f"  test={self.test},"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t182" href="#t182">182</a></span><span class="t">            <span class="str">f"  line={self.line},"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t183" href="#t183">183</a></span><span class="t">            <span class="str">f"  fit={self.fit},"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t184" href="#t184">184</a></span><span class="t">            <span class="str">f"  axfrm={self.axfrm},"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t185" href="#t185">185</a></span><span class="t">            <span class="str">f"  itst={self.itst},itnd={self.itnd},itdel={self.itdel},"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t186" href="#t186">186</a></span><span class="t">            <span class="str">"&amp;end"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t187" href="#t187">187</a></span><span class="t">            <span class="str">"2 1 -1 0 0"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t188" href="#t188">188</a></span><span class="t">            <span class="str">f"{self.s1range}"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t189" href="#t189">189</a></span><span class="t">            <span class="str">f"{self.s2range}"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t190" href="#t190">190</a></span><span class="t">            <span class="str">"!"</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t191" href="#t191">191</a></span><span class="t">        <span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t192" href="#t192">192</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">cmd</span> <span class="op">=</span> <span class="op">[</span><span class="str">"\n"</span><span class="op">.</span><span class="nam">join</span><span class="op">(</span><span class="nam">instructions</span><span class="op">)</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t193" href="#t193">193</a></span><span class="t">        <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="str">'Creating command line with instructions and required arguments'</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t194" href="#t194">194</a></span><span class="t">               <span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">global_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t195" href="#t195">195</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t196" href="#t196">196</a></span><span class="t">        <span class="com"># Run Biobb block</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t197" href="#t197">197</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">run_biobb</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t198" href="#t198">198</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t199" href="#t199">199</a></span><span class="t">        <span class="com"># change back to original directory</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t200" href="#t200">200</a></span><span class="t">        <span class="nam">os</span><span class="op">.</span><span class="nam">chdir</span><span class="op">(</span><span class="nam">original_directory</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t201" href="#t201">201</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t202" href="#t202">202</a></span><span class="t">        <span class="com"># create zipfile and write output inside</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t203" href="#t203">203</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">"out"</span><span class="op">]</span><span class="op">[</span><span class="str">"output_zip_path"</span><span class="op">]</span> <span class="key">is</span> <span class="key">not</span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t204" href="#t204">204</a></span><span class="t">            <span class="nam">zf</span> <span class="op">=</span> <span class="nam">zipfile</span><span class="op">.</span><span class="nam">ZipFile</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t205" href="#t205">205</a></span><span class="t">                <span class="nam">Path</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">"out"</span><span class="op">]</span><span class="op">[</span><span class="str">"output_zip_path"</span><span class="op">]</span><span class="op">)</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t206" href="#t206">206</a></span><span class="t">                <span class="str">"w"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t207" href="#t207">207</a></span><span class="t">            <span class="key">for</span> <span class="nam">curves_outfile</span> <span class="key">in</span> <span class="nam">Path</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span><span class="op">)</span><span class="op">.</span><span class="nam">glob</span><span class="op">(</span><span class="str">"curves_output*"</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t208" href="#t208">208</a></span><span class="t">                <span class="key">if</span> <span class="nam">curves_outfile</span><span class="op">.</span><span class="nam">suffix</span> <span class="key">not</span> <span class="key">in</span> <span class="op">(</span><span class="str">".cda"</span><span class="op">,</span> <span class="str">".lis"</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t209" href="#t209">209</a></span><span class="t">                    <span class="nam">zf</span><span class="op">.</span><span class="nam">write</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t210" href="#t210">210</a></span><span class="t">                        <span class="nam">curves_outfile</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t211" href="#t211">211</a></span><span class="t">                        <span class="nam">arcname</span><span class="op">=</span><span class="nam">curves_outfile</span><span class="op">.</span><span class="nam">name</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t212" href="#t212">212</a></span><span class="t">            <span class="nam">zf</span><span class="op">.</span><span class="nam">close</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t213" href="#t213">213</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t214" href="#t214">214</a></span><span class="t">        <span class="com"># rename cda and lis files</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t215" href="#t215">215</a></span><span class="t">        <span class="op">(</span><span class="nam">Path</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span><span class="op">)</span> <span class="op">/</span> <span class="str">"curves_output.cda"</span><span class="op">)</span><span class="op">.</span><span class="nam">rename</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t216" href="#t216">216</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">"out"</span><span class="op">]</span><span class="op">[</span><span class="str">"output_cda_path"</span><span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t217" href="#t217">217</a></span><span class="t">        <span class="op">(</span><span class="nam">Path</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span><span class="op">)</span> <span class="op">/</span> <span class="str">"curves_output.lis"</span><span class="op">)</span><span class="op">.</span><span class="nam">rename</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t218" href="#t218">218</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">"out"</span><span class="op">]</span><span class="op">[</span><span class="str">"output_lis_path"</span><span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t219" href="#t219">219</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t220" href="#t220">220</a></span><span class="t">        <span class="com"># Remove temporary file(s)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t221" href="#t221">221</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_files</span><span class="op">.</span><span class="nam">extend</span><span class="op">(</span><span class="op">[</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t222" href="#t222">222</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"unique_dir"</span><span class="op">)</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t223" href="#t223">223</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t224" href="#t224">224</a></span><span class="t">        <span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t225" href="#t225">225</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">remove_tmp_files</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t226" href="#t226">226</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t227" href="#t227">227</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_arguments</span><span class="op">(</span><span class="nam">output_files_created</span><span class="op">=</span><span class="key">True</span><span class="op">,</span> <span class="nam">raise_exception</span><span class="op">=</span><span class="key">False</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t228" href="#t228">228</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t229" href="#t229">229</a></span><span class="t">        <span class="key">return</span> <span class="nam">self</span><span class="op">.</span><span class="nam">return_code</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t230" href="#t230">230</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t19" href="#t19">19</a></span><span class="t"><span class="str">    | The Cur+ program is used to analyze the structure of nucleic acids and their complexes.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t20" href="#t20">20</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t21" href="#t21">21</a></span><span class="t"><span class="str">    Args:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t22" href="#t22">22</a></span><span class="t"><span class="str">        input_struc_path (str): Trajectory or PDB input file. File type: input. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/curvesplus/structure.stripped.trj>`_. Accepted formats: trj (edam:format_3910), pdb (edam:format_1476), netcdf (edam:format_3650), nc (edam:format_3650).</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t23" href="#t23">23</a></span><span class="t"><span class="str">        input_top_path (str) (Optional): Topology file, needed along with .trj file (optional). File type: input. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/curvesplus/structure.stripped.top>`_. Accepted formats: top (edam:format_3881).</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t24" href="#t24">24</a></span><span class="t"><span class="str">        output_cda_path (str): Filename for Curves+ output .cda file. File type: output. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/reference/curvesplus/curves_trj_output.cda>`_. Accepted formats: cda (edam:format_2330).</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t25" href="#t25">25</a></span><span class="t"><span class="str">        output_lis_path (str): Filename for Curves+ output .lis file. File type: output. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/reference/curvesplus/curves_trj_output.lis>`_. Accepted formats: lis (edam:format_2330).</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t26" href="#t26">26</a></span><span class="t"><span class="str">        output_zip_path (str) (Optional): Filename for .zip files containing Curves+ output that is not .cda or .lis files. File type: output. Accepted formats: zip (edam:format_3987).</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t27" href="#t27">27</a></span><span class="t"><span class="str">        properties (dict):</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t28" href="#t28">28</a></span><span class="t"><span class="str">            * **s1range** (*str*) - (None) Range of first strand. Must be specified in the form "start:end".</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t29" href="#t29">29</a></span><span class="t"><span class="str">            * **s2range** (*str*) - (None) Range of second strand. Must be specified in the form "start:end".</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t30" href="#t30">30</a></span><span class="t"><span class="str">            * **stdlib_path** (*str*) - ('standard') Path to Curves' standard library files for nucleotides. If not specified will look for 'standard' files in current directory.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t31" href="#t31">31</a></span><span class="t"><span class="str">            * **itst** (*int*) - (0) Iteration start index.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t32" href="#t32">32</a></span><span class="t"><span class="str">            * **itnd** (*int*) - (0) Iteration end index.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t33" href="#t33">33</a></span><span class="t"><span class="str">            * **itdel** (*int*) - (1) Iteration delimiter.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t34" href="#t34">34</a></span><span class="t"><span class="str">            * **ions** (*bool*) - (False) If True, helicoidal analysis of ions (or solvent molecules) around solute is carried out.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t35" href="#t35">35</a></span><span class="t"><span class="str">            * **test** (*bool*) - (False) If True, provide addition output in .lis file on fitting and axis generation.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t36" href="#t36">36</a></span><span class="t"><span class="str">            * **line** (*bool*) - (False) if True, find the best linear helical axis.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t37" href="#t37">37</a></span><span class="t"><span class="str">            * **fit** (*bool*) - (True) if True, fit a standard bases to the input coordinates (important for MD snapshots to avoid base distortions leading to noisy helical parameters).</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t38" href="#t38">38</a></span><span class="t"><span class="str">            * **axfrm** (*bool*) - (False) if True, generates closely spaced helical axis frames as input for Canal and Canion.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t39" href="#t39">39</a></span><span class="t"><span class="str">            * **binary_path** (*str*) - (Cur+) Path to Curves+ executable, otherwise the program wil look for Cur+ executable in the binaries folder.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t40" href="#t40">40</a></span><span class="t"><span class="str">            * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t41" href="#t41">41</a></span><span class="t"><span class="str">            * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t42" href="#t42">42</a></span><span class="t"><span class="str">    Examples:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t43" href="#t43">43</a></span><span class="t"><span class="str">        This is a use example of how to use the building block from Python::</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t44" href="#t44">44</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t45" href="#t45">45</a></span><span class="t"><span class="str">            from biobb_dna.curvesplus.biobb_curves import biobb_curves</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t46" href="#t46">46</a></span><span class="t"><span class="str">            prop = {</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t47" href="#t47">47</a></span><span class="t"><span class="str">                's1range': '1:12',</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t48" href="#t48">48</a></span><span class="t"><span class="str">                's2range': '24:13',</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t49" href="#t49">49</a></span><span class="t"><span class="str">            }</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t50" href="#t50">50</a></span><span class="t"><span class="str">            biobb_curves(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t51" href="#t51">51</a></span><span class="t"><span class="str">                input_struc_path='/path/to/structure/file.trj',</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t52" href="#t52">52</a></span><span class="t"><span class="str">                input_top_path='/path/to/topology/file.top',</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t53" href="#t53">53</a></span><span class="t"><span class="str">                output_cda_path='/path/to/output/file.cda',</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t54" href="#t54">54</a></span><span class="t"><span class="str">                output_lis_path='/path/to/output/file.lis',</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t55" href="#t55">55</a></span><span class="t"><span class="str">                properties=prop)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t56" href="#t56">56</a></span><span class="t"><span class="str">    Info:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t57" href="#t57">57</a></span><span class="t"><span class="str">        * wrapped_software:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t58" href="#t58">58</a></span><span class="t"><span class="str">            * name: Curves</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t59" href="#t59">59</a></span><span class="t"><span class="str">            * version: >=2.6</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t60" href="#t60">60</a></span><span class="t"><span class="str">            * license: BSD 3-Clause</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t61" href="#t61">61</a></span><span class="t"><span class="str">        * ontology:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t62" href="#t62">62</a></span><span class="t"><span class="str">            * name: EDAM</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t63" href="#t63">63</a></span><span class="t"><span class="str">            * schema: http://edamontology.org/EDAM.owl</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t64" href="#t64">64</a></span><span class="t"><span class="str">    """</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t65" href="#t65">65</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t66" href="#t66">66</a></span><span class="t">    <span class="key">def</span> <span class="nam">__init__</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t67" href="#t67">67</a></span><span class="t">            <span class="nam">self</span><span class="op">,</span> <span class="nam">input_struc_path</span><span class="op">,</span> <span class="nam">output_lis_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t68" href="#t68">68</a></span><span class="t">            <span class="nam">output_cda_path</span><span class="op">,</span> <span class="nam">output_zip_path</span><span class="op">=</span><span class="key">None</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t69" href="#t69">69</a></span><span class="t">            <span class="nam">input_top_path</span><span class="op">=</span><span class="key">None</span><span class="op">,</span> <span class="nam">properties</span><span class="op">=</span><span class="key">None</span><span class="op">,</span> <span class="op">**</span><span class="nam">kwargs</span><span class="op">)</span> <span class="op">-></span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t70" href="#t70">70</a></span><span class="t">        <span class="nam">properties</span> <span class="op">=</span> <span class="nam">properties</span> <span class="key">or</span> <span class="op">{</span><span class="op">}</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t71" href="#t71">71</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t72" href="#t72">72</a></span><span class="t">        <span class="com"># Call parent class constructor</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t73" href="#t73">73</a></span><span class="t">        <span class="nam">super</span><span class="op">(</span><span class="op">)</span><span class="op">.</span><span class="nam">__init__</span><span class="op">(</span><span class="nam">properties</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t74" href="#t74">74</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">locals_var_dict</span> <span class="op">=</span> <span class="nam">locals</span><span class="op">(</span><span class="op">)</span><span class="op">.</span><span class="nam">copy</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t75" href="#t75">75</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t76" href="#t76">76</a></span><span class="t">        <span class="com"># Input/Output files</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t77" href="#t77">77</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span> <span class="op">=</span> <span class="op">{</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t78" href="#t78">78</a></span><span class="t">            <span class="str">'in'</span><span class="op">:</span> <span class="op">{</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t79" href="#t79">79</a></span><span class="t">                <span class="str">'input_struc_path'</span><span class="op">:</span> <span class="nam">input_struc_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t80" href="#t80">80</a></span><span class="t">                <span class="str">'input_top_path'</span><span class="op">:</span> <span class="nam">input_top_path</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t81" href="#t81">81</a></span><span class="t">            <span class="op">}</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t82" href="#t82">82</a></span><span class="t">            <span class="str">'out'</span><span class="op">:</span> <span class="op">{</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t83" href="#t83">83</a></span><span class="t">                <span class="str">'output_lis_path'</span><span class="op">:</span> <span class="nam">output_lis_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t84" href="#t84">84</a></span><span class="t">                <span class="str">'output_cda_path'</span><span class="op">:</span> <span class="nam">output_cda_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t85" href="#t85">85</a></span><span class="t">                <span class="str">'output_zip_path'</span><span class="op">:</span> <span class="nam">output_zip_path</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t86" href="#t86">86</a></span><span class="t">            <span class="op">}</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t87" href="#t87">87</a></span><span class="t">        <span class="op">}</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t88" href="#t88">88</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t89" href="#t89">89</a></span><span class="t">        <span class="com"># Properties specific for BB</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t90" href="#t90">90</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">s1range</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'s1range'</span><span class="op">,</span> <span class="key">None</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t91" href="#t91">91</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">binary_path</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'binary_path'</span><span class="op">,</span> <span class="str">'Cur+'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t92" href="#t92">92</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">stdlib_path</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'stdlib_path'</span><span class="op">,</span> <span class="key">None</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t93" href="#t93">93</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">s2range</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'s2range'</span><span class="op">,</span> <span class="key">None</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t94" href="#t94">94</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">itst</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'itst'</span><span class="op">,</span> <span class="num">0</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t95" href="#t95">95</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">itnd</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'itnd'</span><span class="op">,</span> <span class="num">0</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t96" href="#t96">96</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">itdel</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'itdel'</span><span class="op">,</span> <span class="num">1</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t97" href="#t97">97</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">ions</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'ions'</span><span class="op">,</span> <span class="str">'.f.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t98" href="#t98">98</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">test</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'test'</span><span class="op">,</span> <span class="str">'.f.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t99" href="#t99">99</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">line</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'line'</span><span class="op">,</span> <span class="str">'.f.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t100" href="#t100">100</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">fit</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'fit'</span><span class="op">,</span> <span class="str">'.t.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t101" href="#t101">101</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">axfrm</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'axfrm'</span><span class="op">,</span> <span class="str">'.f.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t102" href="#t102">102</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">properties</span> <span class="op">=</span> <span class="nam">properties</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t103" href="#t103">103</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t104" href="#t104">104</a></span><span class="t">        <span class="com"># Check the properties</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t105" href="#t105">105</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_properties</span><span class="op">(</span><span class="nam">properties</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t106" href="#t106">106</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_arguments</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t107" href="#t107">107</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t108" href="#t108">108</a></span><span class="t">    <span class="op">@</span><span class="nam">launchlogger</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t109" href="#t109">109</a></span><span class="t">    <span class="key">def</span> <span class="nam">launch</span><span class="op">(</span><span class="nam">self</span><span class="op">)</span> <span class="op">-></span> <span class="nam">int</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t110" href="#t110">110</a></span><span class="t">        <span class="str">"""Execute the :class:`Curves &lt;biobb_dna.curvesplus.biobb_curves.Curves>` object."""</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t111" href="#t111">111</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t112" href="#t112">112</a></span><span class="t">        <span class="com"># Setup Biobb</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t113" href="#t113">113</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">check_restart</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t114" href="#t114">114</a></span><span class="t">            <span class="key">return</span> <span class="num">0</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t115" href="#t115">115</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">stage_files</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t116" href="#t116">116</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t117" href="#t117">117</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">s1range</span> <span class="key">is</span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t118" href="#t118">118</a></span><span class="t">            <span class="key">raise</span> <span class="nam">ValueError</span><span class="op">(</span><span class="str">"property 's1range' must be specified!"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t119" href="#t119">119</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">s2range</span> <span class="key">is</span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t120" href="#t120">120</a></span><span class="t">            <span class="com"># compute s2range if not provided</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t121" href="#t121">121</a></span><span class="t">            <span class="nam">range1_end</span> <span class="op">=</span> <span class="nam">int</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">s1range</span><span class="op">.</span><span class="nam">split</span><span class="op">(</span><span class="str">":"</span><span class="op">)</span><span class="op">[</span><span class="num">1</span><span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t122" href="#t122">122</a></span><span class="t">            <span class="nam">s2start</span> <span class="op">=</span> <span class="nam">range1_end</span> <span class="op">+</span> <span class="num">1</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t123" href="#t123">123</a></span><span class="t">            <span class="nam">s2end</span> <span class="op">=</span> <span class="num">2</span> <span class="op">*</span> <span class="nam">range1_end</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t124" href="#t124">124</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">s2range</span> <span class="op">=</span> <span class="str">f"{s2end}:{s2start}"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t125" href="#t125">125</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t126" href="#t126">126</a></span><span class="t">        <span class="com"># check standard library files location if not provided</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t127" href="#t127">127</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">stdlib_path</span> <span class="key">is</span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t128" href="#t128">128</a></span><span class="t">            <span class="key">if</span> <span class="nam">os</span><span class="op">.</span><span class="nam">getenv</span><span class="op">(</span><span class="str">"CONDA_PREFIX"</span><span class="op">,</span> <span class="key">False</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t129" href="#t129">129</a></span><span class="t">                <span class="nam">curves_aux_path</span> <span class="op">=</span> <span class="nam">Path</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t130" href="#t130">130</a></span><span class="t">                    <span class="nam">os</span><span class="op">.</span><span class="nam">getenv</span><span class="op">(</span><span class="str">"CONDA_PREFIX"</span><span class="op">)</span><span class="op">)</span> <span class="op">/</span> <span class="str">".curvesplus"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t131" href="#t131">131</a></span><span class="t">                <span class="com"># check if .curvesplus directory is in $CONDA_PREFIX</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t132" href="#t132">132</a></span><span class="t">                <span class="key">if</span> <span class="nam">curves_aux_path</span><span class="op">.</span><span class="nam">exists</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t133" href="#t133">133</a></span><span class="t">                    <span class="key">if</span> <span class="nam">len</span><span class="op">(</span><span class="nam">list</span><span class="op">(</span><span class="nam">curves_aux_path</span><span class="op">.</span><span class="nam">glob</span><span class="op">(</span><span class="str">"standard_*.lib"</span><span class="op">)</span><span class="op">)</span><span class="op">)</span> <span class="op">!=</span> <span class="num">3</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t134" href="#t134">134</a></span><span class="t">                        <span class="key">raise</span> <span class="nam">FileNotFoundError</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t135" href="#t135">135</a></span><span class="t">                            <span class="str">"One or all standard library files "</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t136" href="#t136">136</a></span><span class="t">                            <span class="str">f"missing from {curves_aux_path}! "</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t137" href="#t137">137</a></span><span class="t">                            <span class="str">"Check files standard_b.lib, "</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t138" href="#t138">138</a></span><span class="t">                            <span class="str">"standard_s.lib and standard_i.lib exist."</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t139" href="#t139">139</a></span><span class="t">                    <span class="nam">self</span><span class="op">.</span><span class="nam">stdlib_path</span> <span class="op">=</span> <span class="nam">curves_aux_path</span> <span class="op">/</span> <span class="str">"standard"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t140" href="#t140">140</a></span><span class="t">                <span class="key">else</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t141" href="#t141">141</a></span><span class="t">                    <span class="key">raise</span> <span class="nam">FileNotFoundError</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t142" href="#t142">142</a></span><span class="t">                        <span class="str">".curvesplus directory not found in "</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t143" href="#t143">143</a></span><span class="t">                        <span class="str">f"{os.getenv('CONDA_PREFIX')} !"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t144" href="#t144">144</a></span><span class="t">                        <span class="str">"Please indicate where standard_*.lib files are "</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t145" href="#t145">145</a></span><span class="t">                        <span class="str">"located with the stdlib_path property."</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t146" href="#t146">146</a></span><span class="t">            <span class="key">else</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t147" href="#t147">147</a></span><span class="t">                <span class="com"># CONDA_PREFIX undefined</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t148" href="#t148">148</a></span><span class="t">                <span class="nam">self</span><span class="op">.</span><span class="nam">stdlib_path</span> <span class="op">=</span> <span class="nam">Path</span><span class="op">.</span><span class="nam">cwd</span><span class="op">(</span><span class="op">)</span> <span class="op">/</span> <span class="str">"standard"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t149" href="#t149">149</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t150" href="#t150">150</a></span><span class="t">        <span class="com"># Creating temporary folder</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t151" href="#t151">151</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span> <span class="op">=</span> <span class="nam">fu</span><span class="op">.</span><span class="nam">create_unique_dir</span><span class="op">(</span><span class="nam">prefix</span><span class="op">=</span><span class="str">"curves_"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t152" href="#t152">152</a></span><span class="t">        <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="str">'Creating %s temporary folder'</span> <span class="op">%</span> <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t153" href="#t153">153</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t154" href="#t154">154</a></span><span class="t">        <span class="com"># copy input files to temporary folder</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t155" href="#t155">155</a></span><span class="t">        <span class="nam">shutil</span><span class="op">.</span><span class="nam">copy</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'input_struc_path'</span><span class="op">]</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t156" href="#t156">156</a></span><span class="t">        <span class="nam">tmp_struc_input</span> <span class="op">=</span> <span class="nam">Path</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'input_struc_path'</span><span class="op">]</span><span class="op">)</span><span class="op">.</span><span class="nam">name</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t157" href="#t157">157</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'input_top_path'</span><span class="op">]</span> <span class="key">is</span> <span class="key">not</span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t158" href="#t158">158</a></span><span class="t">            <span class="nam">shutil</span><span class="op">.</span><span class="nam">copy</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'input_top_path'</span><span class="op">]</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t159" href="#t159">159</a></span><span class="t">            <span class="nam">tmp_top_input</span> <span class="op">=</span> <span class="nam">Path</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'input_top_path'</span><span class="op">]</span><span class="op">)</span><span class="op">.</span><span class="nam">name</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t160" href="#t160">160</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t161" href="#t161">161</a></span><span class="t">        <span class="com"># change directory to temporary folder</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t162" href="#t162">162</a></span><span class="t">        <span class="nam">original_directory</span> <span class="op">=</span> <span class="nam">os</span><span class="op">.</span><span class="nam">getcwd</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t163" href="#t163">163</a></span><span class="t">        <span class="nam">os</span><span class="op">.</span><span class="nam">chdir</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t164" href="#t164">164</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t165" href="#t165">165</a></span><span class="t">        <span class="com"># create intructions</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t166" href="#t166">166</a></span><span class="t">        <span class="nam">instructions</span> <span class="op">=</span> <span class="op">[</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t167" href="#t167">167</a></span><span class="t">            <span class="str">f"{self.binary_path} &lt;&lt;! "</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t168" href="#t168">168</a></span><span class="t">            <span class="str">"&amp;inp"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t169" href="#t169">169</a></span><span class="t">            <span class="str">f"  file={tmp_struc_input},"</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t170" href="#t170">170</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'input_top_path'</span><span class="op">]</span> <span class="key">is</span> <span class="key">not</span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t171" href="#t171">171</a></span><span class="t">            <span class="com"># add topology file if needed</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t172" href="#t172">172</a></span><span class="t">            <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="str">'Appending provided topology to command'</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t173" href="#t173">173</a></span><span class="t">                   <span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">global_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t174" href="#t174">174</a></span><span class="t">            <span class="nam">instructions</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t175" href="#t175">175</a></span><span class="t">                <span class="str">f"  ftop={tmp_top_input},"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t176" href="#t176">176</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t177" href="#t177">177</a></span><span class="t">        <span class="com"># create intructions</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t178" href="#t178">178</a></span><span class="t">        <span class="nam">instructions</span> <span class="op">=</span> <span class="nam">instructions</span> <span class="op">+</span> <span class="op">[</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t179" href="#t179">179</a></span><span class="t">            <span class="str">"  lis='curves_output',"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t180" href="#t180">180</a></span><span class="t">            <span class="str">f"  lib={self.stdlib_path},"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t181" href="#t181">181</a></span><span class="t">            <span class="str">f"  ions={self.ions},"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t182" href="#t182">182</a></span><span class="t">            <span class="str">f"  test={self.test},"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t183" href="#t183">183</a></span><span class="t">            <span class="str">f"  line={self.line},"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t184" href="#t184">184</a></span><span class="t">            <span class="str">f"  fit={self.fit},"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t185" href="#t185">185</a></span><span class="t">            <span class="str">f"  axfrm={self.axfrm},"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t186" href="#t186">186</a></span><span class="t">            <span class="str">f"  itst={self.itst},itnd={self.itnd},itdel={self.itdel},"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t187" href="#t187">187</a></span><span class="t">            <span class="str">"&amp;end"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t188" href="#t188">188</a></span><span class="t">            <span class="str">"2 1 -1 0 0"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t189" href="#t189">189</a></span><span class="t">            <span class="str">f"{self.s1range}"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t190" href="#t190">190</a></span><span class="t">            <span class="str">f"{self.s2range}"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t191" href="#t191">191</a></span><span class="t">            <span class="str">"!"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t192" href="#t192">192</a></span><span class="t">        <span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t193" href="#t193">193</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">cmd</span> <span class="op">=</span> <span class="op">[</span><span class="str">"\n"</span><span class="op">.</span><span class="nam">join</span><span class="op">(</span><span class="nam">instructions</span><span class="op">)</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t194" href="#t194">194</a></span><span class="t">        <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="str">'Creating command line with instructions and required arguments'</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t195" href="#t195">195</a></span><span class="t">               <span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">global_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t196" href="#t196">196</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t197" href="#t197">197</a></span><span class="t">        <span class="com"># Run Biobb block</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t198" href="#t198">198</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">run_biobb</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t199" href="#t199">199</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t200" href="#t200">200</a></span><span class="t">        <span class="com"># change back to original directory</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t201" href="#t201">201</a></span><span class="t">        <span class="nam">os</span><span class="op">.</span><span class="nam">chdir</span><span class="op">(</span><span class="nam">original_directory</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t202" href="#t202">202</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t203" href="#t203">203</a></span><span class="t">        <span class="com"># create zipfile and write output inside</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t204" href="#t204">204</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">"out"</span><span class="op">]</span><span class="op">[</span><span class="str">"output_zip_path"</span><span class="op">]</span> <span class="key">is</span> <span class="key">not</span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t205" href="#t205">205</a></span><span class="t">            <span class="nam">zf</span> <span class="op">=</span> <span class="nam">zipfile</span><span class="op">.</span><span class="nam">ZipFile</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t206" href="#t206">206</a></span><span class="t">                <span class="nam">Path</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">"out"</span><span class="op">]</span><span class="op">[</span><span class="str">"output_zip_path"</span><span class="op">]</span><span class="op">)</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t207" href="#t207">207</a></span><span class="t">                <span class="str">"w"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t208" href="#t208">208</a></span><span class="t">            <span class="key">for</span> <span class="nam">curves_outfile</span> <span class="key">in</span> <span class="nam">Path</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span><span class="op">)</span><span class="op">.</span><span class="nam">glob</span><span class="op">(</span><span class="str">"curves_output*"</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t209" href="#t209">209</a></span><span class="t">                <span class="key">if</span> <span class="nam">curves_outfile</span><span class="op">.</span><span class="nam">suffix</span> <span class="key">not</span> <span class="key">in</span> <span class="op">(</span><span class="str">".cda"</span><span class="op">,</span> <span class="str">".lis"</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t210" href="#t210">210</a></span><span class="t">                    <span class="nam">zf</span><span class="op">.</span><span class="nam">write</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t211" href="#t211">211</a></span><span class="t">                        <span class="nam">curves_outfile</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t212" href="#t212">212</a></span><span class="t">                        <span class="nam">arcname</span><span class="op">=</span><span class="nam">curves_outfile</span><span class="op">.</span><span class="nam">name</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t213" href="#t213">213</a></span><span class="t">            <span class="nam">zf</span><span class="op">.</span><span class="nam">close</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t214" href="#t214">214</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t215" href="#t215">215</a></span><span class="t">        <span class="com"># rename cda and lis files</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t216" href="#t216">216</a></span><span class="t">        <span class="op">(</span><span class="nam">Path</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span><span class="op">)</span> <span class="op">/</span> <span class="str">"curves_output.cda"</span><span class="op">)</span><span class="op">.</span><span class="nam">rename</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t217" href="#t217">217</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">"out"</span><span class="op">]</span><span class="op">[</span><span class="str">"output_cda_path"</span><span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t218" href="#t218">218</a></span><span class="t">        <span class="op">(</span><span class="nam">Path</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span><span class="op">)</span> <span class="op">/</span> <span class="str">"curves_output.lis"</span><span class="op">)</span><span class="op">.</span><span class="nam">rename</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t219" href="#t219">219</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">"out"</span><span class="op">]</span><span class="op">[</span><span class="str">"output_lis_path"</span><span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t220" href="#t220">220</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t221" href="#t221">221</a></span><span class="t">        <span class="com"># Remove temporary file(s)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t222" href="#t222">222</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_files</span><span class="op">.</span><span class="nam">extend</span><span class="op">(</span><span class="op">[</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t223" href="#t223">223</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"unique_dir"</span><span class="op">)</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t224" href="#t224">224</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t225" href="#t225">225</a></span><span class="t">        <span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t226" href="#t226">226</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">remove_tmp_files</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t227" href="#t227">227</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t228" href="#t228">228</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_arguments</span><span class="op">(</span><span class="nam">output_files_created</span><span class="op">=</span><span class="key">True</span><span class="op">,</span> <span class="nam">raise_exception</span><span class="op">=</span><span class="key">False</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t229" href="#t229">229</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t230" href="#t230">230</a></span><span class="t">        <span class="key">return</span> <span class="nam">self</span><span class="op">.</span><span class="nam">return_code</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t231" href="#t231">231</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t232" href="#t232">232</a></span><span class="t"><span class="key">def</span> <span class="nam">biobb_curves</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t233" href="#t233">233</a></span><span class="t">        <span class="nam">input_struc_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span> <span class="nam">output_lis_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span> <span class="nam">output_cda_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t234" href="#t234">234</a></span><span class="t">        <span class="nam">input_top_path</span><span class="op">:</span> <span class="nam">str</span> <span class="op">=</span> <span class="key">None</span><span class="op">,</span> <span class="nam">output_zip_path</span><span class="op">:</span> <span class="nam">str</span> <span class="op">=</span> <span class="key">None</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t235" href="#t235">235</a></span><span class="t">        <span class="nam">properties</span><span class="op">:</span> <span class="nam">dict</span> <span class="op">=</span> <span class="key">None</span><span class="op">,</span> <span class="op">**</span><span class="nam">kwargs</span><span class="op">)</span> <span class="op">-></span> <span class="nam">int</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t236" href="#t236">236</a></span><span class="t">    <span class="str">"""Create :class:`Curves &lt;biobb_dna.curvesplus.biobb_curves.Curves>` class and</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t237" href="#t237">237</a></span><span class="t"><span class="str">    execute the :meth:`launch() &lt;biobb_dna.curvesplus.biobb_curves.Curves.launch>` method."""</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t238" href="#t238">238</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t239" href="#t239">239</a></span><span class="t">    <span class="key">return</span> <span class="nam">Curves</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t240" href="#t240">240</a></span><span class="t">        <span class="nam">input_struc_path</span><span class="op">=</span><span class="nam">input_struc_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t241" href="#t241">241</a></span><span class="t">        <span class="nam">input_top_path</span><span class="op">=</span><span class="nam">input_top_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t242" href="#t242">242</a></span><span class="t">        <span class="nam">output_lis_path</span><span class="op">=</span><span class="nam">output_lis_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t243" href="#t243">243</a></span><span class="t">        <span class="nam">output_cda_path</span><span class="op">=</span><span class="nam">output_cda_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t244" href="#t244">244</a></span><span class="t">        <span class="nam">output_zip_path</span><span class="op">=</span><span class="nam">output_zip_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t245" href="#t245">245</a></span><span class="t">        <span class="nam">properties</span><span class="op">=</span><span class="nam">properties</span><span class="op">,</span> <span class="op">**</span><span class="nam">kwargs</span><span class="op">)</span><span class="op">.</span><span class="nam">launch</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t246" href="#t246">246</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t232" href="#t232">232</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t233" href="#t233">233</a></span><span class="t"><span class="key">def</span> <span class="nam">biobb_curves</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t234" href="#t234">234</a></span><span class="t">        <span class="nam">input_struc_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span> <span class="nam">output_lis_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span> <span class="nam">output_cda_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t235" href="#t235">235</a></span><span class="t">        <span class="nam">input_top_path</span><span class="op">:</span> <span class="nam">str</span> <span class="op">=</span> <span class="key">None</span><span class="op">,</span> <span class="nam">output_zip_path</span><span class="op">:</span> <span class="nam">str</span> <span class="op">=</span> <span class="key">None</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t236" href="#t236">236</a></span><span class="t">        <span class="nam">properties</span><span class="op">:</span> <span class="nam">dict</span> <span class="op">=</span> <span class="key">None</span><span class="op">,</span> <span class="op">**</span><span class="nam">kwargs</span><span class="op">)</span> <span class="op">-></span> <span class="nam">int</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t237" href="#t237">237</a></span><span class="t">    <span class="str">"""Create :class:`Curves &lt;biobb_dna.curvesplus.biobb_curves.Curves>` class and</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t238" href="#t238">238</a></span><span class="t"><span class="str">    execute the :meth:`launch() &lt;biobb_dna.curvesplus.biobb_curves.Curves.launch>` method."""</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t239" href="#t239">239</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t240" href="#t240">240</a></span><span class="t">    <span class="key">return</span> <span class="nam">Curves</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t241" href="#t241">241</a></span><span class="t">        <span class="nam">input_struc_path</span><span class="op">=</span><span class="nam">input_struc_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t242" href="#t242">242</a></span><span class="t">        <span class="nam">input_top_path</span><span class="op">=</span><span class="nam">input_top_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t243" href="#t243">243</a></span><span class="t">        <span class="nam">output_lis_path</span><span class="op">=</span><span class="nam">output_lis_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t244" href="#t244">244</a></span><span class="t">        <span class="nam">output_cda_path</span><span class="op">=</span><span class="nam">output_cda_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t245" href="#t245">245</a></span><span class="t">        <span class="nam">output_zip_path</span><span class="op">=</span><span class="nam">output_zip_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t246" href="#t246">246</a></span><span class="t">        <span class="nam">properties</span><span class="op">=</span><span class="nam">properties</span><span class="op">,</span> <span class="op">**</span><span class="nam">kwargs</span><span class="op">)</span><span class="op">.</span><span class="nam">launch</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t247" href="#t247">247</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t248" href="#t248">248</a></span><span class="t"><span class="key">def</span> <span class="nam">main</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t249" href="#t249">249</a></span><span class="t">    <span class="str">"""Command line execution of this building block. Please check the command line documentation."""</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t250" href="#t250">250</a></span><span class="t">    <span class="nam">parser</span> <span class="op">=</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">ArgumentParser</span><span class="op">(</span><span class="nam">description</span><span class="op">=</span><span class="str">'Execute Cur+ form the Curves+ software suite.'</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t251" href="#t251">251</a></span><span class="t">                                     <span class="nam">formatter_class</span><span class="op">=</span><span class="key">lambda</span> <span class="nam">prog</span><span class="op">:</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">RawTextHelpFormatter</span><span class="op">(</span><span class="nam">prog</span><span class="op">,</span> <span class="nam">width</span><span class="op">=</span><span class="num">99999</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t252" href="#t252">252</a></span><span class="t">    <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--config'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">False</span><span class="op">,</span> <span class="nam">help</span><span class="op">=</span><span class="str">'Configuration file'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t253" href="#t253">253</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t254" href="#t254">254</a></span><span class="t">    <span class="nam">required_args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument_group</span><span class="op">(</span><span class="str">'required arguments'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t255" href="#t255">255</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--input_struc_path'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t256" href="#t256">256</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Trajectory or PDB input file. Accepted formats: trj, pdb.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t257" href="#t257">257</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--output_cda_path'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t258" href="#t258">258</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Filename to give to output .cda file. Accepted formats: str.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t259" href="#t259">259</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--output_lis_path'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t260" href="#t260">260</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Filename to give to output .lis file. Accepted formats: str.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t261" href="#t261">261</a></span><span class="t">    <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--input_top_path'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">False</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t262" href="#t262">262</a></span><span class="t">                        <span class="nam">help</span><span class="op">=</span><span class="str">'Topology file, needed along with .trj file (optional). Accepted formats: top.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t263" href="#t263">263</a></span><span class="t">    <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--output_zip_path'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">False</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t264" href="#t264">264</a></span><span class="t">                        <span class="nam">help</span><span class="op">=</span><span class="str">'Filename to give to output files (except .cda and .lis files). Accepted formats: str.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t265" href="#t265">265</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t266" href="#t266">266</a></span><span class="t">    <span class="nam">args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">parse_args</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t267" href="#t267">267</a></span><span class="t">    <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="op">=</span> <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="key">or</span> <span class="str">"{}"</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t268" href="#t268">268</a></span><span class="t">    <span class="nam">properties</span> <span class="op">=</span> <span class="nam">settings</span><span class="op">.</span><span class="nam">ConfReader</span><span class="op">(</span><span class="nam">config</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">config</span><span class="op">)</span><span class="op">.</span><span class="nam">get_prop_dic</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t269" href="#t269">269</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t270" href="#t270">270</a></span><span class="t">    <span class="nam">biobb_curves</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t271" href="#t271">271</a></span><span class="t">        <span class="nam">input_struc_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_struc_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t272" href="#t272">272</a></span><span class="t">        <span class="nam">input_top_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_top_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t273" href="#t273">273</a></span><span class="t">        <span class="nam">output_cda_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">output_cda_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t274" href="#t274">274</a></span><span class="t">        <span class="nam">output_lis_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">output_lis_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t275" href="#t275">275</a></span><span class="t">        <span class="nam">output_zip_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">output_zip_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t276" href="#t276">276</a></span><span class="t">        <span class="nam">properties</span><span class="op">=</span><span class="nam">properties</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t277" href="#t277">277</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t248" href="#t248">248</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t249" href="#t249">249</a></span><span class="t"><span class="key">def</span> <span class="nam">main</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t250" href="#t250">250</a></span><span class="t">    <span class="str">"""Command line execution of this building block. Please check the command line documentation."""</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t251" href="#t251">251</a></span><span class="t">    <span class="nam">parser</span> <span class="op">=</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">ArgumentParser</span><span class="op">(</span><span class="nam">description</span><span class="op">=</span><span class="str">'Execute Cur+ form the Curves+ software suite.'</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t252" href="#t252">252</a></span><span class="t">                                     <span class="nam">formatter_class</span><span class="op">=</span><span class="key">lambda</span> <span class="nam">prog</span><span class="op">:</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">RawTextHelpFormatter</span><span class="op">(</span><span class="nam">prog</span><span class="op">,</span> <span class="nam">width</span><span class="op">=</span><span class="num">99999</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t253" href="#t253">253</a></span><span class="t">    <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--config'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">False</span><span class="op">,</span> <span class="nam">help</span><span class="op">=</span><span class="str">'Configuration file'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t254" href="#t254">254</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t255" href="#t255">255</a></span><span class="t">    <span class="nam">required_args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument_group</span><span class="op">(</span><span class="str">'required arguments'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t256" href="#t256">256</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--input_struc_path'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t257" href="#t257">257</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Trajectory or PDB input file. Accepted formats: trj, pdb.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t258" href="#t258">258</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--output_cda_path'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t259" href="#t259">259</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Filename to give to output .cda file. Accepted formats: str.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t260" href="#t260">260</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--output_lis_path'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t261" href="#t261">261</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Filename to give to output .lis file. Accepted formats: str.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t262" href="#t262">262</a></span><span class="t">    <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--input_top_path'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">False</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t263" href="#t263">263</a></span><span class="t">                        <span class="nam">help</span><span class="op">=</span><span class="str">'Topology file, needed along with .trj file (optional). Accepted formats: top.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t264" href="#t264">264</a></span><span class="t">    <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--output_zip_path'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">False</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t265" href="#t265">265</a></span><span class="t">                        <span class="nam">help</span><span class="op">=</span><span class="str">'Filename to give to output files (except .cda and .lis files). Accepted formats: str.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t266" href="#t266">266</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t267" href="#t267">267</a></span><span class="t">    <span class="nam">args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">parse_args</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t268" href="#t268">268</a></span><span class="t">    <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="op">=</span> <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="key">or</span> <span class="str">"{}"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t269" href="#t269">269</a></span><span class="t">    <span class="nam">properties</span> <span class="op">=</span> <span class="nam">settings</span><span class="op">.</span><span class="nam">ConfReader</span><span class="op">(</span><span class="nam">config</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">config</span><span class="op">)</span><span class="op">.</span><span class="nam">get_prop_dic</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t270" href="#t270">270</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t271" href="#t271">271</a></span><span class="t">    <span class="nam">biobb_curves</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t272" href="#t272">272</a></span><span class="t">        <span class="nam">input_struc_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_struc_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t273" href="#t273">273</a></span><span class="t">        <span class="nam">input_top_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_top_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t274" href="#t274">274</a></span><span class="t">        <span class="nam">output_cda_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">output_cda_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t275" href="#t275">275</a></span><span class="t">        <span class="nam">output_lis_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">output_lis_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t276" href="#t276">276</a></span><span class="t">        <span class="nam">output_zip_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">output_zip_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t277" href="#t277">277</a></span><span class="t">        <span class="nam">properties</span><span class="op">=</span><span class="nam">properties</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t278" href="#t278">278</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t279" href="#t279">279</a></span><span class="t"><span class="key">if</span> <span class="nam">__name__</span> <span class="op">==</span> <span class="str">'__main__'</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t280" href="#t280">280</a></span><span class="t">    <span class="nam">main</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t279" href="#t279">279</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t280" href="#t280">280</a></span><span class="t"><span class="key">if</span> <span class="nam">__name__</span> <span class="op">==</span> <span class="str">'__main__'</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t281" href="#t281">281</a></span><span class="t">    <span class="nam">main</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
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 <footer>
     <div class="content">
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             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.5.1">coverage.py v7.5.1</a>,
-            created at 2024-05-07 09:06 +0000
+            created at 2024-05-24 09:29 +0000
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@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_159731231e5c9c9d___init___py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.5.1">coverage.py v7.5.1</a>,
-            created at 2024-05-07 09:06 +0000
+            created at 2024-05-24 09:29 +0000
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             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -93,7 +93,7 @@ <h2>
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             &nbsp; &nbsp; &nbsp;
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-            created at 2024-05-07 09:06 +0000
+            created at 2024-05-24 09:29 +0000
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diff --git a/coverage/z_8030ef0ea5bfd6aa_test_canal_py.html b/coverage/z_8030ef0ea5bfd6aa_test_canal_py.html
index 0ef8304b..933533e7 100644
--- a/coverage/z_8030ef0ea5bfd6aa_test_canal_py.html
+++ b/coverage/z_8030ef0ea5bfd6aa_test_canal_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_8030ef0ea5bfd6aa_test_canion_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
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-            created at 2024-05-07 09:06 +0000
+            created at 2024-05-24 09:29 +0000
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         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -110,7 +110,7 @@ <h2>
             <a class="nav" href="z_8030ef0ea5bfd6aa_test_canion_py.html">&#xbb; next</a>
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+            created at 2024-05-24 09:29 +0000
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diff --git a/coverage/z_8030ef0ea5bfd6aa_test_canion_py.html b/coverage/z_8030ef0ea5bfd6aa_test_canion_py.html
index 54c833d5..2965269e 100644
--- a/coverage/z_8030ef0ea5bfd6aa_test_canion_py.html
+++ b/coverage/z_8030ef0ea5bfd6aa_test_canion_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_8030ef0ea5bfd6aa_test_curves_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
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-            created at 2024-05-07 09:06 +0000
+            created at 2024-05-24 09:29 +0000
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@@ -110,7 +110,7 @@ <h2>
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+            created at 2024-05-24 09:29 +0000
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diff --git a/coverage/z_8030ef0ea5bfd6aa_test_curves_py.html b/coverage/z_8030ef0ea5bfd6aa_test_curves_py.html
index ca772599..dfaddb55 100644
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+++ b/coverage/z_8030ef0ea5bfd6aa_test_curves_py.html
@@ -65,7 +65,7 @@ <h2>
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             &nbsp; &nbsp; &nbsp;
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-            created at 2024-05-07 09:06 +0000
+            created at 2024-05-24 09:29 +0000
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             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -110,7 +110,7 @@ <h2>
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             &nbsp; &nbsp; &nbsp;
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-            created at 2024-05-07 09:06 +0000
+            created at 2024-05-24 09:29 +0000
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diff --git a/coverage/z_833b0317e3c43dca___init___py.html b/coverage/z_833b0317e3c43dca___init___py.html
index 818ae15f..3a65766e 100644
--- a/coverage/z_833b0317e3c43dca___init___py.html
+++ b/coverage/z_833b0317e3c43dca___init___py.html
@@ -65,7 +65,7 @@ <h2>
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             &nbsp; &nbsp; &nbsp;
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-            created at 2024-05-07 09:06 +0000
+            created at 2024-05-24 09:29 +0000
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             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -89,7 +89,7 @@ <h2>
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             &nbsp; &nbsp; &nbsp;
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-            created at 2024-05-07 09:06 +0000
+            created at 2024-05-24 09:29 +0000
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diff --git a/coverage/z_833b0317e3c43dca_constants_py.html b/coverage/z_833b0317e3c43dca_constants_py.html
index 413a3a91..51422612 100644
--- a/coverage/z_833b0317e3c43dca_constants_py.html
+++ b/coverage/z_833b0317e3c43dca_constants_py.html
@@ -65,7 +65,7 @@ <h2>
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             &nbsp; &nbsp; &nbsp;
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-            created at 2024-05-07 09:06 +0000
+            created at 2024-05-24 09:29 +0000
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@@ -162,7 +162,7 @@ <h2>
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+            created at 2024-05-24 09:29 +0000
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index bbe46589..e9e80d04 100644
--- a/coverage/z_833b0317e3c43dca_loader_py.html
+++ b/coverage/z_833b0317e3c43dca_loader_py.html
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+            created at 2024-05-24 09:29 +0000
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+            created at 2024-05-24 09:29 +0000
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diff --git a/coverage/z_833b0317e3c43dca_transform_py.html b/coverage/z_833b0317e3c43dca_transform_py.html
index dd3a3f27..930281bc 100644
--- a/coverage/z_833b0317e3c43dca_transform_py.html
+++ b/coverage/z_833b0317e3c43dca_transform_py.html
@@ -65,7 +65,7 @@ <h2>
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             &nbsp; &nbsp; &nbsp;
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-            created at 2024-05-07 09:06 +0000
+            created at 2024-05-24 09:29 +0000
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@@ -102,7 +102,7 @@ <h2>
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+            created at 2024-05-24 09:29 +0000
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diff --git a/coverage/z_8a2a7f872cf1434f___init___py.html b/coverage/z_8a2a7f872cf1434f___init___py.html
index 71dd7bb8..0f4e864e 100644
--- a/coverage/z_8a2a7f872cf1434f___init___py.html
+++ b/coverage/z_8a2a7f872cf1434f___init___py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_8a2a7f872cf1434f_interbpcorr_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
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-            created at 2024-05-07 09:06 +0000
+            created at 2024-05-24 09:29 +0000
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@@ -94,7 +94,7 @@ <h2>
             <a class="nav" href="z_8a2a7f872cf1434f_interbpcorr_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
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-            created at 2024-05-07 09:06 +0000
+            created at 2024-05-24 09:29 +0000
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diff --git a/coverage/z_8a2a7f872cf1434f_interbpcorr_py.html b/coverage/z_8a2a7f872cf1434f_interbpcorr_py.html
index a1fb91e0..c44c3a92 100644
--- a/coverage/z_8a2a7f872cf1434f_interbpcorr_py.html
+++ b/coverage/z_8a2a7f872cf1434f_interbpcorr_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_8a2a7f872cf1434f_interhpcorr_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
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-            created at 2024-05-07 09:06 +0000
+            created at 2024-05-24 09:29 +0000
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         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -103,314 +103,315 @@ <h2>
     <p class="pln"><span class="n"><a id="t21" href="#t21">21</a></span><span class="t">    <span class="str">"""</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t22" href="#t22">22</a></span><span class="t"><span class="str">    | biobb_dna InterBasePairCorrelation</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t23" href="#t23">23</a></span><span class="t"><span class="str">    | Calculate correlation between all base pairs of a single sequence and for a single helical parameter.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t24" href="#t24">24</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t25" href="#t25">25</a></span><span class="t"><span class="str">    Args:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t26" href="#t26">26</a></span><span class="t"><span class="str">        input_filename_shift (str): Path to .ser file with data for helical parameter 'shift'. File type: input. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/correlation/canal_output_shift.ser>`_. Accepted formats: ser (edam:format_2330).</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t27" href="#t27">27</a></span><span class="t"><span class="str">        input_filename_slide (str): Path to .ser file with data for helical parameter 'slide'. File type: input. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/correlation/canal_output_slide.ser>`_. Accepted formats: ser (edam:format_2330).</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t28" href="#t28">28</a></span><span class="t"><span class="str">        input_filename_rise (str): Path to .ser file with data for helical parameter 'rise'. File type: input. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/correlation/canal_output_rise.ser>`_. Accepted formats: ser (edam:format_2330).</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t29" href="#t29">29</a></span><span class="t"><span class="str">        input_filename_tilt (str): Path to .ser file with data for helical parameter 'tilt'. File type: input. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/correlation/canal_output_tilt.ser>`_. Accepted formats: ser (edam:format_2330).</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t30" href="#t30">30</a></span><span class="t"><span class="str">        input_filename_roll (str): Path to .ser file with data for helical parameter 'roll'. File type: input. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/correlation/canal_output_roll.ser>`_. Accepted formats: ser (edam:format_2330).</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t31" href="#t31">31</a></span><span class="t"><span class="str">        input_filename_twist (str): Path to .ser file with data for helical parameter 'twist'. File type: input. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/correlation/canal_output_twist.ser>`_. Accepted formats: ser (edam:format_2330).</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t32" href="#t32">32</a></span><span class="t"><span class="str">        output_csv_path (str): Path to directory where output is saved. File type: output. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/reference/correlation/inter_bpcorr_ref.csv>`_. Accepted formats: csv (edam:format_3752).</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t33" href="#t33">33</a></span><span class="t"><span class="str">        output_jpg_path (str): Path to .jpg file where output is saved. File type: output. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/reference/correlation/inter_bpcorr_ref.jpg>`_. Accepted formats: jpg (edam:format_3579).</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t34" href="#t34">34</a></span><span class="t"><span class="str">        properties (dict):</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t35" href="#t35">35</a></span><span class="t"><span class="str">            * **sequence** (*str*) - (None) Nucleic acid sequence for the input .ser file. Length of sequence is expected to be the same as the total number of columns in the .ser file, minus the index column (even if later on a subset of columns is selected with the *seqpos* option).</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t36" href="#t36">36</a></span><span class="t"><span class="str">            * **seqpos** (*list*) - (None) list of sequence positions (columns indices starting by 0) to analyze.  If not specified it will analyse the complete sequence.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t37" href="#t37">37</a></span><span class="t"><span class="str">            * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t38" href="#t38">38</a></span><span class="t"><span class="str">            * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t39" href="#t39">39</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t40" href="#t40">40</a></span><span class="t"><span class="str">    Examples:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t41" href="#t41">41</a></span><span class="t"><span class="str">        This is a use example of how to use the building block from Python::</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t42" href="#t42">42</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t43" href="#t43">43</a></span><span class="t"><span class="str">            from biobb_dna.interbp_correlations.interbpcorr import interbpcorr</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t44" href="#t44">44</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t45" href="#t45">45</a></span><span class="t"><span class="str">            interbpcorr(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t46" href="#t46">46</a></span><span class="t"><span class="str">                input_filename_shift='path/to/input/shift.ser',</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t47" href="#t47">47</a></span><span class="t"><span class="str">                input_filename_slide='path/to/input/slide.ser',</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t48" href="#t48">48</a></span><span class="t"><span class="str">                input_filename_rise='path/to/input/slide.ser',</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t49" href="#t49">49</a></span><span class="t"><span class="str">                input_filename_tilt='path/to/input/tilt.ser',</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t50" href="#t50">50</a></span><span class="t"><span class="str">                input_filename_roll='path/to/input/roll.ser',</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t51" href="#t51">51</a></span><span class="t"><span class="str">                input_filename_twist='path/to/input/twist.ser',</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t52" href="#t52">52</a></span><span class="t"><span class="str">                output_csv_path='path/to/output/file.csv',</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t53" href="#t53">53</a></span><span class="t"><span class="str">                output_jpg_path='path/to/output/plot.jpg',</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t54" href="#t54">54</a></span><span class="t"><span class="str">                properties=prop)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t55" href="#t55">55</a></span><span class="t"><span class="str">    Info:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t56" href="#t56">56</a></span><span class="t"><span class="str">        * wrapped_software:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t57" href="#t57">57</a></span><span class="t"><span class="str">            * name: In house</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t58" href="#t58">58</a></span><span class="t"><span class="str">            * license: Apache-2.0</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t59" href="#t59">59</a></span><span class="t"><span class="str">        * ontology:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t60" href="#t60">60</a></span><span class="t"><span class="str">            * name: EDAM</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t61" href="#t61">61</a></span><span class="t"><span class="str">            * schema: http://edamontology.org/EDAM.owl</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t62" href="#t62">62</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t63" href="#t63">63</a></span><span class="t"><span class="str">    """</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t64" href="#t64">64</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t65" href="#t65">65</a></span><span class="t">    <span class="key">def</span> <span class="nam">__init__</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t66" href="#t66">66</a></span><span class="t">            <span class="nam">self</span><span class="op">,</span> <span class="nam">input_filename_shift</span><span class="op">,</span> <span class="nam">input_filename_slide</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t67" href="#t67">67</a></span><span class="t">            <span class="nam">input_filename_rise</span><span class="op">,</span> <span class="nam">input_filename_tilt</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t68" href="#t68">68</a></span><span class="t">            <span class="nam">input_filename_roll</span><span class="op">,</span> <span class="nam">input_filename_twist</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t69" href="#t69">69</a></span><span class="t">            <span class="nam">output_csv_path</span><span class="op">,</span> <span class="nam">output_jpg_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t70" href="#t70">70</a></span><span class="t">            <span class="nam">properties</span><span class="op">=</span><span class="key">None</span><span class="op">,</span> <span class="op">**</span><span class="nam">kwargs</span><span class="op">)</span> <span class="op">-></span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t71" href="#t71">71</a></span><span class="t">        <span class="nam">properties</span> <span class="op">=</span> <span class="nam">properties</span> <span class="key">or</span> <span class="op">{</span><span class="op">}</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t72" href="#t72">72</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t73" href="#t73">73</a></span><span class="t">        <span class="com"># Call parent class constructor</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t74" href="#t74">74</a></span><span class="t">        <span class="nam">super</span><span class="op">(</span><span class="op">)</span><span class="op">.</span><span class="nam">__init__</span><span class="op">(</span><span class="nam">properties</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t75" href="#t75">75</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">locals_var_dict</span> <span class="op">=</span> <span class="nam">locals</span><span class="op">(</span><span class="op">)</span><span class="op">.</span><span class="nam">copy</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t76" href="#t76">76</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t77" href="#t77">77</a></span><span class="t">        <span class="com"># Input/Output files</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t78" href="#t78">78</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span> <span class="op">=</span> <span class="op">{</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t79" href="#t79">79</a></span><span class="t">            <span class="str">'in'</span><span class="op">:</span> <span class="op">{</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t80" href="#t80">80</a></span><span class="t">                <span class="str">'input_filename_shift'</span><span class="op">:</span> <span class="nam">input_filename_shift</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t81" href="#t81">81</a></span><span class="t">                <span class="str">'input_filename_slide'</span><span class="op">:</span> <span class="nam">input_filename_slide</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t82" href="#t82">82</a></span><span class="t">                <span class="str">'input_filename_rise'</span><span class="op">:</span> <span class="nam">input_filename_rise</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t83" href="#t83">83</a></span><span class="t">                <span class="str">'input_filename_tilt'</span><span class="op">:</span> <span class="nam">input_filename_tilt</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t84" href="#t84">84</a></span><span class="t">                <span class="str">'input_filename_roll'</span><span class="op">:</span> <span class="nam">input_filename_roll</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t85" href="#t85">85</a></span><span class="t">                <span class="str">'input_filename_twist'</span><span class="op">:</span> <span class="nam">input_filename_twist</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t86" href="#t86">86</a></span><span class="t">            <span class="op">}</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t87" href="#t87">87</a></span><span class="t">            <span class="str">'out'</span><span class="op">:</span> <span class="op">{</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t88" href="#t88">88</a></span><span class="t">                <span class="str">'output_csv_path'</span><span class="op">:</span> <span class="nam">output_csv_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t89" href="#t89">89</a></span><span class="t">                <span class="str">'output_jpg_path'</span><span class="op">:</span> <span class="nam">output_jpg_path</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t90" href="#t90">90</a></span><span class="t">            <span class="op">}</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t91" href="#t91">91</a></span><span class="t">        <span class="op">}</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t92" href="#t92">92</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t93" href="#t93">93</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">properties</span> <span class="op">=</span> <span class="nam">properties</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t94" href="#t94">94</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"sequence"</span><span class="op">,</span> <span class="key">None</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t95" href="#t95">95</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"seqpos"</span><span class="op">,</span> <span class="key">None</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t96" href="#t96">96</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t97" href="#t97">97</a></span><span class="t">        <span class="com"># Check the properties</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t98" href="#t98">98</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_properties</span><span class="op">(</span><span class="nam">properties</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t99" href="#t99">99</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_arguments</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t100" href="#t100">100</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t101" href="#t101">101</a></span><span class="t">    <span class="op">@</span><span class="nam">launchlogger</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t102" href="#t102">102</a></span><span class="t">    <span class="key">def</span> <span class="nam">launch</span><span class="op">(</span><span class="nam">self</span><span class="op">)</span> <span class="op">-></span> <span class="nam">int</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t103" href="#t103">103</a></span><span class="t">        <span class="str">"""Execute the :class:`HelParCorrelation &lt;correlations.interbpcorr.InterBasePairCorrelation>` object."""</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t104" href="#t104">104</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t105" href="#t105">105</a></span><span class="t">        <span class="com"># Setup Biobb</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t106" href="#t106">106</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">check_restart</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t107" href="#t107">107</a></span><span class="t">            <span class="key">return</span> <span class="num">0</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t108" href="#t108">108</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">stage_files</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t109" href="#t109">109</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t110" href="#t110">110</a></span><span class="t">        <span class="com"># check sequence</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t111" href="#t111">111</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span> <span class="key">is</span> <span class="key">None</span> <span class="key">or</span> <span class="nam">len</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span><span class="op">)</span> <span class="op">&lt;</span> <span class="num">2</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t112" href="#t112">112</a></span><span class="t">            <span class="key">raise</span> <span class="nam">ValueError</span><span class="op">(</span><span class="str">"sequence is null or too short!"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t113" href="#t113">113</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t114" href="#t114">114</a></span><span class="t">        <span class="com"># check seqpos</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t115" href="#t115">115</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span> <span class="key">is</span> <span class="key">not</span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t116" href="#t116">116</a></span><span class="t">            <span class="key">if</span> <span class="key">not</span> <span class="op">(</span><span class="nam">isinstance</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">,</span> <span class="nam">list</span><span class="op">)</span> <span class="key">and</span> <span class="nam">len</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">)</span> <span class="op">></span> <span class="num">1</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t117" href="#t117">117</a></span><span class="t">                <span class="key">raise</span> <span class="nam">ValueError</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t118" href="#t118">118</a></span><span class="t">                    <span class="str">"seqpos must be a list of at least two integers"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t119" href="#t119">119</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t120" href="#t120">120</a></span><span class="t">        <span class="com"># Creating temporary folder</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t121" href="#t121">121</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span> <span class="op">=</span> <span class="nam">fu</span><span class="op">.</span><span class="nam">create_unique_dir</span><span class="op">(</span><span class="nam">prefix</span><span class="op">=</span><span class="str">"bpcorrelation_"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t122" href="#t122">122</a></span><span class="t">        <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="str">'Creating %s temporary folder'</span> <span class="op">%</span> <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t123" href="#t123">123</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t124" href="#t124">124</a></span><span class="t">        <span class="com"># read input</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t125" href="#t125">125</a></span><span class="t">        <span class="nam">shift</span> <span class="op">=</span> <span class="nam">read_series</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t126" href="#t126">126</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">"in"</span><span class="op">]</span><span class="op">[</span><span class="str">"input_filename_shift"</span><span class="op">]</span><span class="op">,</span> <span class="nam">usecols</span><span class="op">=</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t127" href="#t127">127</a></span><span class="t">        <span class="nam">slide</span> <span class="op">=</span> <span class="nam">read_series</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t128" href="#t128">128</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">"in"</span><span class="op">]</span><span class="op">[</span><span class="str">"input_filename_slide"</span><span class="op">]</span><span class="op">,</span> <span class="nam">usecols</span><span class="op">=</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t129" href="#t129">129</a></span><span class="t">        <span class="nam">rise</span> <span class="op">=</span> <span class="nam">read_series</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t130" href="#t130">130</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">"in"</span><span class="op">]</span><span class="op">[</span><span class="str">"input_filename_rise"</span><span class="op">]</span><span class="op">,</span> <span class="nam">usecols</span><span class="op">=</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t131" href="#t131">131</a></span><span class="t">        <span class="nam">tilt</span> <span class="op">=</span> <span class="nam">read_series</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t132" href="#t132">132</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">"in"</span><span class="op">]</span><span class="op">[</span><span class="str">"input_filename_tilt"</span><span class="op">]</span><span class="op">,</span> <span class="nam">usecols</span><span class="op">=</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t133" href="#t133">133</a></span><span class="t">        <span class="nam">roll</span> <span class="op">=</span> <span class="nam">read_series</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t134" href="#t134">134</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">"in"</span><span class="op">]</span><span class="op">[</span><span class="str">"input_filename_roll"</span><span class="op">]</span><span class="op">,</span> <span class="nam">usecols</span><span class="op">=</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t135" href="#t135">135</a></span><span class="t">        <span class="nam">twist</span> <span class="op">=</span> <span class="nam">read_series</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t136" href="#t136">136</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">"in"</span><span class="op">]</span><span class="op">[</span><span class="str">"input_filename_twist"</span><span class="op">]</span><span class="op">,</span> <span class="nam">usecols</span><span class="op">=</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t137" href="#t137">137</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t138" href="#t138">138</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span> <span class="key">is</span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t139" href="#t139">139</a></span><span class="t">            <span class="com"># drop first and last columns</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t140" href="#t140">140</a></span><span class="t">            <span class="nam">shift</span> <span class="op">=</span> <span class="nam">shift</span><span class="op">[</span><span class="nam">shift</span><span class="op">.</span><span class="nam">columns</span><span class="op">[</span><span class="num">1</span><span class="op">:</span><span class="op">-</span><span class="num">2</span><span class="op">]</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t141" href="#t141">141</a></span><span class="t">            <span class="nam">slide</span> <span class="op">=</span> <span class="nam">slide</span><span class="op">[</span><span class="nam">slide</span><span class="op">.</span><span class="nam">columns</span><span class="op">[</span><span class="num">1</span><span class="op">:</span><span class="op">-</span><span class="num">2</span><span class="op">]</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t142" href="#t142">142</a></span><span class="t">            <span class="nam">rise</span> <span class="op">=</span> <span class="nam">rise</span><span class="op">[</span><span class="nam">rise</span><span class="op">.</span><span class="nam">columns</span><span class="op">[</span><span class="num">1</span><span class="op">:</span><span class="op">-</span><span class="num">2</span><span class="op">]</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t143" href="#t143">143</a></span><span class="t">            <span class="nam">tilt</span> <span class="op">=</span> <span class="nam">tilt</span><span class="op">[</span><span class="nam">tilt</span><span class="op">.</span><span class="nam">columns</span><span class="op">[</span><span class="num">1</span><span class="op">:</span><span class="op">-</span><span class="num">2</span><span class="op">]</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t144" href="#t144">144</a></span><span class="t">            <span class="nam">roll</span> <span class="op">=</span> <span class="nam">roll</span><span class="op">[</span><span class="nam">roll</span><span class="op">.</span><span class="nam">columns</span><span class="op">[</span><span class="num">1</span><span class="op">:</span><span class="op">-</span><span class="num">2</span><span class="op">]</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t145" href="#t145">145</a></span><span class="t">            <span class="nam">twist</span> <span class="op">=</span> <span class="nam">twist</span><span class="op">[</span><span class="nam">twist</span><span class="op">.</span><span class="nam">columns</span><span class="op">[</span><span class="num">1</span><span class="op">:</span><span class="op">-</span><span class="num">2</span><span class="op">]</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t146" href="#t146">146</a></span><span class="t">            <span class="nam">labels</span> <span class="op">=</span> <span class="op">[</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t147" href="#t147">147</a></span><span class="t">                <span class="str">f"{i+1}_{self.sequence[i:i+2]}"</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">range</span><span class="op">(</span><span class="num">1</span><span class="op">,</span> <span class="nam">len</span><span class="op">(</span><span class="nam">shift</span><span class="op">.</span><span class="nam">columns</span><span class="op">)</span> <span class="op">+</span> <span class="num">1</span><span class="op">)</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t148" href="#t148">148</a></span><span class="t">            <span class="nam">corr_index</span> <span class="op">=</span> <span class="op">[</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t149" href="#t149">149</a></span><span class="t">                <span class="str">f"{self.sequence[i:i+3]}"</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">range</span><span class="op">(</span><span class="num">1</span><span class="op">,</span> <span class="nam">len</span><span class="op">(</span><span class="nam">shift</span><span class="op">.</span><span class="nam">columns</span><span class="op">)</span> <span class="op">+</span> <span class="num">1</span><span class="op">)</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t150" href="#t150">150</a></span><span class="t">        <span class="key">else</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t151" href="#t151">151</a></span><span class="t">            <span class="nam">labels</span> <span class="op">=</span> <span class="op">[</span><span class="str">f"{i+1}_{self.sequence[i:i+2]}"</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t152" href="#t152">152</a></span><span class="t">            <span class="nam">corr_index</span> <span class="op">=</span> <span class="op">[</span><span class="str">f"{self.sequence[i:i+3]}"</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t153" href="#t153">153</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t154" href="#t154">154</a></span><span class="t">        <span class="com"># rename duplicated subunits</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t155" href="#t155">155</a></span><span class="t">        <span class="nam">shift</span><span class="op">.</span><span class="nam">columns</span> <span class="op">=</span> <span class="nam">labels</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t156" href="#t156">156</a></span><span class="t">        <span class="nam">slide</span><span class="op">.</span><span class="nam">columns</span> <span class="op">=</span> <span class="nam">labels</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t157" href="#t157">157</a></span><span class="t">        <span class="nam">rise</span><span class="op">.</span><span class="nam">columns</span> <span class="op">=</span> <span class="nam">labels</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t158" href="#t158">158</a></span><span class="t">        <span class="nam">tilt</span><span class="op">.</span><span class="nam">columns</span> <span class="op">=</span> <span class="nam">labels</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t159" href="#t159">159</a></span><span class="t">        <span class="nam">roll</span><span class="op">.</span><span class="nam">columns</span> <span class="op">=</span> <span class="nam">labels</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t160" href="#t160">160</a></span><span class="t">        <span class="nam">twist</span><span class="op">.</span><span class="nam">columns</span> <span class="op">=</span> <span class="nam">labels</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t161" href="#t161">161</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t162" href="#t162">162</a></span><span class="t">        <span class="com"># set names to each dataset</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t163" href="#t163">163</a></span><span class="t">        <span class="nam">shift</span><span class="op">.</span><span class="nam">name</span> <span class="op">=</span> <span class="str">"shift"</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t164" href="#t164">164</a></span><span class="t">        <span class="nam">slide</span><span class="op">.</span><span class="nam">name</span> <span class="op">=</span> <span class="str">"slide"</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t165" href="#t165">165</a></span><span class="t">        <span class="nam">rise</span><span class="op">.</span><span class="nam">name</span> <span class="op">=</span> <span class="str">"rise"</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t166" href="#t166">166</a></span><span class="t">        <span class="nam">tilt</span><span class="op">.</span><span class="nam">name</span> <span class="op">=</span> <span class="str">"tilt"</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t167" href="#t167">167</a></span><span class="t">        <span class="nam">roll</span><span class="op">.</span><span class="nam">name</span> <span class="op">=</span> <span class="str">"roll"</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t168" href="#t168">168</a></span><span class="t">        <span class="nam">twist</span><span class="op">.</span><span class="nam">name</span> <span class="op">=</span> <span class="str">"twist"</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t169" href="#t169">169</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t170" href="#t170">170</a></span><span class="t">        <span class="com"># get correlation between neighboring basepairs among all helical parameters</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t171" href="#t171">171</a></span><span class="t">        <span class="nam">results</span> <span class="op">=</span> <span class="op">{</span><span class="op">}</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t172" href="#t172">172</a></span><span class="t">        <span class="nam">datasets</span> <span class="op">=</span> <span class="op">[</span><span class="nam">shift</span><span class="op">,</span> <span class="nam">slide</span><span class="op">,</span> <span class="nam">rise</span><span class="op">,</span> <span class="nam">tilt</span><span class="op">,</span> <span class="nam">roll</span><span class="op">,</span> <span class="nam">twist</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t173" href="#t173">173</a></span><span class="t">        <span class="key">for</span> <span class="nam">ser1</span><span class="op">,</span> <span class="nam">ser2</span> <span class="key">in</span> <span class="nam">product</span><span class="op">(</span><span class="nam">datasets</span><span class="op">,</span> <span class="nam">datasets</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t174" href="#t174">174</a></span><span class="t">            <span class="nam">ser2_shifted</span> <span class="op">=</span> <span class="nam">ser2</span><span class="op">.</span><span class="nam">shift</span><span class="op">(</span><span class="nam">axis</span><span class="op">=</span><span class="num">1</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t175" href="#t175">175</a></span><span class="t">            <span class="nam">ser2_shifted</span><span class="op">[</span><span class="nam">labels</span><span class="op">[</span><span class="num">0</span><span class="op">]</span><span class="op">]</span> <span class="op">=</span> <span class="nam">ser2</span><span class="op">[</span><span class="nam">labels</span><span class="op">[</span><span class="op">-</span><span class="num">1</span><span class="op">]</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t176" href="#t176">176</a></span><span class="t">            <span class="key">if</span> <span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t177" href="#t177">177</a></span><span class="t">                    <span class="nam">ser1</span><span class="op">.</span><span class="nam">name</span> <span class="key">in</span> <span class="nam">constants</span><span class="op">.</span><span class="nam">hp_angular</span> <span class="key">and</span> <span class="nam">ser2</span><span class="op">.</span><span class="nam">name</span> <span class="key">in</span> <span class="nam">constants</span><span class="op">.</span><span class="nam">hp_angular</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t178" href="#t178">178</a></span><span class="t">                <span class="nam">method</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">circular</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t179" href="#t179">179</a></span><span class="t">            <span class="key">elif</span> <span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t180" href="#t180">180</a></span><span class="t">                <span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t181" href="#t181">181</a></span><span class="t">                    <span class="nam">ser1</span><span class="op">.</span><span class="nam">name</span> <span class="key">in</span> <span class="nam">constants</span><span class="op">.</span><span class="nam">hp_angular</span> <span class="key">and</span> <span class="key">not</span> <span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t182" href="#t182">182</a></span><span class="t">                        <span class="nam">ser2</span><span class="op">.</span><span class="nam">name</span> <span class="key">in</span> <span class="nam">constants</span><span class="op">.</span><span class="nam">hp_angular</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t183" href="#t183">183</a></span><span class="t">                <span class="op">)</span> <span class="key">or</span> <span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t184" href="#t184">184</a></span><span class="t">                    <span class="nam">ser2</span><span class="op">.</span><span class="nam">name</span> <span class="key">in</span> <span class="nam">constants</span><span class="op">.</span><span class="nam">hp_angular</span> <span class="key">and</span> <span class="key">not</span> <span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t185" href="#t185">185</a></span><span class="t">                        <span class="nam">ser1</span><span class="op">.</span><span class="nam">name</span> <span class="key">in</span> <span class="nam">constants</span><span class="op">.</span><span class="nam">hp_angular</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t186" href="#t186">186</a></span><span class="t">                <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t187" href="#t187">187</a></span><span class="t">            <span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t188" href="#t188">188</a></span><span class="t">                <span class="nam">method</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">circlineal</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t189" href="#t189">189</a></span><span class="t">            <span class="key">else</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t190" href="#t190">190</a></span><span class="t">                <span class="nam">method</span> <span class="op">=</span> <span class="str">"pearson"</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t191" href="#t191">191</a></span><span class="t">            <span class="nam">corr_data</span> <span class="op">=</span> <span class="nam">ser1</span><span class="op">.</span><span class="nam">corrwith</span><span class="op">(</span><span class="nam">ser2_shifted</span><span class="op">,</span> <span class="nam">method</span><span class="op">=</span><span class="nam">method</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t192" href="#t192">192</a></span><span class="t">            <span class="nam">corr_data</span><span class="op">.</span><span class="nam">index</span> <span class="op">=</span> <span class="nam">corr_index</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t193" href="#t193">193</a></span><span class="t">            <span class="nam">results</span><span class="op">[</span><span class="str">f"{ser1.name}/{ser2.name}"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">corr_data</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t194" href="#t194">194</a></span><span class="t">        <span class="nam">result_df</span> <span class="op">=</span> <span class="nam">pd</span><span class="op">.</span><span class="nam">DataFrame</span><span class="op">.</span><span class="nam">from_dict</span><span class="op">(</span><span class="nam">results</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t195" href="#t195">195</a></span><span class="t">        <span class="nam">result_df</span><span class="op">.</span><span class="nam">index</span> <span class="op">=</span> <span class="nam">corr_index</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t196" href="#t196">196</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t197" href="#t197">197</a></span><span class="t">        <span class="com"># save csv data</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t198" href="#t198">198</a></span><span class="t">        <span class="nam">result_df</span><span class="op">.</span><span class="nam">to_csv</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">"out"</span><span class="op">]</span><span class="op">[</span><span class="str">"output_csv_path"</span><span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t199" href="#t199">199</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t200" href="#t200">200</a></span><span class="t">        <span class="com"># create heatmap</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t201" href="#t201">201</a></span><span class="t">        <span class="nam">cmap</span> <span class="op">=</span> <span class="nam">plt</span><span class="op">.</span><span class="nam">get_cmap</span><span class="op">(</span><span class="str">"bwr"</span><span class="op">)</span><span class="op">.</span><span class="nam">copy</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t202" href="#t202">202</a></span><span class="t">        <span class="nam">bounds</span> <span class="op">=</span> <span class="op">[</span><span class="op">-</span><span class="num">1</span><span class="op">,</span> <span class="op">-</span><span class="num">.8</span><span class="op">,</span> <span class="op">-</span><span class="num">.6</span><span class="op">,</span> <span class="op">-</span><span class="num">.4</span><span class="op">,</span> <span class="op">-</span><span class="num">.2</span><span class="op">,</span> <span class="num">.2</span><span class="op">,</span> <span class="num">.4</span><span class="op">,</span> <span class="num">.6</span><span class="op">,</span> <span class="num">.8</span><span class="op">,</span> <span class="num">1</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t203" href="#t203">203</a></span><span class="t">        <span class="nam">num</span> <span class="op">=</span> <span class="nam">cmap</span><span class="op">.</span><span class="nam">N</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t204" href="#t204">204</a></span><span class="t">        <span class="nam">norm</span> <span class="op">=</span> <span class="nam">mpl</span><span class="op">.</span><span class="nam">colors</span><span class="op">.</span><span class="nam">BoundaryNorm</span><span class="op">(</span><span class="nam">bounds</span><span class="op">,</span> <span class="nam">num</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t205" href="#t205">205</a></span><span class="t">        <span class="nam">cmap</span><span class="op">.</span><span class="nam">set_bad</span><span class="op">(</span><span class="nam">color</span><span class="op">=</span><span class="str">"gainsboro"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t206" href="#t206">206</a></span><span class="t">        <span class="nam">fig</span><span class="op">,</span> <span class="nam">ax</span> <span class="op">=</span> <span class="nam">plt</span><span class="op">.</span><span class="nam">subplots</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t207" href="#t207">207</a></span><span class="t">            <span class="num">1</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t24" href="#t24">24</a></span><span class="t"><span class="str">    | Calculate correlation between neighboring base pairs and pairs of helical parameters.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t25" href="#t25">25</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t26" href="#t26">26</a></span><span class="t"><span class="str">    Args:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t27" href="#t27">27</a></span><span class="t"><span class="str">        input_filename_shift (str): Path to .ser file with data for helical parameter 'shift'. File type: input. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/correlation/canal_output_shift.ser>`_. Accepted formats: ser (edam:format_2330).</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t28" href="#t28">28</a></span><span class="t"><span class="str">        input_filename_slide (str): Path to .ser file with data for helical parameter 'slide'. File type: input. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/correlation/canal_output_slide.ser>`_. Accepted formats: ser (edam:format_2330).</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t29" href="#t29">29</a></span><span class="t"><span class="str">        input_filename_rise (str): Path to .ser file with data for helical parameter 'rise'. File type: input. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/correlation/canal_output_rise.ser>`_. Accepted formats: ser (edam:format_2330).</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t30" href="#t30">30</a></span><span class="t"><span class="str">        input_filename_tilt (str): Path to .ser file with data for helical parameter 'tilt'. File type: input. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/correlation/canal_output_tilt.ser>`_. Accepted formats: ser (edam:format_2330).</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t31" href="#t31">31</a></span><span class="t"><span class="str">        input_filename_roll (str): Path to .ser file with data for helical parameter 'roll'. File type: input. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/correlation/canal_output_roll.ser>`_. Accepted formats: ser (edam:format_2330).</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t32" href="#t32">32</a></span><span class="t"><span class="str">        input_filename_twist (str): Path to .ser file with data for helical parameter 'twist'. File type: input. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/correlation/canal_output_twist.ser>`_. Accepted formats: ser (edam:format_2330).</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t33" href="#t33">33</a></span><span class="t"><span class="str">        output_csv_path (str): Path to directory where output is saved. File type: output. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/reference/correlation/inter_bpcorr_ref.csv>`_. Accepted formats: csv (edam:format_3752).</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t34" href="#t34">34</a></span><span class="t"><span class="str">        output_jpg_path (str): Path to .jpg file where output is saved. File type: output. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/reference/correlation/inter_bpcorr_ref.jpg>`_. Accepted formats: jpg (edam:format_3579).</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t35" href="#t35">35</a></span><span class="t"><span class="str">        properties (dict):</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t36" href="#t36">36</a></span><span class="t"><span class="str">            * **sequence** (*str*) - (None) Nucleic acid sequence for the input .ser file. Length of sequence is expected to be the same as the total number of columns in the .ser file, minus the index column (even if later on a subset of columns is selected with the *seqpos* option).</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t37" href="#t37">37</a></span><span class="t"><span class="str">            * **seqpos** (*list*) - (None) list of sequence positions (columns indices starting by 0) to analyze.  If not specified it will analyse the complete sequence.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t38" href="#t38">38</a></span><span class="t"><span class="str">            * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t39" href="#t39">39</a></span><span class="t"><span class="str">            * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t40" href="#t40">40</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t41" href="#t41">41</a></span><span class="t"><span class="str">    Examples:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t42" href="#t42">42</a></span><span class="t"><span class="str">        This is a use example of how to use the building block from Python::</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t43" href="#t43">43</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t44" href="#t44">44</a></span><span class="t"><span class="str">            from biobb_dna.interbp_correlations.interbpcorr import interbpcorr</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t45" href="#t45">45</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t46" href="#t46">46</a></span><span class="t"><span class="str">            interbpcorr(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t47" href="#t47">47</a></span><span class="t"><span class="str">                input_filename_shift='path/to/input/shift.ser',</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t48" href="#t48">48</a></span><span class="t"><span class="str">                input_filename_slide='path/to/input/slide.ser',</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t49" href="#t49">49</a></span><span class="t"><span class="str">                input_filename_rise='path/to/input/slide.ser',</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t50" href="#t50">50</a></span><span class="t"><span class="str">                input_filename_tilt='path/to/input/tilt.ser',</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t51" href="#t51">51</a></span><span class="t"><span class="str">                input_filename_roll='path/to/input/roll.ser',</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t52" href="#t52">52</a></span><span class="t"><span class="str">                input_filename_twist='path/to/input/twist.ser',</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t53" href="#t53">53</a></span><span class="t"><span class="str">                output_csv_path='path/to/output/file.csv',</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t54" href="#t54">54</a></span><span class="t"><span class="str">                output_jpg_path='path/to/output/plot.jpg',</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t55" href="#t55">55</a></span><span class="t"><span class="str">                properties=prop)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t56" href="#t56">56</a></span><span class="t"><span class="str">    Info:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t57" href="#t57">57</a></span><span class="t"><span class="str">        * wrapped_software:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t58" href="#t58">58</a></span><span class="t"><span class="str">            * name: In house</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t59" href="#t59">59</a></span><span class="t"><span class="str">            * license: Apache-2.0</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t60" href="#t60">60</a></span><span class="t"><span class="str">        * ontology:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t61" href="#t61">61</a></span><span class="t"><span class="str">            * name: EDAM</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t62" href="#t62">62</a></span><span class="t"><span class="str">            * schema: http://edamontology.org/EDAM.owl</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t63" href="#t63">63</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t64" href="#t64">64</a></span><span class="t"><span class="str">    """</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t65" href="#t65">65</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t66" href="#t66">66</a></span><span class="t">    <span class="key">def</span> <span class="nam">__init__</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t67" href="#t67">67</a></span><span class="t">            <span class="nam">self</span><span class="op">,</span> <span class="nam">input_filename_shift</span><span class="op">,</span> <span class="nam">input_filename_slide</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t68" href="#t68">68</a></span><span class="t">            <span class="nam">input_filename_rise</span><span class="op">,</span> <span class="nam">input_filename_tilt</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t69" href="#t69">69</a></span><span class="t">            <span class="nam">input_filename_roll</span><span class="op">,</span> <span class="nam">input_filename_twist</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t70" href="#t70">70</a></span><span class="t">            <span class="nam">output_csv_path</span><span class="op">,</span> <span class="nam">output_jpg_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t71" href="#t71">71</a></span><span class="t">            <span class="nam">properties</span><span class="op">=</span><span class="key">None</span><span class="op">,</span> <span class="op">**</span><span class="nam">kwargs</span><span class="op">)</span> <span class="op">-></span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t72" href="#t72">72</a></span><span class="t">        <span class="nam">properties</span> <span class="op">=</span> <span class="nam">properties</span> <span class="key">or</span> <span class="op">{</span><span class="op">}</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t73" href="#t73">73</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t74" href="#t74">74</a></span><span class="t">        <span class="com"># Call parent class constructor</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t75" href="#t75">75</a></span><span class="t">        <span class="nam">super</span><span class="op">(</span><span class="op">)</span><span class="op">.</span><span class="nam">__init__</span><span class="op">(</span><span class="nam">properties</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t76" href="#t76">76</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">locals_var_dict</span> <span class="op">=</span> <span class="nam">locals</span><span class="op">(</span><span class="op">)</span><span class="op">.</span><span class="nam">copy</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t77" href="#t77">77</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t78" href="#t78">78</a></span><span class="t">        <span class="com"># Input/Output files</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t79" href="#t79">79</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span> <span class="op">=</span> <span class="op">{</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t80" href="#t80">80</a></span><span class="t">            <span class="str">'in'</span><span class="op">:</span> <span class="op">{</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t81" href="#t81">81</a></span><span class="t">                <span class="str">'input_filename_shift'</span><span class="op">:</span> <span class="nam">input_filename_shift</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t82" href="#t82">82</a></span><span class="t">                <span class="str">'input_filename_slide'</span><span class="op">:</span> <span class="nam">input_filename_slide</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t83" href="#t83">83</a></span><span class="t">                <span class="str">'input_filename_rise'</span><span class="op">:</span> <span class="nam">input_filename_rise</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t84" href="#t84">84</a></span><span class="t">                <span class="str">'input_filename_tilt'</span><span class="op">:</span> <span class="nam">input_filename_tilt</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t85" href="#t85">85</a></span><span class="t">                <span class="str">'input_filename_roll'</span><span class="op">:</span> <span class="nam">input_filename_roll</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t86" href="#t86">86</a></span><span class="t">                <span class="str">'input_filename_twist'</span><span class="op">:</span> <span class="nam">input_filename_twist</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t87" href="#t87">87</a></span><span class="t">            <span class="op">}</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t88" href="#t88">88</a></span><span class="t">            <span class="str">'out'</span><span class="op">:</span> <span class="op">{</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t89" href="#t89">89</a></span><span class="t">                <span class="str">'output_csv_path'</span><span class="op">:</span> <span class="nam">output_csv_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t90" href="#t90">90</a></span><span class="t">                <span class="str">'output_jpg_path'</span><span class="op">:</span> <span class="nam">output_jpg_path</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t91" href="#t91">91</a></span><span class="t">            <span class="op">}</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t92" href="#t92">92</a></span><span class="t">        <span class="op">}</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t93" href="#t93">93</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t94" href="#t94">94</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">properties</span> <span class="op">=</span> <span class="nam">properties</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t95" href="#t95">95</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"sequence"</span><span class="op">,</span> <span class="key">None</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t96" href="#t96">96</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"seqpos"</span><span class="op">,</span> <span class="key">None</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t97" href="#t97">97</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t98" href="#t98">98</a></span><span class="t">        <span class="com"># Check the properties</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t99" href="#t99">99</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_properties</span><span class="op">(</span><span class="nam">properties</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t100" href="#t100">100</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_arguments</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t101" href="#t101">101</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t102" href="#t102">102</a></span><span class="t">    <span class="op">@</span><span class="nam">launchlogger</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t103" href="#t103">103</a></span><span class="t">    <span class="key">def</span> <span class="nam">launch</span><span class="op">(</span><span class="nam">self</span><span class="op">)</span> <span class="op">-></span> <span class="nam">int</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t104" href="#t104">104</a></span><span class="t">        <span class="str">"""Execute the :class:`HelParCorrelation &lt;correlations.interbpcorr.InterBasePairCorrelation>` object."""</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t105" href="#t105">105</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t106" href="#t106">106</a></span><span class="t">        <span class="com"># Setup Biobb</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t107" href="#t107">107</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">check_restart</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t108" href="#t108">108</a></span><span class="t">            <span class="key">return</span> <span class="num">0</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t109" href="#t109">109</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">stage_files</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t110" href="#t110">110</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t111" href="#t111">111</a></span><span class="t">        <span class="com"># check sequence</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t112" href="#t112">112</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span> <span class="key">is</span> <span class="key">None</span> <span class="key">or</span> <span class="nam">len</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span><span class="op">)</span> <span class="op">&lt;</span> <span class="num">2</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t113" href="#t113">113</a></span><span class="t">            <span class="key">raise</span> <span class="nam">ValueError</span><span class="op">(</span><span class="str">"sequence is null or too short!"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t114" href="#t114">114</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t115" href="#t115">115</a></span><span class="t">        <span class="com"># check seqpos</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t116" href="#t116">116</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span> <span class="key">is</span> <span class="key">not</span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t117" href="#t117">117</a></span><span class="t">            <span class="key">if</span> <span class="key">not</span> <span class="op">(</span><span class="nam">isinstance</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">,</span> <span class="nam">list</span><span class="op">)</span> <span class="key">and</span> <span class="nam">len</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">)</span> <span class="op">></span> <span class="num">1</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t118" href="#t118">118</a></span><span class="t">                <span class="key">raise</span> <span class="nam">ValueError</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t119" href="#t119">119</a></span><span class="t">                    <span class="str">"seqpos must be a list of at least two integers"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t120" href="#t120">120</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t121" href="#t121">121</a></span><span class="t">        <span class="com"># Creating temporary folder</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t122" href="#t122">122</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span> <span class="op">=</span> <span class="nam">fu</span><span class="op">.</span><span class="nam">create_unique_dir</span><span class="op">(</span><span class="nam">prefix</span><span class="op">=</span><span class="str">"bpcorrelation_"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t123" href="#t123">123</a></span><span class="t">        <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="str">'Creating %s temporary folder'</span> <span class="op">%</span> <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t124" href="#t124">124</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t125" href="#t125">125</a></span><span class="t">        <span class="com"># read input</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t126" href="#t126">126</a></span><span class="t">        <span class="nam">shift</span> <span class="op">=</span> <span class="nam">read_series</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t127" href="#t127">127</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">"in"</span><span class="op">]</span><span class="op">[</span><span class="str">"input_filename_shift"</span><span class="op">]</span><span class="op">,</span> <span class="nam">usecols</span><span class="op">=</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t128" href="#t128">128</a></span><span class="t">        <span class="nam">slide</span> <span class="op">=</span> <span class="nam">read_series</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t129" href="#t129">129</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">"in"</span><span class="op">]</span><span class="op">[</span><span class="str">"input_filename_slide"</span><span class="op">]</span><span class="op">,</span> <span class="nam">usecols</span><span class="op">=</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t130" href="#t130">130</a></span><span class="t">        <span class="nam">rise</span> <span class="op">=</span> <span class="nam">read_series</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t131" href="#t131">131</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">"in"</span><span class="op">]</span><span class="op">[</span><span class="str">"input_filename_rise"</span><span class="op">]</span><span class="op">,</span> <span class="nam">usecols</span><span class="op">=</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t132" href="#t132">132</a></span><span class="t">        <span class="nam">tilt</span> <span class="op">=</span> <span class="nam">read_series</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t133" href="#t133">133</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">"in"</span><span class="op">]</span><span class="op">[</span><span class="str">"input_filename_tilt"</span><span class="op">]</span><span class="op">,</span> <span class="nam">usecols</span><span class="op">=</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t134" href="#t134">134</a></span><span class="t">        <span class="nam">roll</span> <span class="op">=</span> <span class="nam">read_series</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t135" href="#t135">135</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">"in"</span><span class="op">]</span><span class="op">[</span><span class="str">"input_filename_roll"</span><span class="op">]</span><span class="op">,</span> <span class="nam">usecols</span><span class="op">=</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t136" href="#t136">136</a></span><span class="t">        <span class="nam">twist</span> <span class="op">=</span> <span class="nam">read_series</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t137" href="#t137">137</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">"in"</span><span class="op">]</span><span class="op">[</span><span class="str">"input_filename_twist"</span><span class="op">]</span><span class="op">,</span> <span class="nam">usecols</span><span class="op">=</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t138" href="#t138">138</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t139" href="#t139">139</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span> <span class="key">is</span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t140" href="#t140">140</a></span><span class="t">            <span class="com"># drop first and last columns</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t141" href="#t141">141</a></span><span class="t">            <span class="nam">shift</span> <span class="op">=</span> <span class="nam">shift</span><span class="op">[</span><span class="nam">shift</span><span class="op">.</span><span class="nam">columns</span><span class="op">[</span><span class="num">1</span><span class="op">:</span><span class="op">-</span><span class="num">2</span><span class="op">]</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t142" href="#t142">142</a></span><span class="t">            <span class="nam">slide</span> <span class="op">=</span> <span class="nam">slide</span><span class="op">[</span><span class="nam">slide</span><span class="op">.</span><span class="nam">columns</span><span class="op">[</span><span class="num">1</span><span class="op">:</span><span class="op">-</span><span class="num">2</span><span class="op">]</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t143" href="#t143">143</a></span><span class="t">            <span class="nam">rise</span> <span class="op">=</span> <span class="nam">rise</span><span class="op">[</span><span class="nam">rise</span><span class="op">.</span><span class="nam">columns</span><span class="op">[</span><span class="num">1</span><span class="op">:</span><span class="op">-</span><span class="num">2</span><span class="op">]</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t144" href="#t144">144</a></span><span class="t">            <span class="nam">tilt</span> <span class="op">=</span> <span class="nam">tilt</span><span class="op">[</span><span class="nam">tilt</span><span class="op">.</span><span class="nam">columns</span><span class="op">[</span><span class="num">1</span><span class="op">:</span><span class="op">-</span><span class="num">2</span><span class="op">]</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t145" href="#t145">145</a></span><span class="t">            <span class="nam">roll</span> <span class="op">=</span> <span class="nam">roll</span><span class="op">[</span><span class="nam">roll</span><span class="op">.</span><span class="nam">columns</span><span class="op">[</span><span class="num">1</span><span class="op">:</span><span class="op">-</span><span class="num">2</span><span class="op">]</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t146" href="#t146">146</a></span><span class="t">            <span class="nam">twist</span> <span class="op">=</span> <span class="nam">twist</span><span class="op">[</span><span class="nam">twist</span><span class="op">.</span><span class="nam">columns</span><span class="op">[</span><span class="num">1</span><span class="op">:</span><span class="op">-</span><span class="num">2</span><span class="op">]</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t147" href="#t147">147</a></span><span class="t">            <span class="nam">labels</span> <span class="op">=</span> <span class="op">[</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t148" href="#t148">148</a></span><span class="t">                <span class="str">f"{i+1}_{self.sequence[i:i+2]}"</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">range</span><span class="op">(</span><span class="num">1</span><span class="op">,</span> <span class="nam">len</span><span class="op">(</span><span class="nam">shift</span><span class="op">.</span><span class="nam">columns</span><span class="op">)</span> <span class="op">+</span> <span class="num">1</span><span class="op">)</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t149" href="#t149">149</a></span><span class="t">            <span class="nam">corr_index</span> <span class="op">=</span> <span class="op">[</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t150" href="#t150">150</a></span><span class="t">                <span class="str">f"{self.sequence[i:i+3]}"</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">range</span><span class="op">(</span><span class="num">1</span><span class="op">,</span> <span class="nam">len</span><span class="op">(</span><span class="nam">shift</span><span class="op">.</span><span class="nam">columns</span><span class="op">)</span> <span class="op">+</span> <span class="num">1</span><span class="op">)</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t151" href="#t151">151</a></span><span class="t">        <span class="key">else</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t152" href="#t152">152</a></span><span class="t">            <span class="nam">labels</span> <span class="op">=</span> <span class="op">[</span><span class="str">f"{i+1}_{self.sequence[i:i+2]}"</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t153" href="#t153">153</a></span><span class="t">            <span class="nam">corr_index</span> <span class="op">=</span> <span class="op">[</span><span class="str">f"{self.sequence[i:i+3]}"</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t154" href="#t154">154</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t155" href="#t155">155</a></span><span class="t">        <span class="com"># rename duplicated subunits</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t156" href="#t156">156</a></span><span class="t">        <span class="nam">shift</span><span class="op">.</span><span class="nam">columns</span> <span class="op">=</span> <span class="nam">labels</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t157" href="#t157">157</a></span><span class="t">        <span class="nam">slide</span><span class="op">.</span><span class="nam">columns</span> <span class="op">=</span> <span class="nam">labels</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t158" href="#t158">158</a></span><span class="t">        <span class="nam">rise</span><span class="op">.</span><span class="nam">columns</span> <span class="op">=</span> <span class="nam">labels</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t159" href="#t159">159</a></span><span class="t">        <span class="nam">tilt</span><span class="op">.</span><span class="nam">columns</span> <span class="op">=</span> <span class="nam">labels</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t160" href="#t160">160</a></span><span class="t">        <span class="nam">roll</span><span class="op">.</span><span class="nam">columns</span> <span class="op">=</span> <span class="nam">labels</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t161" href="#t161">161</a></span><span class="t">        <span class="nam">twist</span><span class="op">.</span><span class="nam">columns</span> <span class="op">=</span> <span class="nam">labels</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t162" href="#t162">162</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t163" href="#t163">163</a></span><span class="t">        <span class="com"># set names to each dataset</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t164" href="#t164">164</a></span><span class="t">        <span class="nam">shift</span><span class="op">.</span><span class="nam">name</span> <span class="op">=</span> <span class="str">"shift"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t165" href="#t165">165</a></span><span class="t">        <span class="nam">slide</span><span class="op">.</span><span class="nam">name</span> <span class="op">=</span> <span class="str">"slide"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t166" href="#t166">166</a></span><span class="t">        <span class="nam">rise</span><span class="op">.</span><span class="nam">name</span> <span class="op">=</span> <span class="str">"rise"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t167" href="#t167">167</a></span><span class="t">        <span class="nam">tilt</span><span class="op">.</span><span class="nam">name</span> <span class="op">=</span> <span class="str">"tilt"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t168" href="#t168">168</a></span><span class="t">        <span class="nam">roll</span><span class="op">.</span><span class="nam">name</span> <span class="op">=</span> <span class="str">"roll"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t169" href="#t169">169</a></span><span class="t">        <span class="nam">twist</span><span class="op">.</span><span class="nam">name</span> <span class="op">=</span> <span class="str">"twist"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t170" href="#t170">170</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t171" href="#t171">171</a></span><span class="t">        <span class="com"># get correlation between neighboring basepairs among all helical parameters</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t172" href="#t172">172</a></span><span class="t">        <span class="nam">results</span> <span class="op">=</span> <span class="op">{</span><span class="op">}</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t173" href="#t173">173</a></span><span class="t">        <span class="nam">datasets</span> <span class="op">=</span> <span class="op">[</span><span class="nam">shift</span><span class="op">,</span> <span class="nam">slide</span><span class="op">,</span> <span class="nam">rise</span><span class="op">,</span> <span class="nam">tilt</span><span class="op">,</span> <span class="nam">roll</span><span class="op">,</span> <span class="nam">twist</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t174" href="#t174">174</a></span><span class="t">        <span class="key">for</span> <span class="nam">ser1</span><span class="op">,</span> <span class="nam">ser2</span> <span class="key">in</span> <span class="nam">product</span><span class="op">(</span><span class="nam">datasets</span><span class="op">,</span> <span class="nam">datasets</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t175" href="#t175">175</a></span><span class="t">            <span class="nam">ser2_shifted</span> <span class="op">=</span> <span class="nam">ser2</span><span class="op">.</span><span class="nam">shift</span><span class="op">(</span><span class="nam">axis</span><span class="op">=</span><span class="num">1</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t176" href="#t176">176</a></span><span class="t">            <span class="nam">ser2_shifted</span><span class="op">[</span><span class="nam">labels</span><span class="op">[</span><span class="num">0</span><span class="op">]</span><span class="op">]</span> <span class="op">=</span> <span class="nam">ser2</span><span class="op">[</span><span class="nam">labels</span><span class="op">[</span><span class="op">-</span><span class="num">1</span><span class="op">]</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t177" href="#t177">177</a></span><span class="t">            <span class="key">if</span> <span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t178" href="#t178">178</a></span><span class="t">                    <span class="nam">ser1</span><span class="op">.</span><span class="nam">name</span> <span class="key">in</span> <span class="nam">constants</span><span class="op">.</span><span class="nam">hp_angular</span> <span class="key">and</span> <span class="nam">ser2</span><span class="op">.</span><span class="nam">name</span> <span class="key">in</span> <span class="nam">constants</span><span class="op">.</span><span class="nam">hp_angular</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t179" href="#t179">179</a></span><span class="t">                <span class="nam">method</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">circular</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t180" href="#t180">180</a></span><span class="t">            <span class="key">elif</span> <span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t181" href="#t181">181</a></span><span class="t">                <span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t182" href="#t182">182</a></span><span class="t">                    <span class="nam">ser1</span><span class="op">.</span><span class="nam">name</span> <span class="key">in</span> <span class="nam">constants</span><span class="op">.</span><span class="nam">hp_angular</span> <span class="key">and</span> <span class="key">not</span> <span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t183" href="#t183">183</a></span><span class="t">                        <span class="nam">ser2</span><span class="op">.</span><span class="nam">name</span> <span class="key">in</span> <span class="nam">constants</span><span class="op">.</span><span class="nam">hp_angular</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t184" href="#t184">184</a></span><span class="t">                <span class="op">)</span> <span class="key">or</span> <span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t185" href="#t185">185</a></span><span class="t">                    <span class="nam">ser2</span><span class="op">.</span><span class="nam">name</span> <span class="key">in</span> <span class="nam">constants</span><span class="op">.</span><span class="nam">hp_angular</span> <span class="key">and</span> <span class="key">not</span> <span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t186" href="#t186">186</a></span><span class="t">                        <span class="nam">ser1</span><span class="op">.</span><span class="nam">name</span> <span class="key">in</span> <span class="nam">constants</span><span class="op">.</span><span class="nam">hp_angular</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t187" href="#t187">187</a></span><span class="t">                <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t188" href="#t188">188</a></span><span class="t">            <span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t189" href="#t189">189</a></span><span class="t">                <span class="nam">method</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">circlineal</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t190" href="#t190">190</a></span><span class="t">            <span class="key">else</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t191" href="#t191">191</a></span><span class="t">                <span class="nam">method</span> <span class="op">=</span> <span class="str">"pearson"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t192" href="#t192">192</a></span><span class="t">            <span class="nam">corr_data</span> <span class="op">=</span> <span class="nam">ser1</span><span class="op">.</span><span class="nam">corrwith</span><span class="op">(</span><span class="nam">ser2_shifted</span><span class="op">,</span> <span class="nam">method</span><span class="op">=</span><span class="nam">method</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t193" href="#t193">193</a></span><span class="t">            <span class="nam">corr_data</span><span class="op">.</span><span class="nam">index</span> <span class="op">=</span> <span class="nam">corr_index</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t194" href="#t194">194</a></span><span class="t">            <span class="nam">results</span><span class="op">[</span><span class="str">f"{ser1.name}/{ser2.name}"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">corr_data</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t195" href="#t195">195</a></span><span class="t">        <span class="nam">result_df</span> <span class="op">=</span> <span class="nam">pd</span><span class="op">.</span><span class="nam">DataFrame</span><span class="op">.</span><span class="nam">from_dict</span><span class="op">(</span><span class="nam">results</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t196" href="#t196">196</a></span><span class="t">        <span class="nam">result_df</span><span class="op">.</span><span class="nam">index</span> <span class="op">=</span> <span class="nam">corr_index</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t197" href="#t197">197</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t198" href="#t198">198</a></span><span class="t">        <span class="com"># save csv data</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t199" href="#t199">199</a></span><span class="t">        <span class="nam">result_df</span><span class="op">.</span><span class="nam">to_csv</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">"out"</span><span class="op">]</span><span class="op">[</span><span class="str">"output_csv_path"</span><span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t200" href="#t200">200</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t201" href="#t201">201</a></span><span class="t">        <span class="com"># create heatmap</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t202" href="#t202">202</a></span><span class="t">        <span class="nam">cmap</span> <span class="op">=</span> <span class="nam">plt</span><span class="op">.</span><span class="nam">get_cmap</span><span class="op">(</span><span class="str">"bwr"</span><span class="op">)</span><span class="op">.</span><span class="nam">copy</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t203" href="#t203">203</a></span><span class="t">        <span class="nam">bounds</span> <span class="op">=</span> <span class="op">[</span><span class="op">-</span><span class="num">1</span><span class="op">,</span> <span class="op">-</span><span class="num">.8</span><span class="op">,</span> <span class="op">-</span><span class="num">.6</span><span class="op">,</span> <span class="op">-</span><span class="num">.4</span><span class="op">,</span> <span class="op">-</span><span class="num">.2</span><span class="op">,</span> <span class="num">.2</span><span class="op">,</span> <span class="num">.4</span><span class="op">,</span> <span class="num">.6</span><span class="op">,</span> <span class="num">.8</span><span class="op">,</span> <span class="num">1</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t204" href="#t204">204</a></span><span class="t">        <span class="nam">num</span> <span class="op">=</span> <span class="nam">cmap</span><span class="op">.</span><span class="nam">N</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t205" href="#t205">205</a></span><span class="t">        <span class="nam">norm</span> <span class="op">=</span> <span class="nam">mpl</span><span class="op">.</span><span class="nam">colors</span><span class="op">.</span><span class="nam">BoundaryNorm</span><span class="op">(</span><span class="nam">bounds</span><span class="op">,</span> <span class="nam">num</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t206" href="#t206">206</a></span><span class="t">        <span class="nam">cmap</span><span class="op">.</span><span class="nam">set_bad</span><span class="op">(</span><span class="nam">color</span><span class="op">=</span><span class="str">"gainsboro"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t207" href="#t207">207</a></span><span class="t">        <span class="nam">fig</span><span class="op">,</span> <span class="nam">ax</span> <span class="op">=</span> <span class="nam">plt</span><span class="op">.</span><span class="nam">subplots</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t208" href="#t208">208</a></span><span class="t">            <span class="num">1</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t209" href="#t209">209</a></span><span class="t">            <span class="nam">dpi</span><span class="op">=</span><span class="num">300</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t210" href="#t210">210</a></span><span class="t">            <span class="nam">figsize</span><span class="op">=</span><span class="op">(</span><span class="num">7.5</span><span class="op">,</span> <span class="num">5</span><span class="op">)</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t211" href="#t211">211</a></span><span class="t">            <span class="nam">tight_layout</span><span class="op">=</span><span class="key">True</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t212" href="#t212">212</a></span><span class="t">        <span class="nam">im</span> <span class="op">=</span> <span class="nam">ax</span><span class="op">.</span><span class="nam">imshow</span><span class="op">(</span><span class="nam">result_df</span><span class="op">,</span> <span class="nam">cmap</span><span class="op">=</span><span class="nam">cmap</span><span class="op">,</span> <span class="nam">norm</span><span class="op">=</span><span class="nam">norm</span><span class="op">,</span> <span class="nam">aspect</span><span class="op">=</span><span class="str">'auto'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t213" href="#t213">213</a></span><span class="t">        <span class="nam">plt</span><span class="op">.</span><span class="nam">colorbar</span><span class="op">(</span><span class="nam">im</span><span class="op">,</span> <span class="nam">ticks</span><span class="op">=</span><span class="op">[</span><span class="op">-</span><span class="num">1</span><span class="op">,</span> <span class="op">-</span><span class="num">.8</span><span class="op">,</span> <span class="op">-</span><span class="num">.6</span><span class="op">,</span> <span class="op">-</span><span class="num">.4</span><span class="op">,</span> <span class="op">-</span><span class="num">.2</span><span class="op">,</span> <span class="num">.2</span><span class="op">,</span> <span class="num">.4</span><span class="op">,</span> <span class="num">.6</span><span class="op">,</span> <span class="num">.8</span><span class="op">,</span> <span class="num">1</span><span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t214" href="#t214">214</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t215" href="#t215">215</a></span><span class="t">        <span class="com"># axes</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t216" href="#t216">216</a></span><span class="t">        <span class="nam">xlocs</span> <span class="op">=</span> <span class="nam">np</span><span class="op">.</span><span class="nam">arange</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">result_df</span><span class="op">.</span><span class="nam">columns</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t217" href="#t217">217</a></span><span class="t">        <span class="nam">_</span> <span class="op">=</span> <span class="nam">ax</span><span class="op">.</span><span class="nam">set_xticks</span><span class="op">(</span><span class="nam">xlocs</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t218" href="#t218">218</a></span><span class="t">        <span class="nam">_</span> <span class="op">=</span> <span class="nam">ax</span><span class="op">.</span><span class="nam">set_xticklabels</span><span class="op">(</span><span class="nam">result_df</span><span class="op">.</span><span class="nam">columns</span><span class="op">.</span><span class="nam">to_list</span><span class="op">(</span><span class="op">)</span><span class="op">,</span> <span class="nam">rotation</span><span class="op">=</span><span class="num">90</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t219" href="#t219">219</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t220" href="#t220">220</a></span><span class="t">        <span class="nam">ylocs</span> <span class="op">=</span> <span class="nam">np</span><span class="op">.</span><span class="nam">arange</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">result_df</span><span class="op">.</span><span class="nam">index</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t221" href="#t221">221</a></span><span class="t">        <span class="nam">_</span> <span class="op">=</span> <span class="nam">ax</span><span class="op">.</span><span class="nam">set_yticks</span><span class="op">(</span><span class="nam">ylocs</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t222" href="#t222">222</a></span><span class="t">        <span class="nam">_</span> <span class="op">=</span> <span class="nam">ax</span><span class="op">.</span><span class="nam">set_yticklabels</span><span class="op">(</span><span class="nam">result_df</span><span class="op">.</span><span class="nam">index</span><span class="op">.</span><span class="nam">to_list</span><span class="op">(</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t223" href="#t223">223</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t224" href="#t224">224</a></span><span class="t">        <span class="nam">ax</span><span class="op">.</span><span class="nam">set_title</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t225" href="#t225">225</a></span><span class="t">            <span class="str">"Correlation for neighboring basepairs "</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t226" href="#t226">226</a></span><span class="t">            <span class="str">"and pairs of helical parameters"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t227" href="#t227">227</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t228" href="#t228">228</a></span><span class="t">        <span class="nam">fig</span><span class="op">.</span><span class="nam">tight_layout</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t229" href="#t229">229</a></span><span class="t">        <span class="nam">fig</span><span class="op">.</span><span class="nam">savefig</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t230" href="#t230">230</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'out'</span><span class="op">]</span><span class="op">[</span><span class="str">'output_jpg_path'</span><span class="op">]</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t231" href="#t231">231</a></span><span class="t">            <span class="nam">format</span><span class="op">=</span><span class="str">"jpg"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t232" href="#t232">232</a></span><span class="t">        <span class="nam">plt</span><span class="op">.</span><span class="nam">close</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t233" href="#t233">233</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t234" href="#t234">234</a></span><span class="t">        <span class="com"># Remove temporary file(s)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t235" href="#t235">235</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_files</span><span class="op">.</span><span class="nam">extend</span><span class="op">(</span><span class="op">[</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t236" href="#t236">236</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"unique_dir"</span><span class="op">)</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t237" href="#t237">237</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t238" href="#t238">238</a></span><span class="t">        <span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t239" href="#t239">239</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">remove_tmp_files</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t240" href="#t240">240</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t241" href="#t241">241</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_arguments</span><span class="op">(</span><span class="nam">output_files_created</span><span class="op">=</span><span class="key">True</span><span class="op">,</span> <span class="nam">raise_exception</span><span class="op">=</span><span class="key">False</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t242" href="#t242">242</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t243" href="#t243">243</a></span><span class="t">        <span class="key">return</span> <span class="num">0</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t244" href="#t244">244</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t245" href="#t245">245</a></span><span class="t">    <span class="op">@</span><span class="nam">staticmethod</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t246" href="#t246">246</a></span><span class="t">    <span class="key">def</span> <span class="nam">circular</span><span class="op">(</span><span class="nam">x1</span><span class="op">,</span> <span class="nam">x2</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t247" href="#t247">247</a></span><span class="t">        <span class="nam">x1</span> <span class="op">=</span> <span class="nam">x1</span> <span class="op">*</span> <span class="nam">np</span><span class="op">.</span><span class="nam">pi</span> <span class="op">/</span> <span class="num">180</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t248" href="#t248">248</a></span><span class="t">        <span class="nam">x2</span> <span class="op">=</span> <span class="nam">x2</span> <span class="op">*</span> <span class="nam">np</span><span class="op">.</span><span class="nam">pi</span> <span class="op">/</span> <span class="num">180</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t249" href="#t249">249</a></span><span class="t">        <span class="nam">diff_1</span> <span class="op">=</span> <span class="nam">np</span><span class="op">.</span><span class="nam">sin</span><span class="op">(</span><span class="nam">x1</span> <span class="op">-</span> <span class="nam">x1</span><span class="op">.</span><span class="nam">mean</span><span class="op">(</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t250" href="#t250">250</a></span><span class="t">        <span class="nam">diff_2</span> <span class="op">=</span> <span class="nam">np</span><span class="op">.</span><span class="nam">sin</span><span class="op">(</span><span class="nam">x2</span> <span class="op">-</span> <span class="nam">x2</span><span class="op">.</span><span class="nam">mean</span><span class="op">(</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t251" href="#t251">251</a></span><span class="t">        <span class="nam">num</span> <span class="op">=</span> <span class="op">(</span><span class="nam">diff_1</span> <span class="op">*</span> <span class="nam">diff_2</span><span class="op">)</span><span class="op">.</span><span class="nam">sum</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t252" href="#t252">252</a></span><span class="t">        <span class="nam">den</span> <span class="op">=</span> <span class="nam">np</span><span class="op">.</span><span class="nam">sqrt</span><span class="op">(</span><span class="op">(</span><span class="nam">diff_1</span> <span class="op">**</span> <span class="num">2</span><span class="op">)</span><span class="op">.</span><span class="nam">sum</span><span class="op">(</span><span class="op">)</span> <span class="op">*</span> <span class="op">(</span><span class="nam">diff_2</span> <span class="op">**</span> <span class="num">2</span><span class="op">)</span><span class="op">.</span><span class="nam">sum</span><span class="op">(</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t253" href="#t253">253</a></span><span class="t">        <span class="key">return</span> <span class="nam">num</span> <span class="op">/</span> <span class="nam">den</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t254" href="#t254">254</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t255" href="#t255">255</a></span><span class="t">    <span class="op">@</span><span class="nam">staticmethod</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t256" href="#t256">256</a></span><span class="t">    <span class="key">def</span> <span class="nam">circlineal</span><span class="op">(</span><span class="nam">x1</span><span class="op">,</span> <span class="nam">x2</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t257" href="#t257">257</a></span><span class="t">        <span class="nam">x2</span> <span class="op">=</span> <span class="nam">x2</span> <span class="op">*</span> <span class="nam">np</span><span class="op">.</span><span class="nam">pi</span> <span class="op">/</span> <span class="num">180</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t258" href="#t258">258</a></span><span class="t">        <span class="nam">rc</span> <span class="op">=</span> <span class="nam">np</span><span class="op">.</span><span class="nam">corrcoef</span><span class="op">(</span><span class="nam">x1</span><span class="op">,</span> <span class="nam">np</span><span class="op">.</span><span class="nam">cos</span><span class="op">(</span><span class="nam">x2</span><span class="op">)</span><span class="op">)</span><span class="op">[</span><span class="num">1</span><span class="op">,</span> <span class="num">0</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t259" href="#t259">259</a></span><span class="t">        <span class="nam">rs</span> <span class="op">=</span> <span class="nam">np</span><span class="op">.</span><span class="nam">corrcoef</span><span class="op">(</span><span class="nam">x1</span><span class="op">,</span> <span class="nam">np</span><span class="op">.</span><span class="nam">sin</span><span class="op">(</span><span class="nam">x2</span><span class="op">)</span><span class="op">)</span><span class="op">[</span><span class="num">1</span><span class="op">,</span> <span class="num">0</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t260" href="#t260">260</a></span><span class="t">        <span class="nam">rcs</span> <span class="op">=</span> <span class="nam">np</span><span class="op">.</span><span class="nam">corrcoef</span><span class="op">(</span><span class="nam">np</span><span class="op">.</span><span class="nam">sin</span><span class="op">(</span><span class="nam">x2</span><span class="op">)</span><span class="op">,</span> <span class="nam">np</span><span class="op">.</span><span class="nam">cos</span><span class="op">(</span><span class="nam">x2</span><span class="op">)</span><span class="op">)</span><span class="op">[</span><span class="num">1</span><span class="op">,</span> <span class="num">0</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t261" href="#t261">261</a></span><span class="t">        <span class="nam">num</span> <span class="op">=</span> <span class="op">(</span><span class="nam">rc</span> <span class="op">**</span> <span class="num">2</span><span class="op">)</span> <span class="op">+</span> <span class="op">(</span><span class="nam">rs</span> <span class="op">**</span> <span class="num">2</span><span class="op">)</span> <span class="op">-</span> <span class="num">2</span> <span class="op">*</span> <span class="nam">rc</span> <span class="op">*</span> <span class="nam">rs</span> <span class="op">*</span> <span class="nam">rcs</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t262" href="#t262">262</a></span><span class="t">        <span class="nam">den</span> <span class="op">=</span> <span class="num">1</span> <span class="op">-</span> <span class="op">(</span><span class="nam">rcs</span> <span class="op">**</span> <span class="num">2</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t263" href="#t263">263</a></span><span class="t">        <span class="nam">correlation</span> <span class="op">=</span> <span class="nam">np</span><span class="op">.</span><span class="nam">sqrt</span><span class="op">(</span><span class="nam">num</span> <span class="op">/</span> <span class="nam">den</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t264" href="#t264">264</a></span><span class="t">        <span class="key">if</span> <span class="nam">np</span><span class="op">.</span><span class="nam">corrcoef</span><span class="op">(</span><span class="nam">x1</span><span class="op">,</span> <span class="nam">x2</span><span class="op">)</span><span class="op">[</span><span class="num">1</span><span class="op">,</span> <span class="num">0</span><span class="op">]</span> <span class="op">&lt;</span> <span class="num">0</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t265" href="#t265">265</a></span><span class="t">            <span class="nam">correlation</span> <span class="op">*=</span> <span class="op">-</span><span class="num">1</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t266" href="#t266">266</a></span><span class="t">        <span class="key">return</span> <span class="nam">correlation</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t267" href="#t267">267</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t209" href="#t209">209</a></span><span class="t">            <span class="num">1</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t210" href="#t210">210</a></span><span class="t">            <span class="nam">dpi</span><span class="op">=</span><span class="num">300</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t211" href="#t211">211</a></span><span class="t">            <span class="nam">figsize</span><span class="op">=</span><span class="op">(</span><span class="num">7.5</span><span class="op">,</span> <span class="num">5</span><span class="op">)</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t212" href="#t212">212</a></span><span class="t">            <span class="nam">tight_layout</span><span class="op">=</span><span class="key">True</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t213" href="#t213">213</a></span><span class="t">        <span class="nam">im</span> <span class="op">=</span> <span class="nam">ax</span><span class="op">.</span><span class="nam">imshow</span><span class="op">(</span><span class="nam">result_df</span><span class="op">,</span> <span class="nam">cmap</span><span class="op">=</span><span class="nam">cmap</span><span class="op">,</span> <span class="nam">norm</span><span class="op">=</span><span class="nam">norm</span><span class="op">,</span> <span class="nam">aspect</span><span class="op">=</span><span class="str">'auto'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t214" href="#t214">214</a></span><span class="t">        <span class="nam">plt</span><span class="op">.</span><span class="nam">colorbar</span><span class="op">(</span><span class="nam">im</span><span class="op">,</span> <span class="nam">ticks</span><span class="op">=</span><span class="op">[</span><span class="op">-</span><span class="num">1</span><span class="op">,</span> <span class="op">-</span><span class="num">.8</span><span class="op">,</span> <span class="op">-</span><span class="num">.6</span><span class="op">,</span> <span class="op">-</span><span class="num">.4</span><span class="op">,</span> <span class="op">-</span><span class="num">.2</span><span class="op">,</span> <span class="num">.2</span><span class="op">,</span> <span class="num">.4</span><span class="op">,</span> <span class="num">.6</span><span class="op">,</span> <span class="num">.8</span><span class="op">,</span> <span class="num">1</span><span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t215" href="#t215">215</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t216" href="#t216">216</a></span><span class="t">        <span class="com"># axes</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t217" href="#t217">217</a></span><span class="t">        <span class="nam">xlocs</span> <span class="op">=</span> <span class="nam">np</span><span class="op">.</span><span class="nam">arange</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">result_df</span><span class="op">.</span><span class="nam">columns</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t218" href="#t218">218</a></span><span class="t">        <span class="nam">_</span> <span class="op">=</span> <span class="nam">ax</span><span class="op">.</span><span class="nam">set_xticks</span><span class="op">(</span><span class="nam">xlocs</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t219" href="#t219">219</a></span><span class="t">        <span class="nam">_</span> <span class="op">=</span> <span class="nam">ax</span><span class="op">.</span><span class="nam">set_xticklabels</span><span class="op">(</span><span class="nam">result_df</span><span class="op">.</span><span class="nam">columns</span><span class="op">.</span><span class="nam">to_list</span><span class="op">(</span><span class="op">)</span><span class="op">,</span> <span class="nam">rotation</span><span class="op">=</span><span class="num">90</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t220" href="#t220">220</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t221" href="#t221">221</a></span><span class="t">        <span class="nam">ylocs</span> <span class="op">=</span> <span class="nam">np</span><span class="op">.</span><span class="nam">arange</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">result_df</span><span class="op">.</span><span class="nam">index</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t222" href="#t222">222</a></span><span class="t">        <span class="nam">_</span> <span class="op">=</span> <span class="nam">ax</span><span class="op">.</span><span class="nam">set_yticks</span><span class="op">(</span><span class="nam">ylocs</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t223" href="#t223">223</a></span><span class="t">        <span class="nam">_</span> <span class="op">=</span> <span class="nam">ax</span><span class="op">.</span><span class="nam">set_yticklabels</span><span class="op">(</span><span class="nam">result_df</span><span class="op">.</span><span class="nam">index</span><span class="op">.</span><span class="nam">to_list</span><span class="op">(</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t224" href="#t224">224</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t225" href="#t225">225</a></span><span class="t">        <span class="nam">ax</span><span class="op">.</span><span class="nam">set_title</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t226" href="#t226">226</a></span><span class="t">            <span class="str">"Correlation for neighboring basepairs "</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t227" href="#t227">227</a></span><span class="t">            <span class="str">"and pairs of helical parameters"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t228" href="#t228">228</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t229" href="#t229">229</a></span><span class="t">        <span class="nam">fig</span><span class="op">.</span><span class="nam">tight_layout</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t230" href="#t230">230</a></span><span class="t">        <span class="nam">fig</span><span class="op">.</span><span class="nam">savefig</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t231" href="#t231">231</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'out'</span><span class="op">]</span><span class="op">[</span><span class="str">'output_jpg_path'</span><span class="op">]</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t232" href="#t232">232</a></span><span class="t">            <span class="nam">format</span><span class="op">=</span><span class="str">"jpg"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t233" href="#t233">233</a></span><span class="t">        <span class="nam">plt</span><span class="op">.</span><span class="nam">close</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t234" href="#t234">234</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t235" href="#t235">235</a></span><span class="t">        <span class="com"># Remove temporary file(s)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t236" href="#t236">236</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_files</span><span class="op">.</span><span class="nam">extend</span><span class="op">(</span><span class="op">[</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t237" href="#t237">237</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"unique_dir"</span><span class="op">)</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t238" href="#t238">238</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t239" href="#t239">239</a></span><span class="t">        <span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t240" href="#t240">240</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">remove_tmp_files</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t241" href="#t241">241</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t242" href="#t242">242</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_arguments</span><span class="op">(</span><span class="nam">output_files_created</span><span class="op">=</span><span class="key">True</span><span class="op">,</span> <span class="nam">raise_exception</span><span class="op">=</span><span class="key">False</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t243" href="#t243">243</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t244" href="#t244">244</a></span><span class="t">        <span class="key">return</span> <span class="num">0</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t245" href="#t245">245</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t246" href="#t246">246</a></span><span class="t">    <span class="op">@</span><span class="nam">staticmethod</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t247" href="#t247">247</a></span><span class="t">    <span class="key">def</span> <span class="nam">circular</span><span class="op">(</span><span class="nam">x1</span><span class="op">,</span> <span class="nam">x2</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t248" href="#t248">248</a></span><span class="t">        <span class="nam">x1</span> <span class="op">=</span> <span class="nam">x1</span> <span class="op">*</span> <span class="nam">np</span><span class="op">.</span><span class="nam">pi</span> <span class="op">/</span> <span class="num">180</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t249" href="#t249">249</a></span><span class="t">        <span class="nam">x2</span> <span class="op">=</span> <span class="nam">x2</span> <span class="op">*</span> <span class="nam">np</span><span class="op">.</span><span class="nam">pi</span> <span class="op">/</span> <span class="num">180</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t250" href="#t250">250</a></span><span class="t">        <span class="nam">diff_1</span> <span class="op">=</span> <span class="nam">np</span><span class="op">.</span><span class="nam">sin</span><span class="op">(</span><span class="nam">x1</span> <span class="op">-</span> <span class="nam">x1</span><span class="op">.</span><span class="nam">mean</span><span class="op">(</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t251" href="#t251">251</a></span><span class="t">        <span class="nam">diff_2</span> <span class="op">=</span> <span class="nam">np</span><span class="op">.</span><span class="nam">sin</span><span class="op">(</span><span class="nam">x2</span> <span class="op">-</span> <span class="nam">x2</span><span class="op">.</span><span class="nam">mean</span><span class="op">(</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t252" href="#t252">252</a></span><span class="t">        <span class="nam">num</span> <span class="op">=</span> <span class="op">(</span><span class="nam">diff_1</span> <span class="op">*</span> <span class="nam">diff_2</span><span class="op">)</span><span class="op">.</span><span class="nam">sum</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t253" href="#t253">253</a></span><span class="t">        <span class="nam">den</span> <span class="op">=</span> <span class="nam">np</span><span class="op">.</span><span class="nam">sqrt</span><span class="op">(</span><span class="op">(</span><span class="nam">diff_1</span> <span class="op">**</span> <span class="num">2</span><span class="op">)</span><span class="op">.</span><span class="nam">sum</span><span class="op">(</span><span class="op">)</span> <span class="op">*</span> <span class="op">(</span><span class="nam">diff_2</span> <span class="op">**</span> <span class="num">2</span><span class="op">)</span><span class="op">.</span><span class="nam">sum</span><span class="op">(</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t254" href="#t254">254</a></span><span class="t">        <span class="key">return</span> <span class="nam">num</span> <span class="op">/</span> <span class="nam">den</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t255" href="#t255">255</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t256" href="#t256">256</a></span><span class="t">    <span class="op">@</span><span class="nam">staticmethod</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t257" href="#t257">257</a></span><span class="t">    <span class="key">def</span> <span class="nam">circlineal</span><span class="op">(</span><span class="nam">x1</span><span class="op">,</span> <span class="nam">x2</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t258" href="#t258">258</a></span><span class="t">        <span class="nam">x2</span> <span class="op">=</span> <span class="nam">x2</span> <span class="op">*</span> <span class="nam">np</span><span class="op">.</span><span class="nam">pi</span> <span class="op">/</span> <span class="num">180</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t259" href="#t259">259</a></span><span class="t">        <span class="nam">rc</span> <span class="op">=</span> <span class="nam">np</span><span class="op">.</span><span class="nam">corrcoef</span><span class="op">(</span><span class="nam">x1</span><span class="op">,</span> <span class="nam">np</span><span class="op">.</span><span class="nam">cos</span><span class="op">(</span><span class="nam">x2</span><span class="op">)</span><span class="op">)</span><span class="op">[</span><span class="num">1</span><span class="op">,</span> <span class="num">0</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t260" href="#t260">260</a></span><span class="t">        <span class="nam">rs</span> <span class="op">=</span> <span class="nam">np</span><span class="op">.</span><span class="nam">corrcoef</span><span class="op">(</span><span class="nam">x1</span><span class="op">,</span> <span class="nam">np</span><span class="op">.</span><span class="nam">sin</span><span class="op">(</span><span class="nam">x2</span><span class="op">)</span><span class="op">)</span><span class="op">[</span><span class="num">1</span><span class="op">,</span> <span class="num">0</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t261" href="#t261">261</a></span><span class="t">        <span class="nam">rcs</span> <span class="op">=</span> <span class="nam">np</span><span class="op">.</span><span class="nam">corrcoef</span><span class="op">(</span><span class="nam">np</span><span class="op">.</span><span class="nam">sin</span><span class="op">(</span><span class="nam">x2</span><span class="op">)</span><span class="op">,</span> <span class="nam">np</span><span class="op">.</span><span class="nam">cos</span><span class="op">(</span><span class="nam">x2</span><span class="op">)</span><span class="op">)</span><span class="op">[</span><span class="num">1</span><span class="op">,</span> <span class="num">0</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t262" href="#t262">262</a></span><span class="t">        <span class="nam">num</span> <span class="op">=</span> <span class="op">(</span><span class="nam">rc</span> <span class="op">**</span> <span class="num">2</span><span class="op">)</span> <span class="op">+</span> <span class="op">(</span><span class="nam">rs</span> <span class="op">**</span> <span class="num">2</span><span class="op">)</span> <span class="op">-</span> <span class="num">2</span> <span class="op">*</span> <span class="nam">rc</span> <span class="op">*</span> <span class="nam">rs</span> <span class="op">*</span> <span class="nam">rcs</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t263" href="#t263">263</a></span><span class="t">        <span class="nam">den</span> <span class="op">=</span> <span class="num">1</span> <span class="op">-</span> <span class="op">(</span><span class="nam">rcs</span> <span class="op">**</span> <span class="num">2</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t264" href="#t264">264</a></span><span class="t">        <span class="nam">correlation</span> <span class="op">=</span> <span class="nam">np</span><span class="op">.</span><span class="nam">sqrt</span><span class="op">(</span><span class="nam">num</span> <span class="op">/</span> <span class="nam">den</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t265" href="#t265">265</a></span><span class="t">        <span class="key">if</span> <span class="nam">np</span><span class="op">.</span><span class="nam">corrcoef</span><span class="op">(</span><span class="nam">x1</span><span class="op">,</span> <span class="nam">x2</span><span class="op">)</span><span class="op">[</span><span class="num">1</span><span class="op">,</span> <span class="num">0</span><span class="op">]</span> <span class="op">&lt;</span> <span class="num">0</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t266" href="#t266">266</a></span><span class="t">            <span class="nam">correlation</span> <span class="op">*=</span> <span class="op">-</span><span class="num">1</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t267" href="#t267">267</a></span><span class="t">        <span class="key">return</span> <span class="nam">correlation</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t268" href="#t268">268</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t269" href="#t269">269</a></span><span class="t"><span class="key">def</span> <span class="nam">interbpcorr</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t270" href="#t270">270</a></span><span class="t">        <span class="nam">input_filename_shift</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span> <span class="nam">input_filename_slide</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t271" href="#t271">271</a></span><span class="t">        <span class="nam">input_filename_rise</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span> <span class="nam">input_filename_tilt</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t272" href="#t272">272</a></span><span class="t">        <span class="nam">input_filename_roll</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span> <span class="nam">input_filename_twist</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t273" href="#t273">273</a></span><span class="t">        <span class="nam">output_csv_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span> <span class="nam">output_jpg_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t274" href="#t274">274</a></span><span class="t">        <span class="nam">properties</span><span class="op">:</span> <span class="nam">dict</span> <span class="op">=</span> <span class="key">None</span><span class="op">,</span> <span class="op">**</span><span class="nam">kwargs</span><span class="op">)</span> <span class="op">-></span> <span class="nam">int</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t275" href="#t275">275</a></span><span class="t">    <span class="str">"""Create :class:`HelParCorrelation &lt;correlations.interbpcorr.InterBasePairCorrelation>` class and</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t276" href="#t276">276</a></span><span class="t"><span class="str">    execute the :meth:`launch() &lt;correlations.interbpcorr.InterBasePairCorrelation.launch>` method."""</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t277" href="#t277">277</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t278" href="#t278">278</a></span><span class="t">    <span class="key">return</span> <span class="nam">InterBasePairCorrelation</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t279" href="#t279">279</a></span><span class="t">        <span class="nam">input_filename_shift</span><span class="op">=</span><span class="nam">input_filename_shift</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t280" href="#t280">280</a></span><span class="t">        <span class="nam">input_filename_slide</span><span class="op">=</span><span class="nam">input_filename_slide</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t281" href="#t281">281</a></span><span class="t">        <span class="nam">input_filename_rise</span><span class="op">=</span><span class="nam">input_filename_rise</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t282" href="#t282">282</a></span><span class="t">        <span class="nam">input_filename_tilt</span><span class="op">=</span><span class="nam">input_filename_tilt</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t283" href="#t283">283</a></span><span class="t">        <span class="nam">input_filename_roll</span><span class="op">=</span><span class="nam">input_filename_roll</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t284" href="#t284">284</a></span><span class="t">        <span class="nam">input_filename_twist</span><span class="op">=</span><span class="nam">input_filename_twist</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t285" href="#t285">285</a></span><span class="t">        <span class="nam">output_csv_path</span><span class="op">=</span><span class="nam">output_csv_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t286" href="#t286">286</a></span><span class="t">        <span class="nam">output_jpg_path</span><span class="op">=</span><span class="nam">output_jpg_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t287" href="#t287">287</a></span><span class="t">        <span class="nam">properties</span><span class="op">=</span><span class="nam">properties</span><span class="op">,</span> <span class="op">**</span><span class="nam">kwargs</span><span class="op">)</span><span class="op">.</span><span class="nam">launch</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t288" href="#t288">288</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t269" href="#t269">269</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t270" href="#t270">270</a></span><span class="t"><span class="key">def</span> <span class="nam">interbpcorr</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t271" href="#t271">271</a></span><span class="t">        <span class="nam">input_filename_shift</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span> <span class="nam">input_filename_slide</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t272" href="#t272">272</a></span><span class="t">        <span class="nam">input_filename_rise</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span> <span class="nam">input_filename_tilt</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t273" href="#t273">273</a></span><span class="t">        <span class="nam">input_filename_roll</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span> <span class="nam">input_filename_twist</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t274" href="#t274">274</a></span><span class="t">        <span class="nam">output_csv_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span> <span class="nam">output_jpg_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t275" href="#t275">275</a></span><span class="t">        <span class="nam">properties</span><span class="op">:</span> <span class="nam">dict</span> <span class="op">=</span> <span class="key">None</span><span class="op">,</span> <span class="op">**</span><span class="nam">kwargs</span><span class="op">)</span> <span class="op">-></span> <span class="nam">int</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t276" href="#t276">276</a></span><span class="t">    <span class="str">"""Create :class:`HelParCorrelation &lt;correlations.interbpcorr.InterBasePairCorrelation>` class and</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t277" href="#t277">277</a></span><span class="t"><span class="str">    execute the :meth:`launch() &lt;correlations.interbpcorr.InterBasePairCorrelation.launch>` method."""</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t278" href="#t278">278</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t279" href="#t279">279</a></span><span class="t">    <span class="key">return</span> <span class="nam">InterBasePairCorrelation</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t280" href="#t280">280</a></span><span class="t">        <span class="nam">input_filename_shift</span><span class="op">=</span><span class="nam">input_filename_shift</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t281" href="#t281">281</a></span><span class="t">        <span class="nam">input_filename_slide</span><span class="op">=</span><span class="nam">input_filename_slide</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t282" href="#t282">282</a></span><span class="t">        <span class="nam">input_filename_rise</span><span class="op">=</span><span class="nam">input_filename_rise</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t283" href="#t283">283</a></span><span class="t">        <span class="nam">input_filename_tilt</span><span class="op">=</span><span class="nam">input_filename_tilt</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t284" href="#t284">284</a></span><span class="t">        <span class="nam">input_filename_roll</span><span class="op">=</span><span class="nam">input_filename_roll</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t285" href="#t285">285</a></span><span class="t">        <span class="nam">input_filename_twist</span><span class="op">=</span><span class="nam">input_filename_twist</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t286" href="#t286">286</a></span><span class="t">        <span class="nam">output_csv_path</span><span class="op">=</span><span class="nam">output_csv_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t287" href="#t287">287</a></span><span class="t">        <span class="nam">output_jpg_path</span><span class="op">=</span><span class="nam">output_jpg_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t288" href="#t288">288</a></span><span class="t">        <span class="nam">properties</span><span class="op">=</span><span class="nam">properties</span><span class="op">,</span> <span class="op">**</span><span class="nam">kwargs</span><span class="op">)</span><span class="op">.</span><span class="nam">launch</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t289" href="#t289">289</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t290" href="#t290">290</a></span><span class="t"><span class="key">def</span> <span class="nam">main</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t291" href="#t291">291</a></span><span class="t">    <span class="str">"""Command line execution of this building block. Please check the command line documentation."""</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t292" href="#t292">292</a></span><span class="t">    <span class="nam">parser</span> <span class="op">=</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">ArgumentParser</span><span class="op">(</span><span class="nam">description</span><span class="op">=</span><span class="str">'Load .ser file from Canal output and calculate correlation between base pairs of the corresponding sequence.'</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t293" href="#t293">293</a></span><span class="t">                                     <span class="nam">formatter_class</span><span class="op">=</span><span class="key">lambda</span> <span class="nam">prog</span><span class="op">:</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">RawTextHelpFormatter</span><span class="op">(</span><span class="nam">prog</span><span class="op">,</span> <span class="nam">width</span><span class="op">=</span><span class="num">99999</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t294" href="#t294">294</a></span><span class="t">    <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--config'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">False</span><span class="op">,</span> <span class="nam">help</span><span class="op">=</span><span class="str">'Configuration file'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t295" href="#t295">295</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t296" href="#t296">296</a></span><span class="t">    <span class="nam">required_args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument_group</span><span class="op">(</span><span class="str">'required arguments'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t297" href="#t297">297</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--input_filename_shift'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t298" href="#t298">298</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Path to ser file for helical parameter shift. Accepted formats: ser.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t299" href="#t299">299</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--input_filename_slide'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t300" href="#t300">300</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Path to ser file for helical parameter slide. Accepted formats: ser.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t301" href="#t301">301</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--input_filename_rise'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t302" href="#t302">302</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Path to ser file for helical parameter rise. Accepted formats: ser.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t303" href="#t303">303</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--input_filename_tilt'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t304" href="#t304">304</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Path to ser file for helical parameter tilt. Accepted formats: ser.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t305" href="#t305">305</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--input_filename_roll'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t306" href="#t306">306</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Path to ser file for helical parameter roll. Accepted formats: ser.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t307" href="#t307">307</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--input_filename_twist'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t308" href="#t308">308</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Path to ser file for helical parameter twist. Accepted formats: ser.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t309" href="#t309">309</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--output_csv_path'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t310" href="#t310">310</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Path to output file. Accepted formats: csv.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t311" href="#t311">311</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--output_jpg_path'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t312" href="#t312">312</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Path to output plot. Accepted formats: jpg.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t313" href="#t313">313</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t314" href="#t314">314</a></span><span class="t">    <span class="nam">args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">parse_args</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t315" href="#t315">315</a></span><span class="t">    <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="op">=</span> <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="key">or</span> <span class="str">"{}"</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t316" href="#t316">316</a></span><span class="t">    <span class="nam">properties</span> <span class="op">=</span> <span class="nam">settings</span><span class="op">.</span><span class="nam">ConfReader</span><span class="op">(</span><span class="nam">config</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">config</span><span class="op">)</span><span class="op">.</span><span class="nam">get_prop_dic</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t317" href="#t317">317</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t318" href="#t318">318</a></span><span class="t">    <span class="nam">interbpcorr</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t319" href="#t319">319</a></span><span class="t">        <span class="nam">input_filename_shift</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_filename_shift</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t320" href="#t320">320</a></span><span class="t">        <span class="nam">input_filename_slide</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_filename_slide</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t321" href="#t321">321</a></span><span class="t">        <span class="nam">input_filename_rise</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_filename_rise</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t322" href="#t322">322</a></span><span class="t">        <span class="nam">input_filename_tilt</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_filename_tilt</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t323" href="#t323">323</a></span><span class="t">        <span class="nam">input_filename_roll</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_filename_roll</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t324" href="#t324">324</a></span><span class="t">        <span class="nam">input_filename_twist</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_filename_twist</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t325" href="#t325">325</a></span><span class="t">        <span class="nam">output_csv_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">output_csv_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t326" href="#t326">326</a></span><span class="t">        <span class="nam">output_jpg_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">output_jpg_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t327" href="#t327">327</a></span><span class="t">        <span class="nam">properties</span><span class="op">=</span><span class="nam">properties</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t328" href="#t328">328</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t290" href="#t290">290</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t291" href="#t291">291</a></span><span class="t"><span class="key">def</span> <span class="nam">main</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t292" href="#t292">292</a></span><span class="t">    <span class="str">"""Command line execution of this building block. Please check the command line documentation."""</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t293" href="#t293">293</a></span><span class="t">    <span class="nam">parser</span> <span class="op">=</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">ArgumentParser</span><span class="op">(</span><span class="nam">description</span><span class="op">=</span><span class="str">'Load .ser file from Canal output and calculate correlation between base pairs of the corresponding sequence.'</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t294" href="#t294">294</a></span><span class="t">                                     <span class="nam">formatter_class</span><span class="op">=</span><span class="key">lambda</span> <span class="nam">prog</span><span class="op">:</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">RawTextHelpFormatter</span><span class="op">(</span><span class="nam">prog</span><span class="op">,</span> <span class="nam">width</span><span class="op">=</span><span class="num">99999</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t295" href="#t295">295</a></span><span class="t">    <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--config'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">False</span><span class="op">,</span> <span class="nam">help</span><span class="op">=</span><span class="str">'Configuration file'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t296" href="#t296">296</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t297" href="#t297">297</a></span><span class="t">    <span class="nam">required_args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument_group</span><span class="op">(</span><span class="str">'required arguments'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t298" href="#t298">298</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--input_filename_shift'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t299" href="#t299">299</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Path to ser file for helical parameter shift. Accepted formats: ser.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t300" href="#t300">300</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--input_filename_slide'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t301" href="#t301">301</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Path to ser file for helical parameter slide. Accepted formats: ser.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t302" href="#t302">302</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--input_filename_rise'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t303" href="#t303">303</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Path to ser file for helical parameter rise. Accepted formats: ser.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t304" href="#t304">304</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--input_filename_tilt'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t305" href="#t305">305</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Path to ser file for helical parameter tilt. Accepted formats: ser.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t306" href="#t306">306</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--input_filename_roll'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t307" href="#t307">307</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Path to ser file for helical parameter roll. Accepted formats: ser.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t308" href="#t308">308</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--input_filename_twist'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t309" href="#t309">309</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Path to ser file for helical parameter twist. Accepted formats: ser.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t310" href="#t310">310</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--output_csv_path'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t311" href="#t311">311</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Path to output file. Accepted formats: csv.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t312" href="#t312">312</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--output_jpg_path'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t313" href="#t313">313</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Path to output plot. Accepted formats: jpg.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t314" href="#t314">314</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t315" href="#t315">315</a></span><span class="t">    <span class="nam">args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">parse_args</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t316" href="#t316">316</a></span><span class="t">    <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="op">=</span> <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="key">or</span> <span class="str">"{}"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t317" href="#t317">317</a></span><span class="t">    <span class="nam">properties</span> <span class="op">=</span> <span class="nam">settings</span><span class="op">.</span><span class="nam">ConfReader</span><span class="op">(</span><span class="nam">config</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">config</span><span class="op">)</span><span class="op">.</span><span class="nam">get_prop_dic</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t318" href="#t318">318</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t319" href="#t319">319</a></span><span class="t">    <span class="nam">interbpcorr</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t320" href="#t320">320</a></span><span class="t">        <span class="nam">input_filename_shift</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_filename_shift</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t321" href="#t321">321</a></span><span class="t">        <span class="nam">input_filename_slide</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_filename_slide</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t322" href="#t322">322</a></span><span class="t">        <span class="nam">input_filename_rise</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_filename_rise</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t323" href="#t323">323</a></span><span class="t">        <span class="nam">input_filename_tilt</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_filename_tilt</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t324" href="#t324">324</a></span><span class="t">        <span class="nam">input_filename_roll</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_filename_roll</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t325" href="#t325">325</a></span><span class="t">        <span class="nam">input_filename_twist</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_filename_twist</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t326" href="#t326">326</a></span><span class="t">        <span class="nam">output_csv_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">output_csv_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t327" href="#t327">327</a></span><span class="t">        <span class="nam">output_jpg_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">output_jpg_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t328" href="#t328">328</a></span><span class="t">        <span class="nam">properties</span><span class="op">=</span><span class="nam">properties</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t329" href="#t329">329</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t330" href="#t330">330</a></span><span class="t"><span class="key">if</span> <span class="nam">__name__</span> <span class="op">==</span> <span class="str">'__main__'</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t331" href="#t331">331</a></span><span class="t">    <span class="nam">main</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t330" href="#t330">330</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t331" href="#t331">331</a></span><span class="t"><span class="key">if</span> <span class="nam">__name__</span> <span class="op">==</span> <span class="str">'__main__'</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t332" href="#t332">332</a></span><span class="t">    <span class="nam">main</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
 </main>
 <footer>
     <div class="content">
@@ -420,7 +421,7 @@ <h2>
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+            created at 2024-05-24 09:29 +0000
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+            created at 2024-05-24 09:29 +0000
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@@ -100,308 +100,309 @@ <h2>
     <p class="pln"><span class="n"><a id="t18" href="#t18">18</a></span><span class="t">    <span class="str">"""</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t19" href="#t19">19</a></span><span class="t"><span class="str">    | biobb_dna InterHelParCorrelation</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t20" href="#t20">20</a></span><span class="t"><span class="str">    | Calculate correlation between helical parameters for a single inter-base pair.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t21" href="#t21">21</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t22" href="#t22">22</a></span><span class="t"><span class="str">    Args:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t23" href="#t23">23</a></span><span class="t"><span class="str">        input_filename_shift (str): Path to .csv file with data for helical parameter 'shift'. File type: input. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/stiffness/series_shift_AA.csv>`_. Accepted formats: csv (edam:format_3752).</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t24" href="#t24">24</a></span><span class="t"><span class="str">        input_filename_slide (str): Path to .csv file with data for helical parameter 'slide'. File type: input. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/stiffness/series_slide_AA.csv>`_. Accepted formats: csv (edam:format_3752).</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t25" href="#t25">25</a></span><span class="t"><span class="str">        input_filename_rise (str): Path to .csv file with data for helical parameter 'rise'. File type: input. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/stiffness/series_rise_AA.csv>`_. Accepted formats: csv (edam:format_3752).</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t26" href="#t26">26</a></span><span class="t"><span class="str">        input_filename_tilt (str): Path to .csv file with data for helical parameter 'tilt'. File type: input. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/stiffness/series_tilt_AA.csv>`_. Accepted formats: csv (edam:format_3752).</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t27" href="#t27">27</a></span><span class="t"><span class="str">        input_filename_roll (str): Path to .csv file with data for helical parameter 'roll'. File type: input. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/stiffness/series_roll_AA.csv>`_. Accepted formats: csv (edam:format_3752).</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t28" href="#t28">28</a></span><span class="t"><span class="str">        input_filename_twist (str): Path to .csv file with data for helical parameter 'twist'. File type: input. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/stiffness/series_twist_AA.csv>`_. Accepted formats: csv (edam:format_3752).</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t29" href="#t29">29</a></span><span class="t"><span class="str">        output_csv_path (str): Path to directory where output is saved. File type: output. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/reference/correlation/inter_hpcorr_ref.csv>`_. Accepted formats: csv (edam:format_3752).</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t30" href="#t30">30</a></span><span class="t"><span class="str">        output_jpg_path (str): Path to .jpg file where output is saved. File type: output. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/reference/correlation/inter_hpcorr_ref.jpg>`_. Accepted formats: jpg (edam:format_3579).</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t31" href="#t31">31</a></span><span class="t"><span class="str">        properties (dict):</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t32" href="#t32">32</a></span><span class="t"><span class="str">            * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t33" href="#t33">33</a></span><span class="t"><span class="str">            * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t34" href="#t34">34</a></span><span class="t"><span class="str">            * **basepair** (*str*) - (None) Name of basepair analyzed.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t35" href="#t35">35</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t36" href="#t36">36</a></span><span class="t"><span class="str">    Examples:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t37" href="#t37">37</a></span><span class="t"><span class="str">        This is a use example of how to use the building block from Python::</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t38" href="#t38">38</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t39" href="#t39">39</a></span><span class="t"><span class="str">            from biobb_dna.interbp_correlations.interhpcorr import interhpcorr</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t40" href="#t40">40</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t41" href="#t41">41</a></span><span class="t"><span class="str">            prop = {</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t42" href="#t42">42</a></span><span class="t"><span class="str">                'basepair': 'AA',</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t43" href="#t43">43</a></span><span class="t"><span class="str">            }</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t44" href="#t44">44</a></span><span class="t"><span class="str">            interhpcorr(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t45" href="#t45">45</a></span><span class="t"><span class="str">                input_filename_shift='path/to/shift.csv',</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t46" href="#t46">46</a></span><span class="t"><span class="str">                input_filename_slide='path/to/slide.csv',</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t47" href="#t47">47</a></span><span class="t"><span class="str">                input_filename_rise='path/to/rise.csv',</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t48" href="#t48">48</a></span><span class="t"><span class="str">                input_filename_tilt='path/to/tilt.csv',</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t49" href="#t49">49</a></span><span class="t"><span class="str">                input_filename_roll='path/to/roll.csv',</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t50" href="#t50">50</a></span><span class="t"><span class="str">                input_filename_twist='path/to/twist.csv',</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t51" href="#t51">51</a></span><span class="t"><span class="str">                output_csv_path='path/to/output/file.csv',</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t52" href="#t52">52</a></span><span class="t"><span class="str">                output_jpg_path='path/to/output/file.jpg',</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t53" href="#t53">53</a></span><span class="t"><span class="str">                properties=prop)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t54" href="#t54">54</a></span><span class="t"><span class="str">    Info:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t55" href="#t55">55</a></span><span class="t"><span class="str">        * wrapped_software:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t56" href="#t56">56</a></span><span class="t"><span class="str">            * name: In house</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t57" href="#t57">57</a></span><span class="t"><span class="str">            * license: Apache-2.0</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t58" href="#t58">58</a></span><span class="t"><span class="str">        * ontology:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t59" href="#t59">59</a></span><span class="t"><span class="str">            * name: EDAM</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t60" href="#t60">60</a></span><span class="t"><span class="str">            * schema: http://edamontology.org/EDAM.owl</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t61" href="#t61">61</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t62" href="#t62">62</a></span><span class="t"><span class="str">    """</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t63" href="#t63">63</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t64" href="#t64">64</a></span><span class="t">    <span class="key">def</span> <span class="nam">__init__</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t65" href="#t65">65</a></span><span class="t">            <span class="nam">self</span><span class="op">,</span> <span class="nam">input_filename_shift</span><span class="op">,</span> <span class="nam">input_filename_slide</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t66" href="#t66">66</a></span><span class="t">            <span class="nam">input_filename_rise</span><span class="op">,</span> <span class="nam">input_filename_tilt</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t67" href="#t67">67</a></span><span class="t">            <span class="nam">input_filename_roll</span><span class="op">,</span> <span class="nam">input_filename_twist</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t68" href="#t68">68</a></span><span class="t">            <span class="nam">output_csv_path</span><span class="op">,</span> <span class="nam">output_jpg_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t69" href="#t69">69</a></span><span class="t">            <span class="nam">properties</span><span class="op">=</span><span class="key">None</span><span class="op">,</span> <span class="op">**</span><span class="nam">kwargs</span><span class="op">)</span> <span class="op">-></span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t70" href="#t70">70</a></span><span class="t">        <span class="nam">properties</span> <span class="op">=</span> <span class="nam">properties</span> <span class="key">or</span> <span class="op">{</span><span class="op">}</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t71" href="#t71">71</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t72" href="#t72">72</a></span><span class="t">        <span class="com"># Call parent class constructor</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t73" href="#t73">73</a></span><span class="t">        <span class="nam">super</span><span class="op">(</span><span class="op">)</span><span class="op">.</span><span class="nam">__init__</span><span class="op">(</span><span class="nam">properties</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t74" href="#t74">74</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">locals_var_dict</span> <span class="op">=</span> <span class="nam">locals</span><span class="op">(</span><span class="op">)</span><span class="op">.</span><span class="nam">copy</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t75" href="#t75">75</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t76" href="#t76">76</a></span><span class="t">        <span class="com"># Input/Output files</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t77" href="#t77">77</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span> <span class="op">=</span> <span class="op">{</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t78" href="#t78">78</a></span><span class="t">            <span class="str">'in'</span><span class="op">:</span> <span class="op">{</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t79" href="#t79">79</a></span><span class="t">                <span class="str">'input_filename_shift'</span><span class="op">:</span> <span class="nam">input_filename_shift</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t80" href="#t80">80</a></span><span class="t">                <span class="str">'input_filename_slide'</span><span class="op">:</span> <span class="nam">input_filename_slide</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t81" href="#t81">81</a></span><span class="t">                <span class="str">'input_filename_rise'</span><span class="op">:</span> <span class="nam">input_filename_rise</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t82" href="#t82">82</a></span><span class="t">                <span class="str">'input_filename_tilt'</span><span class="op">:</span> <span class="nam">input_filename_tilt</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t83" href="#t83">83</a></span><span class="t">                <span class="str">'input_filename_roll'</span><span class="op">:</span> <span class="nam">input_filename_roll</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t84" href="#t84">84</a></span><span class="t">                <span class="str">'input_filename_twist'</span><span class="op">:</span> <span class="nam">input_filename_twist</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t85" href="#t85">85</a></span><span class="t">            <span class="op">}</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t86" href="#t86">86</a></span><span class="t">            <span class="str">'out'</span><span class="op">:</span> <span class="op">{</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t87" href="#t87">87</a></span><span class="t">                <span class="str">'output_csv_path'</span><span class="op">:</span> <span class="nam">output_csv_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t88" href="#t88">88</a></span><span class="t">                <span class="str">'output_jpg_path'</span><span class="op">:</span> <span class="nam">output_jpg_path</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t89" href="#t89">89</a></span><span class="t">            <span class="op">}</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t90" href="#t90">90</a></span><span class="t">        <span class="op">}</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t91" href="#t91">91</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t92" href="#t92">92</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">properties</span> <span class="op">=</span> <span class="nam">properties</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t93" href="#t93">93</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">basepair</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"basepair"</span><span class="op">,</span> <span class="key">None</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t94" href="#t94">94</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t95" href="#t95">95</a></span><span class="t">        <span class="com"># Check the properties</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t96" href="#t96">96</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_properties</span><span class="op">(</span><span class="nam">properties</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t97" href="#t97">97</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_arguments</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t98" href="#t98">98</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t99" href="#t99">99</a></span><span class="t">    <span class="op">@</span><span class="nam">launchlogger</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t100" href="#t100">100</a></span><span class="t">    <span class="key">def</span> <span class="nam">launch</span><span class="op">(</span><span class="nam">self</span><span class="op">)</span> <span class="op">-></span> <span class="nam">int</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t101" href="#t101">101</a></span><span class="t">        <span class="str">"""Execute the :class:`InterHelParCorrelation &lt;interbp_correlations.interhpcorr.InterHelParCorrelation>` object."""</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t102" href="#t102">102</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t103" href="#t103">103</a></span><span class="t">        <span class="com"># Setup Biobb</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t104" href="#t104">104</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">check_restart</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t105" href="#t105">105</a></span><span class="t">            <span class="key">return</span> <span class="num">0</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t106" href="#t106">106</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">stage_files</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t107" href="#t107">107</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t108" href="#t108">108</a></span><span class="t">        <span class="com"># Creating temporary folder</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t109" href="#t109">109</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span> <span class="op">=</span> <span class="nam">fu</span><span class="op">.</span><span class="nam">create_unique_dir</span><span class="op">(</span><span class="nam">prefix</span><span class="op">=</span><span class="str">"hpcorrelation_"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t110" href="#t110">110</a></span><span class="t">        <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="str">'Creating %s temporary folder'</span> <span class="op">%</span> <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t111" href="#t111">111</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t112" href="#t112">112</a></span><span class="t">        <span class="com"># read input</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t113" href="#t113">113</a></span><span class="t">        <span class="nam">shift</span> <span class="op">=</span> <span class="nam">load_data</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">"in"</span><span class="op">]</span><span class="op">[</span><span class="str">"input_filename_shift"</span><span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t114" href="#t114">114</a></span><span class="t">        <span class="nam">slide</span> <span class="op">=</span> <span class="nam">load_data</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">"in"</span><span class="op">]</span><span class="op">[</span><span class="str">"input_filename_slide"</span><span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t115" href="#t115">115</a></span><span class="t">        <span class="nam">rise</span> <span class="op">=</span> <span class="nam">load_data</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">"in"</span><span class="op">]</span><span class="op">[</span><span class="str">"input_filename_rise"</span><span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t116" href="#t116">116</a></span><span class="t">        <span class="nam">tilt</span> <span class="op">=</span> <span class="nam">load_data</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">"in"</span><span class="op">]</span><span class="op">[</span><span class="str">"input_filename_tilt"</span><span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t117" href="#t117">117</a></span><span class="t">        <span class="nam">roll</span> <span class="op">=</span> <span class="nam">load_data</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">"in"</span><span class="op">]</span><span class="op">[</span><span class="str">"input_filename_roll"</span><span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t118" href="#t118">118</a></span><span class="t">        <span class="nam">twist</span> <span class="op">=</span> <span class="nam">load_data</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">"in"</span><span class="op">]</span><span class="op">[</span><span class="str">"input_filename_twist"</span><span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t119" href="#t119">119</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t120" href="#t120">120</a></span><span class="t">        <span class="com"># get basepair</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t121" href="#t121">121</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">basepair</span> <span class="key">is</span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t122" href="#t122">122</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">basepair</span> <span class="op">=</span> <span class="nam">shift</span><span class="op">.</span><span class="nam">columns</span><span class="op">[</span><span class="num">0</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t123" href="#t123">123</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t124" href="#t124">124</a></span><span class="t">        <span class="com"># make matrix</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t125" href="#t125">125</a></span><span class="t">        <span class="nam">coordinates</span> <span class="op">=</span> <span class="op">[</span><span class="str">"shift"</span><span class="op">,</span> <span class="str">"slide"</span><span class="op">,</span> <span class="str">"rise"</span><span class="op">,</span> <span class="str">"tilt"</span><span class="op">,</span> <span class="str">"roll"</span><span class="op">,</span> <span class="str">"twist"</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t126" href="#t126">126</a></span><span class="t">        <span class="nam">corr_matrix</span> <span class="op">=</span> <span class="nam">pd</span><span class="op">.</span><span class="nam">DataFrame</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t127" href="#t127">127</a></span><span class="t">            <span class="nam">np</span><span class="op">.</span><span class="nam">eye</span><span class="op">(</span><span class="num">6</span><span class="op">,</span> <span class="num">6</span><span class="op">)</span><span class="op">,</span> <span class="nam">index</span><span class="op">=</span><span class="nam">coordinates</span><span class="op">,</span> <span class="nam">columns</span><span class="op">=</span><span class="nam">coordinates</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t128" href="#t128">128</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t129" href="#t129">129</a></span><span class="t">        <span class="com"># shift</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t130" href="#t130">130</a></span><span class="t">        <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"shift"</span><span class="op">]</span><span class="op">[</span><span class="str">"slide"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">shift</span><span class="op">.</span><span class="nam">corrwith</span><span class="op">(</span><span class="nam">slide</span><span class="op">,</span> <span class="nam">method</span><span class="op">=</span><span class="str">"pearson"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t131" href="#t131">131</a></span><span class="t">        <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"shift"</span><span class="op">]</span><span class="op">[</span><span class="str">"rise"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">shift</span><span class="op">.</span><span class="nam">corrwith</span><span class="op">(</span><span class="nam">rise</span><span class="op">,</span> <span class="nam">method</span><span class="op">=</span><span class="str">"pearson"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t132" href="#t132">132</a></span><span class="t">        <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"shift"</span><span class="op">]</span><span class="op">[</span><span class="str">"tilt"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">shift</span><span class="op">.</span><span class="nam">corrwith</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t133" href="#t133">133</a></span><span class="t">            <span class="nam">tilt</span><span class="op">,</span> <span class="nam">method</span><span class="op">=</span><span class="nam">self</span><span class="op">.</span><span class="nam">circlineal</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t134" href="#t134">134</a></span><span class="t">        <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"shift"</span><span class="op">]</span><span class="op">[</span><span class="str">"roll"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">shift</span><span class="op">.</span><span class="nam">corrwith</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t135" href="#t135">135</a></span><span class="t">            <span class="nam">roll</span><span class="op">,</span> <span class="nam">method</span><span class="op">=</span><span class="nam">self</span><span class="op">.</span><span class="nam">circlineal</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t136" href="#t136">136</a></span><span class="t">        <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"shift"</span><span class="op">]</span><span class="op">[</span><span class="str">"twist"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">shift</span><span class="op">.</span><span class="nam">corrwith</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t137" href="#t137">137</a></span><span class="t">            <span class="nam">twist</span><span class="op">,</span> <span class="nam">method</span><span class="op">=</span><span class="nam">self</span><span class="op">.</span><span class="nam">circlineal</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t138" href="#t138">138</a></span><span class="t">        <span class="com"># symmetric values</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t139" href="#t139">139</a></span><span class="t">        <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"slide"</span><span class="op">]</span><span class="op">[</span><span class="str">"shift"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"shift"</span><span class="op">]</span><span class="op">[</span><span class="str">"slide"</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t140" href="#t140">140</a></span><span class="t">        <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"rise"</span><span class="op">]</span><span class="op">[</span><span class="str">"shift"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"shift"</span><span class="op">]</span><span class="op">[</span><span class="str">"rise"</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t141" href="#t141">141</a></span><span class="t">        <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"tilt"</span><span class="op">]</span><span class="op">[</span><span class="str">"shift"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"shift"</span><span class="op">]</span><span class="op">[</span><span class="str">"tilt"</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t142" href="#t142">142</a></span><span class="t">        <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"roll"</span><span class="op">]</span><span class="op">[</span><span class="str">"shift"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"shift"</span><span class="op">]</span><span class="op">[</span><span class="str">"roll"</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t143" href="#t143">143</a></span><span class="t">        <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"twist"</span><span class="op">]</span><span class="op">[</span><span class="str">"shift"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"shift"</span><span class="op">]</span><span class="op">[</span><span class="str">"twist"</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t144" href="#t144">144</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t145" href="#t145">145</a></span><span class="t">        <span class="com"># slide</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t146" href="#t146">146</a></span><span class="t">        <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"slide"</span><span class="op">]</span><span class="op">[</span><span class="str">"rise"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">slide</span><span class="op">.</span><span class="nam">corrwith</span><span class="op">(</span><span class="nam">rise</span><span class="op">,</span> <span class="nam">method</span><span class="op">=</span><span class="str">"pearson"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t147" href="#t147">147</a></span><span class="t">        <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"slide"</span><span class="op">]</span><span class="op">[</span><span class="str">"tilt"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">slide</span><span class="op">.</span><span class="nam">corrwith</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t148" href="#t148">148</a></span><span class="t">            <span class="nam">tilt</span><span class="op">,</span> <span class="nam">method</span><span class="op">=</span><span class="nam">self</span><span class="op">.</span><span class="nam">circlineal</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t149" href="#t149">149</a></span><span class="t">        <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"slide"</span><span class="op">]</span><span class="op">[</span><span class="str">"roll"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">slide</span><span class="op">.</span><span class="nam">corrwith</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t150" href="#t150">150</a></span><span class="t">            <span class="nam">roll</span><span class="op">,</span> <span class="nam">method</span><span class="op">=</span><span class="nam">self</span><span class="op">.</span><span class="nam">circlineal</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t151" href="#t151">151</a></span><span class="t">        <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"slide"</span><span class="op">]</span><span class="op">[</span><span class="str">"twist"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">slide</span><span class="op">.</span><span class="nam">corrwith</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t152" href="#t152">152</a></span><span class="t">            <span class="nam">twist</span><span class="op">,</span> <span class="nam">method</span><span class="op">=</span><span class="nam">self</span><span class="op">.</span><span class="nam">circlineal</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t153" href="#t153">153</a></span><span class="t">        <span class="com"># symmetric values</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t154" href="#t154">154</a></span><span class="t">        <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"rise"</span><span class="op">]</span><span class="op">[</span><span class="str">"slide"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"slide"</span><span class="op">]</span><span class="op">[</span><span class="str">"rise"</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t155" href="#t155">155</a></span><span class="t">        <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"tilt"</span><span class="op">]</span><span class="op">[</span><span class="str">"slide"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"slide"</span><span class="op">]</span><span class="op">[</span><span class="str">"tilt"</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t156" href="#t156">156</a></span><span class="t">        <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"roll"</span><span class="op">]</span><span class="op">[</span><span class="str">"slide"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"slide"</span><span class="op">]</span><span class="op">[</span><span class="str">"roll"</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t157" href="#t157">157</a></span><span class="t">        <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"twist"</span><span class="op">]</span><span class="op">[</span><span class="str">"slide"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"slide"</span><span class="op">]</span><span class="op">[</span><span class="str">"twist"</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t158" href="#t158">158</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t159" href="#t159">159</a></span><span class="t">        <span class="com"># rise</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t160" href="#t160">160</a></span><span class="t">        <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"rise"</span><span class="op">]</span><span class="op">[</span><span class="str">"tilt"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">rise</span><span class="op">.</span><span class="nam">corrwith</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t161" href="#t161">161</a></span><span class="t">            <span class="nam">tilt</span><span class="op">,</span> <span class="nam">method</span><span class="op">=</span><span class="nam">self</span><span class="op">.</span><span class="nam">circlineal</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t162" href="#t162">162</a></span><span class="t">        <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"rise"</span><span class="op">]</span><span class="op">[</span><span class="str">"roll"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">rise</span><span class="op">.</span><span class="nam">corrwith</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t163" href="#t163">163</a></span><span class="t">            <span class="nam">roll</span><span class="op">,</span> <span class="nam">method</span><span class="op">=</span><span class="nam">self</span><span class="op">.</span><span class="nam">circlineal</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t164" href="#t164">164</a></span><span class="t">        <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"rise"</span><span class="op">]</span><span class="op">[</span><span class="str">"twist"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">rise</span><span class="op">.</span><span class="nam">corrwith</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t165" href="#t165">165</a></span><span class="t">            <span class="nam">twist</span><span class="op">,</span> <span class="nam">method</span><span class="op">=</span><span class="nam">self</span><span class="op">.</span><span class="nam">circlineal</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t166" href="#t166">166</a></span><span class="t">        <span class="com"># symmetric values</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t167" href="#t167">167</a></span><span class="t">        <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"tilt"</span><span class="op">]</span><span class="op">[</span><span class="str">"rise"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"rise"</span><span class="op">]</span><span class="op">[</span><span class="str">"tilt"</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t168" href="#t168">168</a></span><span class="t">        <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"roll"</span><span class="op">]</span><span class="op">[</span><span class="str">"rise"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"rise"</span><span class="op">]</span><span class="op">[</span><span class="str">"roll"</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t169" href="#t169">169</a></span><span class="t">        <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"twist"</span><span class="op">]</span><span class="op">[</span><span class="str">"rise"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"rise"</span><span class="op">]</span><span class="op">[</span><span class="str">"twist"</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t170" href="#t170">170</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t171" href="#t171">171</a></span><span class="t">        <span class="com"># tilt</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t172" href="#t172">172</a></span><span class="t">        <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"tilt"</span><span class="op">]</span><span class="op">[</span><span class="str">"roll"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">tilt</span><span class="op">.</span><span class="nam">corrwith</span><span class="op">(</span><span class="nam">roll</span><span class="op">,</span> <span class="nam">method</span><span class="op">=</span><span class="nam">self</span><span class="op">.</span><span class="nam">circular</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t173" href="#t173">173</a></span><span class="t">        <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"tilt"</span><span class="op">]</span><span class="op">[</span><span class="str">"twist"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">tilt</span><span class="op">.</span><span class="nam">corrwith</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t174" href="#t174">174</a></span><span class="t">            <span class="nam">twist</span><span class="op">,</span> <span class="nam">method</span><span class="op">=</span><span class="nam">self</span><span class="op">.</span><span class="nam">circular</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t175" href="#t175">175</a></span><span class="t">        <span class="com"># symmetric values</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t176" href="#t176">176</a></span><span class="t">        <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"roll"</span><span class="op">]</span><span class="op">[</span><span class="str">"tilt"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"tilt"</span><span class="op">]</span><span class="op">[</span><span class="str">"roll"</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t177" href="#t177">177</a></span><span class="t">        <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"twist"</span><span class="op">]</span><span class="op">[</span><span class="str">"tilt"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"tilt"</span><span class="op">]</span><span class="op">[</span><span class="str">"twist"</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t178" href="#t178">178</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t179" href="#t179">179</a></span><span class="t">        <span class="com"># roll</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t180" href="#t180">180</a></span><span class="t">        <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"roll"</span><span class="op">]</span><span class="op">[</span><span class="str">"twist"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">roll</span><span class="op">.</span><span class="nam">corrwith</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t181" href="#t181">181</a></span><span class="t">            <span class="nam">twist</span><span class="op">,</span> <span class="nam">method</span><span class="op">=</span><span class="nam">self</span><span class="op">.</span><span class="nam">circular</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t182" href="#t182">182</a></span><span class="t">        <span class="com"># symmetric values</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t183" href="#t183">183</a></span><span class="t">        <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"twist"</span><span class="op">]</span><span class="op">[</span><span class="str">"roll"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"roll"</span><span class="op">]</span><span class="op">[</span><span class="str">"twist"</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t184" href="#t184">184</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t185" href="#t185">185</a></span><span class="t">        <span class="com"># save csv data</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t186" href="#t186">186</a></span><span class="t">        <span class="nam">corr_matrix</span><span class="op">.</span><span class="nam">to_csv</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">"out"</span><span class="op">]</span><span class="op">[</span><span class="str">"output_csv_path"</span><span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t187" href="#t187">187</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t188" href="#t188">188</a></span><span class="t">        <span class="com"># create heatmap</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t189" href="#t189">189</a></span><span class="t">        <span class="nam">fig</span><span class="op">,</span> <span class="nam">axs</span> <span class="op">=</span> <span class="nam">plt</span><span class="op">.</span><span class="nam">subplots</span><span class="op">(</span><span class="num">1</span><span class="op">,</span> <span class="num">1</span><span class="op">,</span> <span class="nam">dpi</span><span class="op">=</span><span class="num">300</span><span class="op">,</span> <span class="nam">tight_layout</span><span class="op">=</span><span class="key">True</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t190" href="#t190">190</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">pcolor</span><span class="op">(</span><span class="nam">corr_matrix</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t191" href="#t191">191</a></span><span class="t">        <span class="com"># Loop over data dimensions and create text annotations.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t192" href="#t192">192</a></span><span class="t">        <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">range</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">corr_matrix</span><span class="op">)</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t193" href="#t193">193</a></span><span class="t">            <span class="key">for</span> <span class="nam">j</span> <span class="key">in</span> <span class="nam">range</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">corr_matrix</span><span class="op">)</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t194" href="#t194">194</a></span><span class="t">                <span class="nam">axs</span><span class="op">.</span><span class="nam">text</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t195" href="#t195">195</a></span><span class="t">                    <span class="nam">j</span><span class="op">+</span><span class="num">.5</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t196" href="#t196">196</a></span><span class="t">                    <span class="nam">i</span><span class="op">+</span><span class="num">.5</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t197" href="#t197">197</a></span><span class="t">                    <span class="str">f"{corr_matrix[coordinates[j]].loc[coordinates[i]]:.2f}"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t198" href="#t198">198</a></span><span class="t">                    <span class="nam">ha</span><span class="op">=</span><span class="str">"center"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t199" href="#t199">199</a></span><span class="t">                    <span class="nam">va</span><span class="op">=</span><span class="str">"center"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t200" href="#t200">200</a></span><span class="t">                    <span class="nam">color</span><span class="op">=</span><span class="str">"w"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t201" href="#t201">201</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_xticks</span><span class="op">(</span><span class="op">[</span><span class="nam">i</span> <span class="op">+</span> <span class="num">0.5</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">range</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">corr_matrix</span><span class="op">)</span><span class="op">)</span><span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t202" href="#t202">202</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_xticklabels</span><span class="op">(</span><span class="nam">corr_matrix</span><span class="op">.</span><span class="nam">columns</span><span class="op">,</span> <span class="nam">rotation</span><span class="op">=</span><span class="num">90</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t203" href="#t203">203</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_yticks</span><span class="op">(</span><span class="op">[</span><span class="nam">i</span><span class="op">+</span><span class="num">0.5</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">range</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">corr_matrix</span><span class="op">)</span><span class="op">)</span><span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t204" href="#t204">204</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_yticklabels</span><span class="op">(</span><span class="nam">corr_matrix</span><span class="op">.</span><span class="nam">index</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t205" href="#t205">205</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_title</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t206" href="#t206">206</a></span><span class="t">            <span class="str">"Helical Parameter Correlation "</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t207" href="#t207">207</a></span><span class="t">            <span class="str">f"for Base Pair Step \'{self.basepair}\'"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t208" href="#t208">208</a></span><span class="t">        <span class="nam">fig</span><span class="op">.</span><span class="nam">tight_layout</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t209" href="#t209">209</a></span><span class="t">        <span class="nam">fig</span><span class="op">.</span><span class="nam">savefig</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t210" href="#t210">210</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'out'</span><span class="op">]</span><span class="op">[</span><span class="str">'output_jpg_path'</span><span class="op">]</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t211" href="#t211">211</a></span><span class="t">            <span class="nam">format</span><span class="op">=</span><span class="str">"jpg"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t212" href="#t212">212</a></span><span class="t">        <span class="nam">plt</span><span class="op">.</span><span class="nam">close</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t213" href="#t213">213</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t214" href="#t214">214</a></span><span class="t">        <span class="com"># Remove temporary file(s)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t215" href="#t215">215</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_files</span><span class="op">.</span><span class="nam">extend</span><span class="op">(</span><span class="op">[</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t216" href="#t216">216</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"unique_dir"</span><span class="op">)</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t217" href="#t217">217</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t218" href="#t218">218</a></span><span class="t">        <span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t219" href="#t219">219</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">remove_tmp_files</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t220" href="#t220">220</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t221" href="#t221">221</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_arguments</span><span class="op">(</span><span class="nam">output_files_created</span><span class="op">=</span><span class="key">True</span><span class="op">,</span> <span class="nam">raise_exception</span><span class="op">=</span><span class="key">False</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t222" href="#t222">222</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t223" href="#t223">223</a></span><span class="t">        <span class="key">return</span> <span class="num">0</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t224" href="#t224">224</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t225" href="#t225">225</a></span><span class="t">    <span class="key">def</span> <span class="nam">get_corr_method</span><span class="op">(</span><span class="nam">self</span><span class="op">,</span> <span class="nam">corrtype1</span><span class="op">,</span> <span class="nam">corrtype2</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t226" href="#t226">226</a></span><span class="t">        <span class="key">if</span> <span class="nam">corrtype1</span> <span class="op">==</span> <span class="str">"circular"</span> <span class="key">and</span> <span class="nam">corrtype2</span> <span class="op">==</span> <span class="str">"linear"</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t227" href="#t227">227</a></span><span class="t">            <span class="nam">method</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">circlineal</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t228" href="#t228">228</a></span><span class="t">        <span class="key">if</span> <span class="nam">corrtype1</span> <span class="op">==</span> <span class="str">"linear"</span> <span class="key">and</span> <span class="nam">corrtype2</span> <span class="op">==</span> <span class="str">"circular"</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t229" href="#t229">229</a></span><span class="t">            <span class="nam">method</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">circlineal</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t230" href="#t230">230</a></span><span class="t">        <span class="key">elif</span> <span class="nam">corrtype1</span> <span class="op">==</span> <span class="str">"circular"</span> <span class="key">and</span> <span class="nam">corrtype2</span> <span class="op">==</span> <span class="str">"circular"</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t231" href="#t231">231</a></span><span class="t">            <span class="nam">method</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">circular</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t232" href="#t232">232</a></span><span class="t">        <span class="key">else</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t233" href="#t233">233</a></span><span class="t">            <span class="nam">method</span> <span class="op">=</span> <span class="str">"pearson"</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t234" href="#t234">234</a></span><span class="t">        <span class="key">return</span> <span class="nam">method</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t235" href="#t235">235</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t236" href="#t236">236</a></span><span class="t">    <span class="op">@</span><span class="nam">staticmethod</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t237" href="#t237">237</a></span><span class="t">    <span class="key">def</span> <span class="nam">circular</span><span class="op">(</span><span class="nam">x1</span><span class="op">,</span> <span class="nam">x2</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t238" href="#t238">238</a></span><span class="t">        <span class="nam">x1</span> <span class="op">=</span> <span class="nam">x1</span> <span class="op">*</span> <span class="nam">np</span><span class="op">.</span><span class="nam">pi</span> <span class="op">/</span> <span class="num">180</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t239" href="#t239">239</a></span><span class="t">        <span class="nam">x2</span> <span class="op">=</span> <span class="nam">x2</span> <span class="op">*</span> <span class="nam">np</span><span class="op">.</span><span class="nam">pi</span> <span class="op">/</span> <span class="num">180</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t240" href="#t240">240</a></span><span class="t">        <span class="nam">diff_1</span> <span class="op">=</span> <span class="nam">np</span><span class="op">.</span><span class="nam">sin</span><span class="op">(</span><span class="nam">x1</span> <span class="op">-</span> <span class="nam">x1</span><span class="op">.</span><span class="nam">mean</span><span class="op">(</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t241" href="#t241">241</a></span><span class="t">        <span class="nam">diff_2</span> <span class="op">=</span> <span class="nam">np</span><span class="op">.</span><span class="nam">sin</span><span class="op">(</span><span class="nam">x2</span> <span class="op">-</span> <span class="nam">x2</span><span class="op">.</span><span class="nam">mean</span><span class="op">(</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t242" href="#t242">242</a></span><span class="t">        <span class="nam">num</span> <span class="op">=</span> <span class="op">(</span><span class="nam">diff_1</span> <span class="op">*</span> <span class="nam">diff_2</span><span class="op">)</span><span class="op">.</span><span class="nam">sum</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t243" href="#t243">243</a></span><span class="t">        <span class="nam">den</span> <span class="op">=</span> <span class="nam">np</span><span class="op">.</span><span class="nam">sqrt</span><span class="op">(</span><span class="op">(</span><span class="nam">diff_1</span> <span class="op">**</span> <span class="num">2</span><span class="op">)</span><span class="op">.</span><span class="nam">sum</span><span class="op">(</span><span class="op">)</span> <span class="op">*</span> <span class="op">(</span><span class="nam">diff_2</span> <span class="op">**</span> <span class="num">2</span><span class="op">)</span><span class="op">.</span><span class="nam">sum</span><span class="op">(</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t244" href="#t244">244</a></span><span class="t">        <span class="key">return</span> <span class="nam">num</span> <span class="op">/</span> <span class="nam">den</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t245" href="#t245">245</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t246" href="#t246">246</a></span><span class="t">    <span class="op">@</span><span class="nam">staticmethod</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t247" href="#t247">247</a></span><span class="t">    <span class="key">def</span> <span class="nam">circlineal</span><span class="op">(</span><span class="nam">x1</span><span class="op">,</span> <span class="nam">x2</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t248" href="#t248">248</a></span><span class="t">        <span class="nam">x2</span> <span class="op">=</span> <span class="nam">x2</span> <span class="op">*</span> <span class="nam">np</span><span class="op">.</span><span class="nam">pi</span> <span class="op">/</span> <span class="num">180</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t249" href="#t249">249</a></span><span class="t">        <span class="nam">rc</span> <span class="op">=</span> <span class="nam">np</span><span class="op">.</span><span class="nam">corrcoef</span><span class="op">(</span><span class="nam">x1</span><span class="op">,</span> <span class="nam">np</span><span class="op">.</span><span class="nam">cos</span><span class="op">(</span><span class="nam">x2</span><span class="op">)</span><span class="op">)</span><span class="op">[</span><span class="num">1</span><span class="op">,</span> <span class="num">0</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t250" href="#t250">250</a></span><span class="t">        <span class="nam">rs</span> <span class="op">=</span> <span class="nam">np</span><span class="op">.</span><span class="nam">corrcoef</span><span class="op">(</span><span class="nam">x1</span><span class="op">,</span> <span class="nam">np</span><span class="op">.</span><span class="nam">sin</span><span class="op">(</span><span class="nam">x2</span><span class="op">)</span><span class="op">)</span><span class="op">[</span><span class="num">1</span><span class="op">,</span> <span class="num">0</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t251" href="#t251">251</a></span><span class="t">        <span class="nam">rcs</span> <span class="op">=</span> <span class="nam">np</span><span class="op">.</span><span class="nam">corrcoef</span><span class="op">(</span><span class="nam">np</span><span class="op">.</span><span class="nam">sin</span><span class="op">(</span><span class="nam">x2</span><span class="op">)</span><span class="op">,</span> <span class="nam">np</span><span class="op">.</span><span class="nam">cos</span><span class="op">(</span><span class="nam">x2</span><span class="op">)</span><span class="op">)</span><span class="op">[</span><span class="num">1</span><span class="op">,</span> <span class="num">0</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t252" href="#t252">252</a></span><span class="t">        <span class="nam">num</span> <span class="op">=</span> <span class="op">(</span><span class="nam">rc</span> <span class="op">**</span> <span class="num">2</span><span class="op">)</span> <span class="op">+</span> <span class="op">(</span><span class="nam">rs</span> <span class="op">**</span> <span class="num">2</span><span class="op">)</span> <span class="op">-</span> <span class="num">2</span> <span class="op">*</span> <span class="nam">rc</span> <span class="op">*</span> <span class="nam">rs</span> <span class="op">*</span> <span class="nam">rcs</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t253" href="#t253">253</a></span><span class="t">        <span class="nam">den</span> <span class="op">=</span> <span class="num">1</span> <span class="op">-</span> <span class="op">(</span><span class="nam">rcs</span> <span class="op">**</span> <span class="num">2</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t254" href="#t254">254</a></span><span class="t">        <span class="nam">correlation</span> <span class="op">=</span> <span class="nam">np</span><span class="op">.</span><span class="nam">sqrt</span><span class="op">(</span><span class="nam">num</span> <span class="op">/</span> <span class="nam">den</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t255" href="#t255">255</a></span><span class="t">        <span class="key">if</span> <span class="nam">np</span><span class="op">.</span><span class="nam">corrcoef</span><span class="op">(</span><span class="nam">x1</span><span class="op">,</span> <span class="nam">x2</span><span class="op">)</span><span class="op">[</span><span class="num">1</span><span class="op">,</span> <span class="num">0</span><span class="op">]</span> <span class="op">&lt;</span> <span class="num">0</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t256" href="#t256">256</a></span><span class="t">            <span class="nam">correlation</span> <span class="op">*=</span> <span class="op">-</span><span class="num">1</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t257" href="#t257">257</a></span><span class="t">        <span class="key">return</span> <span class="nam">correlation</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t258" href="#t258">258</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t21" href="#t21">21</a></span><span class="t"><span class="str">    | Calculate correlation between helical parameters for a single inter-base pair.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t22" href="#t22">22</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t23" href="#t23">23</a></span><span class="t"><span class="str">    Args:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t24" href="#t24">24</a></span><span class="t"><span class="str">        input_filename_shift (str): Path to .csv file with data for helical parameter 'shift'. File type: input. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/stiffness/series_shift_AA.csv>`_. Accepted formats: csv (edam:format_3752).</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t25" href="#t25">25</a></span><span class="t"><span class="str">        input_filename_slide (str): Path to .csv file with data for helical parameter 'slide'. File type: input. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/stiffness/series_slide_AA.csv>`_. Accepted formats: csv (edam:format_3752).</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t26" href="#t26">26</a></span><span class="t"><span class="str">        input_filename_rise (str): Path to .csv file with data for helical parameter 'rise'. File type: input. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/stiffness/series_rise_AA.csv>`_. Accepted formats: csv (edam:format_3752).</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t27" href="#t27">27</a></span><span class="t"><span class="str">        input_filename_tilt (str): Path to .csv file with data for helical parameter 'tilt'. File type: input. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/stiffness/series_tilt_AA.csv>`_. Accepted formats: csv (edam:format_3752).</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t28" href="#t28">28</a></span><span class="t"><span class="str">        input_filename_roll (str): Path to .csv file with data for helical parameter 'roll'. File type: input. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/stiffness/series_roll_AA.csv>`_. Accepted formats: csv (edam:format_3752).</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t29" href="#t29">29</a></span><span class="t"><span class="str">        input_filename_twist (str): Path to .csv file with data for helical parameter 'twist'. File type: input. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/stiffness/series_twist_AA.csv>`_. Accepted formats: csv (edam:format_3752).</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t30" href="#t30">30</a></span><span class="t"><span class="str">        output_csv_path (str): Path to directory where output is saved. File type: output. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/reference/correlation/inter_hpcorr_ref.csv>`_. Accepted formats: csv (edam:format_3752).</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t31" href="#t31">31</a></span><span class="t"><span class="str">        output_jpg_path (str): Path to .jpg file where output is saved. File type: output. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/reference/correlation/inter_hpcorr_ref.jpg>`_. Accepted formats: jpg (edam:format_3579).</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t32" href="#t32">32</a></span><span class="t"><span class="str">        properties (dict):</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t33" href="#t33">33</a></span><span class="t"><span class="str">            * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t34" href="#t34">34</a></span><span class="t"><span class="str">            * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t35" href="#t35">35</a></span><span class="t"><span class="str">            * **basepair** (*str*) - (None) Name of basepair analyzed.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t36" href="#t36">36</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t37" href="#t37">37</a></span><span class="t"><span class="str">    Examples:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t38" href="#t38">38</a></span><span class="t"><span class="str">        This is a use example of how to use the building block from Python::</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t39" href="#t39">39</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t40" href="#t40">40</a></span><span class="t"><span class="str">            from biobb_dna.interbp_correlations.interhpcorr import interhpcorr</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t41" href="#t41">41</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t42" href="#t42">42</a></span><span class="t"><span class="str">            prop = {</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t43" href="#t43">43</a></span><span class="t"><span class="str">                'basepair': 'AA',</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t44" href="#t44">44</a></span><span class="t"><span class="str">            }</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t45" href="#t45">45</a></span><span class="t"><span class="str">            interhpcorr(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t46" href="#t46">46</a></span><span class="t"><span class="str">                input_filename_shift='path/to/shift.csv',</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t47" href="#t47">47</a></span><span class="t"><span class="str">                input_filename_slide='path/to/slide.csv',</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t48" href="#t48">48</a></span><span class="t"><span class="str">                input_filename_rise='path/to/rise.csv',</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t49" href="#t49">49</a></span><span class="t"><span class="str">                input_filename_tilt='path/to/tilt.csv',</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t50" href="#t50">50</a></span><span class="t"><span class="str">                input_filename_roll='path/to/roll.csv',</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t51" href="#t51">51</a></span><span class="t"><span class="str">                input_filename_twist='path/to/twist.csv',</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t52" href="#t52">52</a></span><span class="t"><span class="str">                output_csv_path='path/to/output/file.csv',</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t53" href="#t53">53</a></span><span class="t"><span class="str">                output_jpg_path='path/to/output/file.jpg',</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t54" href="#t54">54</a></span><span class="t"><span class="str">                properties=prop)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t55" href="#t55">55</a></span><span class="t"><span class="str">    Info:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t56" href="#t56">56</a></span><span class="t"><span class="str">        * wrapped_software:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t57" href="#t57">57</a></span><span class="t"><span class="str">            * name: In house</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t58" href="#t58">58</a></span><span class="t"><span class="str">            * license: Apache-2.0</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t59" href="#t59">59</a></span><span class="t"><span class="str">        * ontology:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t60" href="#t60">60</a></span><span class="t"><span class="str">            * name: EDAM</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t61" href="#t61">61</a></span><span class="t"><span class="str">            * schema: http://edamontology.org/EDAM.owl</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t62" href="#t62">62</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t63" href="#t63">63</a></span><span class="t"><span class="str">    """</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t64" href="#t64">64</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t65" href="#t65">65</a></span><span class="t">    <span class="key">def</span> <span class="nam">__init__</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t66" href="#t66">66</a></span><span class="t">            <span class="nam">self</span><span class="op">,</span> <span class="nam">input_filename_shift</span><span class="op">,</span> <span class="nam">input_filename_slide</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t67" href="#t67">67</a></span><span class="t">            <span class="nam">input_filename_rise</span><span class="op">,</span> <span class="nam">input_filename_tilt</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t68" href="#t68">68</a></span><span class="t">            <span class="nam">input_filename_roll</span><span class="op">,</span> <span class="nam">input_filename_twist</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t69" href="#t69">69</a></span><span class="t">            <span class="nam">output_csv_path</span><span class="op">,</span> <span class="nam">output_jpg_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t70" href="#t70">70</a></span><span class="t">            <span class="nam">properties</span><span class="op">=</span><span class="key">None</span><span class="op">,</span> <span class="op">**</span><span class="nam">kwargs</span><span class="op">)</span> <span class="op">-></span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t71" href="#t71">71</a></span><span class="t">        <span class="nam">properties</span> <span class="op">=</span> <span class="nam">properties</span> <span class="key">or</span> <span class="op">{</span><span class="op">}</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t72" href="#t72">72</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t73" href="#t73">73</a></span><span class="t">        <span class="com"># Call parent class constructor</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t74" href="#t74">74</a></span><span class="t">        <span class="nam">super</span><span class="op">(</span><span class="op">)</span><span class="op">.</span><span class="nam">__init__</span><span class="op">(</span><span class="nam">properties</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t75" href="#t75">75</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">locals_var_dict</span> <span class="op">=</span> <span class="nam">locals</span><span class="op">(</span><span class="op">)</span><span class="op">.</span><span class="nam">copy</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t76" href="#t76">76</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t77" href="#t77">77</a></span><span class="t">        <span class="com"># Input/Output files</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t78" href="#t78">78</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span> <span class="op">=</span> <span class="op">{</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t79" href="#t79">79</a></span><span class="t">            <span class="str">'in'</span><span class="op">:</span> <span class="op">{</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t80" href="#t80">80</a></span><span class="t">                <span class="str">'input_filename_shift'</span><span class="op">:</span> <span class="nam">input_filename_shift</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t81" href="#t81">81</a></span><span class="t">                <span class="str">'input_filename_slide'</span><span class="op">:</span> <span class="nam">input_filename_slide</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t82" href="#t82">82</a></span><span class="t">                <span class="str">'input_filename_rise'</span><span class="op">:</span> <span class="nam">input_filename_rise</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t83" href="#t83">83</a></span><span class="t">                <span class="str">'input_filename_tilt'</span><span class="op">:</span> <span class="nam">input_filename_tilt</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t84" href="#t84">84</a></span><span class="t">                <span class="str">'input_filename_roll'</span><span class="op">:</span> <span class="nam">input_filename_roll</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t85" href="#t85">85</a></span><span class="t">                <span class="str">'input_filename_twist'</span><span class="op">:</span> <span class="nam">input_filename_twist</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t86" href="#t86">86</a></span><span class="t">            <span class="op">}</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t87" href="#t87">87</a></span><span class="t">            <span class="str">'out'</span><span class="op">:</span> <span class="op">{</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t88" href="#t88">88</a></span><span class="t">                <span class="str">'output_csv_path'</span><span class="op">:</span> <span class="nam">output_csv_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t89" href="#t89">89</a></span><span class="t">                <span class="str">'output_jpg_path'</span><span class="op">:</span> <span class="nam">output_jpg_path</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t90" href="#t90">90</a></span><span class="t">            <span class="op">}</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t91" href="#t91">91</a></span><span class="t">        <span class="op">}</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t92" href="#t92">92</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t93" href="#t93">93</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">properties</span> <span class="op">=</span> <span class="nam">properties</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t94" href="#t94">94</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">basepair</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"basepair"</span><span class="op">,</span> <span class="key">None</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t95" href="#t95">95</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t96" href="#t96">96</a></span><span class="t">        <span class="com"># Check the properties</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t97" href="#t97">97</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_properties</span><span class="op">(</span><span class="nam">properties</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t98" href="#t98">98</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_arguments</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t99" href="#t99">99</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t100" href="#t100">100</a></span><span class="t">    <span class="op">@</span><span class="nam">launchlogger</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t101" href="#t101">101</a></span><span class="t">    <span class="key">def</span> <span class="nam">launch</span><span class="op">(</span><span class="nam">self</span><span class="op">)</span> <span class="op">-></span> <span class="nam">int</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t102" href="#t102">102</a></span><span class="t">        <span class="str">"""Execute the :class:`InterHelParCorrelation &lt;interbp_correlations.interhpcorr.InterHelParCorrelation>` object."""</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t103" href="#t103">103</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t104" href="#t104">104</a></span><span class="t">        <span class="com"># Setup Biobb</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t105" href="#t105">105</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">check_restart</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t106" href="#t106">106</a></span><span class="t">            <span class="key">return</span> <span class="num">0</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t107" href="#t107">107</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">stage_files</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t108" href="#t108">108</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t109" href="#t109">109</a></span><span class="t">        <span class="com"># Creating temporary folder</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t110" href="#t110">110</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span> <span class="op">=</span> <span class="nam">fu</span><span class="op">.</span><span class="nam">create_unique_dir</span><span class="op">(</span><span class="nam">prefix</span><span class="op">=</span><span class="str">"hpcorrelation_"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t111" href="#t111">111</a></span><span class="t">        <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="str">'Creating %s temporary folder'</span> <span class="op">%</span> <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t112" href="#t112">112</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t113" href="#t113">113</a></span><span class="t">        <span class="com"># read input</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t114" href="#t114">114</a></span><span class="t">        <span class="nam">shift</span> <span class="op">=</span> <span class="nam">load_data</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">"in"</span><span class="op">]</span><span class="op">[</span><span class="str">"input_filename_shift"</span><span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t115" href="#t115">115</a></span><span class="t">        <span class="nam">slide</span> <span class="op">=</span> <span class="nam">load_data</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">"in"</span><span class="op">]</span><span class="op">[</span><span class="str">"input_filename_slide"</span><span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t116" href="#t116">116</a></span><span class="t">        <span class="nam">rise</span> <span class="op">=</span> <span class="nam">load_data</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">"in"</span><span class="op">]</span><span class="op">[</span><span class="str">"input_filename_rise"</span><span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t117" href="#t117">117</a></span><span class="t">        <span class="nam">tilt</span> <span class="op">=</span> <span class="nam">load_data</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">"in"</span><span class="op">]</span><span class="op">[</span><span class="str">"input_filename_tilt"</span><span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t118" href="#t118">118</a></span><span class="t">        <span class="nam">roll</span> <span class="op">=</span> <span class="nam">load_data</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">"in"</span><span class="op">]</span><span class="op">[</span><span class="str">"input_filename_roll"</span><span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t119" href="#t119">119</a></span><span class="t">        <span class="nam">twist</span> <span class="op">=</span> <span class="nam">load_data</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">"in"</span><span class="op">]</span><span class="op">[</span><span class="str">"input_filename_twist"</span><span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t120" href="#t120">120</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t121" href="#t121">121</a></span><span class="t">        <span class="com"># get basepair</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t122" href="#t122">122</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">basepair</span> <span class="key">is</span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t123" href="#t123">123</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">basepair</span> <span class="op">=</span> <span class="nam">shift</span><span class="op">.</span><span class="nam">columns</span><span class="op">[</span><span class="num">0</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t124" href="#t124">124</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t125" href="#t125">125</a></span><span class="t">        <span class="com"># make matrix</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t126" href="#t126">126</a></span><span class="t">        <span class="nam">coordinates</span> <span class="op">=</span> <span class="op">[</span><span class="str">"shift"</span><span class="op">,</span> <span class="str">"slide"</span><span class="op">,</span> <span class="str">"rise"</span><span class="op">,</span> <span class="str">"tilt"</span><span class="op">,</span> <span class="str">"roll"</span><span class="op">,</span> <span class="str">"twist"</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t127" href="#t127">127</a></span><span class="t">        <span class="nam">corr_matrix</span> <span class="op">=</span> <span class="nam">pd</span><span class="op">.</span><span class="nam">DataFrame</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t128" href="#t128">128</a></span><span class="t">            <span class="nam">np</span><span class="op">.</span><span class="nam">eye</span><span class="op">(</span><span class="num">6</span><span class="op">,</span> <span class="num">6</span><span class="op">)</span><span class="op">,</span> <span class="nam">index</span><span class="op">=</span><span class="nam">coordinates</span><span class="op">,</span> <span class="nam">columns</span><span class="op">=</span><span class="nam">coordinates</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t129" href="#t129">129</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t130" href="#t130">130</a></span><span class="t">        <span class="com"># shift</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t131" href="#t131">131</a></span><span class="t">        <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"shift"</span><span class="op">]</span><span class="op">[</span><span class="str">"slide"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">shift</span><span class="op">.</span><span class="nam">corrwith</span><span class="op">(</span><span class="nam">slide</span><span class="op">,</span> <span class="nam">method</span><span class="op">=</span><span class="str">"pearson"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t132" href="#t132">132</a></span><span class="t">        <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"shift"</span><span class="op">]</span><span class="op">[</span><span class="str">"rise"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">shift</span><span class="op">.</span><span class="nam">corrwith</span><span class="op">(</span><span class="nam">rise</span><span class="op">,</span> <span class="nam">method</span><span class="op">=</span><span class="str">"pearson"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t133" href="#t133">133</a></span><span class="t">        <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"shift"</span><span class="op">]</span><span class="op">[</span><span class="str">"tilt"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">shift</span><span class="op">.</span><span class="nam">corrwith</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t134" href="#t134">134</a></span><span class="t">            <span class="nam">tilt</span><span class="op">,</span> <span class="nam">method</span><span class="op">=</span><span class="nam">self</span><span class="op">.</span><span class="nam">circlineal</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t135" href="#t135">135</a></span><span class="t">        <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"shift"</span><span class="op">]</span><span class="op">[</span><span class="str">"roll"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">shift</span><span class="op">.</span><span class="nam">corrwith</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t136" href="#t136">136</a></span><span class="t">            <span class="nam">roll</span><span class="op">,</span> <span class="nam">method</span><span class="op">=</span><span class="nam">self</span><span class="op">.</span><span class="nam">circlineal</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t137" href="#t137">137</a></span><span class="t">        <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"shift"</span><span class="op">]</span><span class="op">[</span><span class="str">"twist"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">shift</span><span class="op">.</span><span class="nam">corrwith</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t138" href="#t138">138</a></span><span class="t">            <span class="nam">twist</span><span class="op">,</span> <span class="nam">method</span><span class="op">=</span><span class="nam">self</span><span class="op">.</span><span class="nam">circlineal</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t139" href="#t139">139</a></span><span class="t">        <span class="com"># symmetric values</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t140" href="#t140">140</a></span><span class="t">        <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"slide"</span><span class="op">]</span><span class="op">[</span><span class="str">"shift"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"shift"</span><span class="op">]</span><span class="op">[</span><span class="str">"slide"</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t141" href="#t141">141</a></span><span class="t">        <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"rise"</span><span class="op">]</span><span class="op">[</span><span class="str">"shift"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"shift"</span><span class="op">]</span><span class="op">[</span><span class="str">"rise"</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t142" href="#t142">142</a></span><span class="t">        <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"tilt"</span><span class="op">]</span><span class="op">[</span><span class="str">"shift"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"shift"</span><span class="op">]</span><span class="op">[</span><span class="str">"tilt"</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t143" href="#t143">143</a></span><span class="t">        <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"roll"</span><span class="op">]</span><span class="op">[</span><span class="str">"shift"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"shift"</span><span class="op">]</span><span class="op">[</span><span class="str">"roll"</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t144" href="#t144">144</a></span><span class="t">        <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"twist"</span><span class="op">]</span><span class="op">[</span><span class="str">"shift"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"shift"</span><span class="op">]</span><span class="op">[</span><span class="str">"twist"</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t145" href="#t145">145</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t146" href="#t146">146</a></span><span class="t">        <span class="com"># slide</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t147" href="#t147">147</a></span><span class="t">        <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"slide"</span><span class="op">]</span><span class="op">[</span><span class="str">"rise"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">slide</span><span class="op">.</span><span class="nam">corrwith</span><span class="op">(</span><span class="nam">rise</span><span class="op">,</span> <span class="nam">method</span><span class="op">=</span><span class="str">"pearson"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t148" href="#t148">148</a></span><span class="t">        <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"slide"</span><span class="op">]</span><span class="op">[</span><span class="str">"tilt"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">slide</span><span class="op">.</span><span class="nam">corrwith</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t149" href="#t149">149</a></span><span class="t">            <span class="nam">tilt</span><span class="op">,</span> <span class="nam">method</span><span class="op">=</span><span class="nam">self</span><span class="op">.</span><span class="nam">circlineal</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t150" href="#t150">150</a></span><span class="t">        <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"slide"</span><span class="op">]</span><span class="op">[</span><span class="str">"roll"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">slide</span><span class="op">.</span><span class="nam">corrwith</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t151" href="#t151">151</a></span><span class="t">            <span class="nam">roll</span><span class="op">,</span> <span class="nam">method</span><span class="op">=</span><span class="nam">self</span><span class="op">.</span><span class="nam">circlineal</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t152" href="#t152">152</a></span><span class="t">        <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"slide"</span><span class="op">]</span><span class="op">[</span><span class="str">"twist"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">slide</span><span class="op">.</span><span class="nam">corrwith</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t153" href="#t153">153</a></span><span class="t">            <span class="nam">twist</span><span class="op">,</span> <span class="nam">method</span><span class="op">=</span><span class="nam">self</span><span class="op">.</span><span class="nam">circlineal</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t154" href="#t154">154</a></span><span class="t">        <span class="com"># symmetric values</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t155" href="#t155">155</a></span><span class="t">        <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"rise"</span><span class="op">]</span><span class="op">[</span><span class="str">"slide"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"slide"</span><span class="op">]</span><span class="op">[</span><span class="str">"rise"</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t156" href="#t156">156</a></span><span class="t">        <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"tilt"</span><span class="op">]</span><span class="op">[</span><span class="str">"slide"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"slide"</span><span class="op">]</span><span class="op">[</span><span class="str">"tilt"</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t157" href="#t157">157</a></span><span class="t">        <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"roll"</span><span class="op">]</span><span class="op">[</span><span class="str">"slide"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"slide"</span><span class="op">]</span><span class="op">[</span><span class="str">"roll"</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t158" href="#t158">158</a></span><span class="t">        <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"twist"</span><span class="op">]</span><span class="op">[</span><span class="str">"slide"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"slide"</span><span class="op">]</span><span class="op">[</span><span class="str">"twist"</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t159" href="#t159">159</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t160" href="#t160">160</a></span><span class="t">        <span class="com"># rise</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t161" href="#t161">161</a></span><span class="t">        <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"rise"</span><span class="op">]</span><span class="op">[</span><span class="str">"tilt"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">rise</span><span class="op">.</span><span class="nam">corrwith</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t162" href="#t162">162</a></span><span class="t">            <span class="nam">tilt</span><span class="op">,</span> <span class="nam">method</span><span class="op">=</span><span class="nam">self</span><span class="op">.</span><span class="nam">circlineal</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t163" href="#t163">163</a></span><span class="t">        <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"rise"</span><span class="op">]</span><span class="op">[</span><span class="str">"roll"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">rise</span><span class="op">.</span><span class="nam">corrwith</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t164" href="#t164">164</a></span><span class="t">            <span class="nam">roll</span><span class="op">,</span> <span class="nam">method</span><span class="op">=</span><span class="nam">self</span><span class="op">.</span><span class="nam">circlineal</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t165" href="#t165">165</a></span><span class="t">        <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"rise"</span><span class="op">]</span><span class="op">[</span><span class="str">"twist"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">rise</span><span class="op">.</span><span class="nam">corrwith</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t166" href="#t166">166</a></span><span class="t">            <span class="nam">twist</span><span class="op">,</span> <span class="nam">method</span><span class="op">=</span><span class="nam">self</span><span class="op">.</span><span class="nam">circlineal</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t167" href="#t167">167</a></span><span class="t">        <span class="com"># symmetric values</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t168" href="#t168">168</a></span><span class="t">        <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"tilt"</span><span class="op">]</span><span class="op">[</span><span class="str">"rise"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"rise"</span><span class="op">]</span><span class="op">[</span><span class="str">"tilt"</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t169" href="#t169">169</a></span><span class="t">        <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"roll"</span><span class="op">]</span><span class="op">[</span><span class="str">"rise"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"rise"</span><span class="op">]</span><span class="op">[</span><span class="str">"roll"</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t170" href="#t170">170</a></span><span class="t">        <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"twist"</span><span class="op">]</span><span class="op">[</span><span class="str">"rise"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"rise"</span><span class="op">]</span><span class="op">[</span><span class="str">"twist"</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t171" href="#t171">171</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t172" href="#t172">172</a></span><span class="t">        <span class="com"># tilt</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t173" href="#t173">173</a></span><span class="t">        <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"tilt"</span><span class="op">]</span><span class="op">[</span><span class="str">"roll"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">tilt</span><span class="op">.</span><span class="nam">corrwith</span><span class="op">(</span><span class="nam">roll</span><span class="op">,</span> <span class="nam">method</span><span class="op">=</span><span class="nam">self</span><span class="op">.</span><span class="nam">circular</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t174" href="#t174">174</a></span><span class="t">        <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"tilt"</span><span class="op">]</span><span class="op">[</span><span class="str">"twist"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">tilt</span><span class="op">.</span><span class="nam">corrwith</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t175" href="#t175">175</a></span><span class="t">            <span class="nam">twist</span><span class="op">,</span> <span class="nam">method</span><span class="op">=</span><span class="nam">self</span><span class="op">.</span><span class="nam">circular</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t176" href="#t176">176</a></span><span class="t">        <span class="com"># symmetric values</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t177" href="#t177">177</a></span><span class="t">        <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"roll"</span><span class="op">]</span><span class="op">[</span><span class="str">"tilt"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"tilt"</span><span class="op">]</span><span class="op">[</span><span class="str">"roll"</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t178" href="#t178">178</a></span><span class="t">        <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"twist"</span><span class="op">]</span><span class="op">[</span><span class="str">"tilt"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"tilt"</span><span class="op">]</span><span class="op">[</span><span class="str">"twist"</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t179" href="#t179">179</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t180" href="#t180">180</a></span><span class="t">        <span class="com"># roll</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t181" href="#t181">181</a></span><span class="t">        <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"roll"</span><span class="op">]</span><span class="op">[</span><span class="str">"twist"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">roll</span><span class="op">.</span><span class="nam">corrwith</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t182" href="#t182">182</a></span><span class="t">            <span class="nam">twist</span><span class="op">,</span> <span class="nam">method</span><span class="op">=</span><span class="nam">self</span><span class="op">.</span><span class="nam">circular</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t183" href="#t183">183</a></span><span class="t">        <span class="com"># symmetric values</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t184" href="#t184">184</a></span><span class="t">        <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"twist"</span><span class="op">]</span><span class="op">[</span><span class="str">"roll"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">corr_matrix</span><span class="op">[</span><span class="str">"roll"</span><span class="op">]</span><span class="op">[</span><span class="str">"twist"</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t185" href="#t185">185</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t186" href="#t186">186</a></span><span class="t">        <span class="com"># save csv data</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t187" href="#t187">187</a></span><span class="t">        <span class="nam">corr_matrix</span><span class="op">.</span><span class="nam">to_csv</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">"out"</span><span class="op">]</span><span class="op">[</span><span class="str">"output_csv_path"</span><span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t188" href="#t188">188</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t189" href="#t189">189</a></span><span class="t">        <span class="com"># create heatmap</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t190" href="#t190">190</a></span><span class="t">        <span class="nam">fig</span><span class="op">,</span> <span class="nam">axs</span> <span class="op">=</span> <span class="nam">plt</span><span class="op">.</span><span class="nam">subplots</span><span class="op">(</span><span class="num">1</span><span class="op">,</span> <span class="num">1</span><span class="op">,</span> <span class="nam">dpi</span><span class="op">=</span><span class="num">300</span><span class="op">,</span> <span class="nam">tight_layout</span><span class="op">=</span><span class="key">True</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t191" href="#t191">191</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">pcolor</span><span class="op">(</span><span class="nam">corr_matrix</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t192" href="#t192">192</a></span><span class="t">        <span class="com"># Loop over data dimensions and create text annotations.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t193" href="#t193">193</a></span><span class="t">        <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">range</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">corr_matrix</span><span class="op">)</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t194" href="#t194">194</a></span><span class="t">            <span class="key">for</span> <span class="nam">j</span> <span class="key">in</span> <span class="nam">range</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">corr_matrix</span><span class="op">)</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t195" href="#t195">195</a></span><span class="t">                <span class="nam">axs</span><span class="op">.</span><span class="nam">text</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t196" href="#t196">196</a></span><span class="t">                    <span class="nam">j</span><span class="op">+</span><span class="num">.5</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t197" href="#t197">197</a></span><span class="t">                    <span class="nam">i</span><span class="op">+</span><span class="num">.5</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t198" href="#t198">198</a></span><span class="t">                    <span class="str">f"{corr_matrix[coordinates[j]].loc[coordinates[i]]:.2f}"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t199" href="#t199">199</a></span><span class="t">                    <span class="nam">ha</span><span class="op">=</span><span class="str">"center"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t200" href="#t200">200</a></span><span class="t">                    <span class="nam">va</span><span class="op">=</span><span class="str">"center"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t201" href="#t201">201</a></span><span class="t">                    <span class="nam">color</span><span class="op">=</span><span class="str">"w"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t202" href="#t202">202</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_xticks</span><span class="op">(</span><span class="op">[</span><span class="nam">i</span> <span class="op">+</span> <span class="num">0.5</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">range</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">corr_matrix</span><span class="op">)</span><span class="op">)</span><span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t203" href="#t203">203</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_xticklabels</span><span class="op">(</span><span class="nam">corr_matrix</span><span class="op">.</span><span class="nam">columns</span><span class="op">,</span> <span class="nam">rotation</span><span class="op">=</span><span class="num">90</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t204" href="#t204">204</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_yticks</span><span class="op">(</span><span class="op">[</span><span class="nam">i</span><span class="op">+</span><span class="num">0.5</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">range</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">corr_matrix</span><span class="op">)</span><span class="op">)</span><span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t205" href="#t205">205</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_yticklabels</span><span class="op">(</span><span class="nam">corr_matrix</span><span class="op">.</span><span class="nam">index</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t206" href="#t206">206</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_title</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t207" href="#t207">207</a></span><span class="t">            <span class="str">"Helical Parameter Correlation "</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t208" href="#t208">208</a></span><span class="t">            <span class="str">f"for Base Pair Step \'{self.basepair}\'"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t209" href="#t209">209</a></span><span class="t">        <span class="nam">fig</span><span class="op">.</span><span class="nam">tight_layout</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t210" href="#t210">210</a></span><span class="t">        <span class="nam">fig</span><span class="op">.</span><span class="nam">savefig</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t211" href="#t211">211</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'out'</span><span class="op">]</span><span class="op">[</span><span class="str">'output_jpg_path'</span><span class="op">]</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t212" href="#t212">212</a></span><span class="t">            <span class="nam">format</span><span class="op">=</span><span class="str">"jpg"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t213" href="#t213">213</a></span><span class="t">        <span class="nam">plt</span><span class="op">.</span><span class="nam">close</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t214" href="#t214">214</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t215" href="#t215">215</a></span><span class="t">        <span class="com"># Remove temporary file(s)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t216" href="#t216">216</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_files</span><span class="op">.</span><span class="nam">extend</span><span class="op">(</span><span class="op">[</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t217" href="#t217">217</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"unique_dir"</span><span class="op">)</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t218" href="#t218">218</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t219" href="#t219">219</a></span><span class="t">        <span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t220" href="#t220">220</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">remove_tmp_files</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t221" href="#t221">221</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t222" href="#t222">222</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_arguments</span><span class="op">(</span><span class="nam">output_files_created</span><span class="op">=</span><span class="key">True</span><span class="op">,</span> <span class="nam">raise_exception</span><span class="op">=</span><span class="key">False</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t223" href="#t223">223</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t224" href="#t224">224</a></span><span class="t">        <span class="key">return</span> <span class="num">0</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t225" href="#t225">225</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t226" href="#t226">226</a></span><span class="t">    <span class="key">def</span> <span class="nam">get_corr_method</span><span class="op">(</span><span class="nam">self</span><span class="op">,</span> <span class="nam">corrtype1</span><span class="op">,</span> <span class="nam">corrtype2</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t227" href="#t227">227</a></span><span class="t">        <span class="key">if</span> <span class="nam">corrtype1</span> <span class="op">==</span> <span class="str">"circular"</span> <span class="key">and</span> <span class="nam">corrtype2</span> <span class="op">==</span> <span class="str">"linear"</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t228" href="#t228">228</a></span><span class="t">            <span class="nam">method</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">circlineal</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t229" href="#t229">229</a></span><span class="t">        <span class="key">if</span> <span class="nam">corrtype1</span> <span class="op">==</span> <span class="str">"linear"</span> <span class="key">and</span> <span class="nam">corrtype2</span> <span class="op">==</span> <span class="str">"circular"</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t230" href="#t230">230</a></span><span class="t">            <span class="nam">method</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">circlineal</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t231" href="#t231">231</a></span><span class="t">        <span class="key">elif</span> <span class="nam">corrtype1</span> <span class="op">==</span> <span class="str">"circular"</span> <span class="key">and</span> <span class="nam">corrtype2</span> <span class="op">==</span> <span class="str">"circular"</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t232" href="#t232">232</a></span><span class="t">            <span class="nam">method</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">circular</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t233" href="#t233">233</a></span><span class="t">        <span class="key">else</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t234" href="#t234">234</a></span><span class="t">            <span class="nam">method</span> <span class="op">=</span> <span class="str">"pearson"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t235" href="#t235">235</a></span><span class="t">        <span class="key">return</span> <span class="nam">method</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t236" href="#t236">236</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t237" href="#t237">237</a></span><span class="t">    <span class="op">@</span><span class="nam">staticmethod</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t238" href="#t238">238</a></span><span class="t">    <span class="key">def</span> <span class="nam">circular</span><span class="op">(</span><span class="nam">x1</span><span class="op">,</span> <span class="nam">x2</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t239" href="#t239">239</a></span><span class="t">        <span class="nam">x1</span> <span class="op">=</span> <span class="nam">x1</span> <span class="op">*</span> <span class="nam">np</span><span class="op">.</span><span class="nam">pi</span> <span class="op">/</span> <span class="num">180</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t240" href="#t240">240</a></span><span class="t">        <span class="nam">x2</span> <span class="op">=</span> <span class="nam">x2</span> <span class="op">*</span> <span class="nam">np</span><span class="op">.</span><span class="nam">pi</span> <span class="op">/</span> <span class="num">180</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t241" href="#t241">241</a></span><span class="t">        <span class="nam">diff_1</span> <span class="op">=</span> <span class="nam">np</span><span class="op">.</span><span class="nam">sin</span><span class="op">(</span><span class="nam">x1</span> <span class="op">-</span> <span class="nam">x1</span><span class="op">.</span><span class="nam">mean</span><span class="op">(</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t242" href="#t242">242</a></span><span class="t">        <span class="nam">diff_2</span> <span class="op">=</span> <span class="nam">np</span><span class="op">.</span><span class="nam">sin</span><span class="op">(</span><span class="nam">x2</span> <span class="op">-</span> <span class="nam">x2</span><span class="op">.</span><span class="nam">mean</span><span class="op">(</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t243" href="#t243">243</a></span><span class="t">        <span class="nam">num</span> <span class="op">=</span> <span class="op">(</span><span class="nam">diff_1</span> <span class="op">*</span> <span class="nam">diff_2</span><span class="op">)</span><span class="op">.</span><span class="nam">sum</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t244" href="#t244">244</a></span><span class="t">        <span class="nam">den</span> <span class="op">=</span> <span class="nam">np</span><span class="op">.</span><span class="nam">sqrt</span><span class="op">(</span><span class="op">(</span><span class="nam">diff_1</span> <span class="op">**</span> <span class="num">2</span><span class="op">)</span><span class="op">.</span><span class="nam">sum</span><span class="op">(</span><span class="op">)</span> <span class="op">*</span> <span class="op">(</span><span class="nam">diff_2</span> <span class="op">**</span> <span class="num">2</span><span class="op">)</span><span class="op">.</span><span class="nam">sum</span><span class="op">(</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t245" href="#t245">245</a></span><span class="t">        <span class="key">return</span> <span class="nam">num</span> <span class="op">/</span> <span class="nam">den</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t246" href="#t246">246</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t247" href="#t247">247</a></span><span class="t">    <span class="op">@</span><span class="nam">staticmethod</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t248" href="#t248">248</a></span><span class="t">    <span class="key">def</span> <span class="nam">circlineal</span><span class="op">(</span><span class="nam">x1</span><span class="op">,</span> <span class="nam">x2</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t249" href="#t249">249</a></span><span class="t">        <span class="nam">x2</span> <span class="op">=</span> <span class="nam">x2</span> <span class="op">*</span> <span class="nam">np</span><span class="op">.</span><span class="nam">pi</span> <span class="op">/</span> <span class="num">180</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t250" href="#t250">250</a></span><span class="t">        <span class="nam">rc</span> <span class="op">=</span> <span class="nam">np</span><span class="op">.</span><span class="nam">corrcoef</span><span class="op">(</span><span class="nam">x1</span><span class="op">,</span> <span class="nam">np</span><span class="op">.</span><span class="nam">cos</span><span class="op">(</span><span class="nam">x2</span><span class="op">)</span><span class="op">)</span><span class="op">[</span><span class="num">1</span><span class="op">,</span> <span class="num">0</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t251" href="#t251">251</a></span><span class="t">        <span class="nam">rs</span> <span class="op">=</span> <span class="nam">np</span><span class="op">.</span><span class="nam">corrcoef</span><span class="op">(</span><span class="nam">x1</span><span class="op">,</span> <span class="nam">np</span><span class="op">.</span><span class="nam">sin</span><span class="op">(</span><span class="nam">x2</span><span class="op">)</span><span class="op">)</span><span class="op">[</span><span class="num">1</span><span class="op">,</span> <span class="num">0</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t252" href="#t252">252</a></span><span class="t">        <span class="nam">rcs</span> <span class="op">=</span> <span class="nam">np</span><span class="op">.</span><span class="nam">corrcoef</span><span class="op">(</span><span class="nam">np</span><span class="op">.</span><span class="nam">sin</span><span class="op">(</span><span class="nam">x2</span><span class="op">)</span><span class="op">,</span> <span class="nam">np</span><span class="op">.</span><span class="nam">cos</span><span class="op">(</span><span class="nam">x2</span><span class="op">)</span><span class="op">)</span><span class="op">[</span><span class="num">1</span><span class="op">,</span> <span class="num">0</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t253" href="#t253">253</a></span><span class="t">        <span class="nam">num</span> <span class="op">=</span> <span class="op">(</span><span class="nam">rc</span> <span class="op">**</span> <span class="num">2</span><span class="op">)</span> <span class="op">+</span> <span class="op">(</span><span class="nam">rs</span> <span class="op">**</span> <span class="num">2</span><span class="op">)</span> <span class="op">-</span> <span class="num">2</span> <span class="op">*</span> <span class="nam">rc</span> <span class="op">*</span> <span class="nam">rs</span> <span class="op">*</span> <span class="nam">rcs</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t254" href="#t254">254</a></span><span class="t">        <span class="nam">den</span> <span class="op">=</span> <span class="num">1</span> <span class="op">-</span> <span class="op">(</span><span class="nam">rcs</span> <span class="op">**</span> <span class="num">2</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t255" href="#t255">255</a></span><span class="t">        <span class="nam">correlation</span> <span class="op">=</span> <span class="nam">np</span><span class="op">.</span><span class="nam">sqrt</span><span class="op">(</span><span class="nam">num</span> <span class="op">/</span> <span class="nam">den</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t256" href="#t256">256</a></span><span class="t">        <span class="key">if</span> <span class="nam">np</span><span class="op">.</span><span class="nam">corrcoef</span><span class="op">(</span><span class="nam">x1</span><span class="op">,</span> <span class="nam">x2</span><span class="op">)</span><span class="op">[</span><span class="num">1</span><span class="op">,</span> <span class="num">0</span><span class="op">]</span> <span class="op">&lt;</span> <span class="num">0</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t257" href="#t257">257</a></span><span class="t">            <span class="nam">correlation</span> <span class="op">*=</span> <span class="op">-</span><span class="num">1</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t258" href="#t258">258</a></span><span class="t">        <span class="key">return</span> <span class="nam">correlation</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t259" href="#t259">259</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t260" href="#t260">260</a></span><span class="t"><span class="key">def</span> <span class="nam">interhpcorr</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t261" href="#t261">261</a></span><span class="t">        <span class="nam">input_filename_shift</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span> <span class="nam">input_filename_slide</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t262" href="#t262">262</a></span><span class="t">        <span class="nam">input_filename_rise</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span> <span class="nam">input_filename_tilt</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t263" href="#t263">263</a></span><span class="t">        <span class="nam">input_filename_roll</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span> <span class="nam">input_filename_twist</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t264" href="#t264">264</a></span><span class="t">        <span class="nam">output_csv_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span> <span class="nam">output_jpg_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t265" href="#t265">265</a></span><span class="t">        <span class="nam">properties</span><span class="op">:</span> <span class="nam">dict</span> <span class="op">=</span> <span class="key">None</span><span class="op">,</span> <span class="op">**</span><span class="nam">kwargs</span><span class="op">)</span> <span class="op">-></span> <span class="nam">int</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t266" href="#t266">266</a></span><span class="t">    <span class="str">"""Create :class:`InterHelParCorrelation &lt;interbp_correlations.interhpcorr.InterHelParCorrelation>` class and</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t267" href="#t267">267</a></span><span class="t"><span class="str">    execute the :meth:`launch() &lt;interbp_correlations.interhpcorr.InterHelParCorrelation.launch>` method."""</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t268" href="#t268">268</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t269" href="#t269">269</a></span><span class="t">    <span class="key">return</span> <span class="nam">InterHelParCorrelation</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t270" href="#t270">270</a></span><span class="t">        <span class="nam">input_filename_shift</span><span class="op">=</span><span class="nam">input_filename_shift</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t271" href="#t271">271</a></span><span class="t">        <span class="nam">input_filename_slide</span><span class="op">=</span><span class="nam">input_filename_slide</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t272" href="#t272">272</a></span><span class="t">        <span class="nam">input_filename_rise</span><span class="op">=</span><span class="nam">input_filename_rise</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t273" href="#t273">273</a></span><span class="t">        <span class="nam">input_filename_tilt</span><span class="op">=</span><span class="nam">input_filename_tilt</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t274" href="#t274">274</a></span><span class="t">        <span class="nam">input_filename_roll</span><span class="op">=</span><span class="nam">input_filename_roll</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t275" href="#t275">275</a></span><span class="t">        <span class="nam">input_filename_twist</span><span class="op">=</span><span class="nam">input_filename_twist</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t276" href="#t276">276</a></span><span class="t">        <span class="nam">output_csv_path</span><span class="op">=</span><span class="nam">output_csv_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t277" href="#t277">277</a></span><span class="t">        <span class="nam">output_jpg_path</span><span class="op">=</span><span class="nam">output_jpg_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t278" href="#t278">278</a></span><span class="t">        <span class="nam">properties</span><span class="op">=</span><span class="nam">properties</span><span class="op">,</span> <span class="op">**</span><span class="nam">kwargs</span><span class="op">)</span><span class="op">.</span><span class="nam">launch</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t279" href="#t279">279</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t260" href="#t260">260</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t261" href="#t261">261</a></span><span class="t"><span class="key">def</span> <span class="nam">interhpcorr</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t262" href="#t262">262</a></span><span class="t">        <span class="nam">input_filename_shift</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span> <span class="nam">input_filename_slide</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t263" href="#t263">263</a></span><span class="t">        <span class="nam">input_filename_rise</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span> <span class="nam">input_filename_tilt</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t264" href="#t264">264</a></span><span class="t">        <span class="nam">input_filename_roll</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span> <span class="nam">input_filename_twist</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t265" href="#t265">265</a></span><span class="t">        <span class="nam">output_csv_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span> <span class="nam">output_jpg_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t266" href="#t266">266</a></span><span class="t">        <span class="nam">properties</span><span class="op">:</span> <span class="nam">dict</span> <span class="op">=</span> <span class="key">None</span><span class="op">,</span> <span class="op">**</span><span class="nam">kwargs</span><span class="op">)</span> <span class="op">-></span> <span class="nam">int</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t267" href="#t267">267</a></span><span class="t">    <span class="str">"""Create :class:`InterHelParCorrelation &lt;interbp_correlations.interhpcorr.InterHelParCorrelation>` class and</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t268" href="#t268">268</a></span><span class="t"><span class="str">    execute the :meth:`launch() &lt;interbp_correlations.interhpcorr.InterHelParCorrelation.launch>` method."""</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t269" href="#t269">269</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t270" href="#t270">270</a></span><span class="t">    <span class="key">return</span> <span class="nam">InterHelParCorrelation</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t271" href="#t271">271</a></span><span class="t">        <span class="nam">input_filename_shift</span><span class="op">=</span><span class="nam">input_filename_shift</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t272" href="#t272">272</a></span><span class="t">        <span class="nam">input_filename_slide</span><span class="op">=</span><span class="nam">input_filename_slide</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t273" href="#t273">273</a></span><span class="t">        <span class="nam">input_filename_rise</span><span class="op">=</span><span class="nam">input_filename_rise</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t274" href="#t274">274</a></span><span class="t">        <span class="nam">input_filename_tilt</span><span class="op">=</span><span class="nam">input_filename_tilt</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t275" href="#t275">275</a></span><span class="t">        <span class="nam">input_filename_roll</span><span class="op">=</span><span class="nam">input_filename_roll</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t276" href="#t276">276</a></span><span class="t">        <span class="nam">input_filename_twist</span><span class="op">=</span><span class="nam">input_filename_twist</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t277" href="#t277">277</a></span><span class="t">        <span class="nam">output_csv_path</span><span class="op">=</span><span class="nam">output_csv_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t278" href="#t278">278</a></span><span class="t">        <span class="nam">output_jpg_path</span><span class="op">=</span><span class="nam">output_jpg_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t279" href="#t279">279</a></span><span class="t">        <span class="nam">properties</span><span class="op">=</span><span class="nam">properties</span><span class="op">,</span> <span class="op">**</span><span class="nam">kwargs</span><span class="op">)</span><span class="op">.</span><span class="nam">launch</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t280" href="#t280">280</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t281" href="#t281">281</a></span><span class="t"><span class="key">def</span> <span class="nam">main</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t282" href="#t282">282</a></span><span class="t">    <span class="str">"""Command line execution of this building block. Please check the command line documentation."""</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t283" href="#t283">283</a></span><span class="t">    <span class="nam">parser</span> <span class="op">=</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">ArgumentParser</span><span class="op">(</span><span class="nam">description</span><span class="op">=</span><span class="str">'Load helical parameter file and save base data individually.'</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t284" href="#t284">284</a></span><span class="t">                                     <span class="nam">formatter_class</span><span class="op">=</span><span class="key">lambda</span> <span class="nam">prog</span><span class="op">:</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">RawTextHelpFormatter</span><span class="op">(</span><span class="nam">prog</span><span class="op">,</span> <span class="nam">width</span><span class="op">=</span><span class="num">99999</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t285" href="#t285">285</a></span><span class="t">    <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--config'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">False</span><span class="op">,</span> <span class="nam">help</span><span class="op">=</span><span class="str">'Configuration file'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t286" href="#t286">286</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t287" href="#t287">287</a></span><span class="t">    <span class="nam">required_args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument_group</span><span class="op">(</span><span class="str">'required arguments'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t288" href="#t288">288</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--input_filename_shift'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t289" href="#t289">289</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Path to csv file with inputs. Accepted formats: csv.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t290" href="#t290">290</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--input_filename_slide'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t291" href="#t291">291</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Path to csv file with inputs. Accepted formats: csv.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t292" href="#t292">292</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--input_filename_rise'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t293" href="#t293">293</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Path to csv file with inputs. Accepted formats: csv.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t294" href="#t294">294</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--input_filename_tilt'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t295" href="#t295">295</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Path to csv file with inputs. Accepted formats: csv.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t296" href="#t296">296</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--input_filename_roll'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t297" href="#t297">297</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Path to csv file with inputs. Accepted formats: csv.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t298" href="#t298">298</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--input_filename_twist'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t299" href="#t299">299</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Path to csv file with inputs. Accepted formats: csv.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t300" href="#t300">300</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--output_csv_path'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t301" href="#t301">301</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Path to output file. Accepted formats: csv.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t302" href="#t302">302</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--output_jpg_path'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t303" href="#t303">303</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Path to output file. Accepted formats: csv.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t304" href="#t304">304</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t305" href="#t305">305</a></span><span class="t">    <span class="nam">args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">parse_args</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t306" href="#t306">306</a></span><span class="t">    <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="op">=</span> <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="key">or</span> <span class="str">"{}"</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t307" href="#t307">307</a></span><span class="t">    <span class="nam">properties</span> <span class="op">=</span> <span class="nam">settings</span><span class="op">.</span><span class="nam">ConfReader</span><span class="op">(</span><span class="nam">config</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">config</span><span class="op">)</span><span class="op">.</span><span class="nam">get_prop_dic</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t308" href="#t308">308</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t309" href="#t309">309</a></span><span class="t">    <span class="nam">interhpcorr</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t310" href="#t310">310</a></span><span class="t">        <span class="nam">input_filename_shift</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_filename_shift</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t311" href="#t311">311</a></span><span class="t">        <span class="nam">input_filename_slide</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_filename_slide</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t312" href="#t312">312</a></span><span class="t">        <span class="nam">input_filename_rise</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_filename_rise</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t313" href="#t313">313</a></span><span class="t">        <span class="nam">input_filename_tilt</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_filename_tilt</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t314" href="#t314">314</a></span><span class="t">        <span class="nam">input_filename_roll</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_filename_roll</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t315" href="#t315">315</a></span><span class="t">        <span class="nam">input_filename_twist</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_filename_twist</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t316" href="#t316">316</a></span><span class="t">        <span class="nam">output_csv_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">output_csv_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t317" href="#t317">317</a></span><span class="t">        <span class="nam">output_jpg_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">output_jpg_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t318" href="#t318">318</a></span><span class="t">        <span class="nam">properties</span><span class="op">=</span><span class="nam">properties</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t319" href="#t319">319</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t281" href="#t281">281</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t282" href="#t282">282</a></span><span class="t"><span class="key">def</span> <span class="nam">main</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t283" href="#t283">283</a></span><span class="t">    <span class="str">"""Command line execution of this building block. Please check the command line documentation."""</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t284" href="#t284">284</a></span><span class="t">    <span class="nam">parser</span> <span class="op">=</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">ArgumentParser</span><span class="op">(</span><span class="nam">description</span><span class="op">=</span><span class="str">'Load helical parameter file and save base data individually.'</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t285" href="#t285">285</a></span><span class="t">                                     <span class="nam">formatter_class</span><span class="op">=</span><span class="key">lambda</span> <span class="nam">prog</span><span class="op">:</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">RawTextHelpFormatter</span><span class="op">(</span><span class="nam">prog</span><span class="op">,</span> <span class="nam">width</span><span class="op">=</span><span class="num">99999</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t286" href="#t286">286</a></span><span class="t">    <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--config'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">False</span><span class="op">,</span> <span class="nam">help</span><span class="op">=</span><span class="str">'Configuration file'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t287" href="#t287">287</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t288" href="#t288">288</a></span><span class="t">    <span class="nam">required_args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument_group</span><span class="op">(</span><span class="str">'required arguments'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t289" href="#t289">289</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--input_filename_shift'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t290" href="#t290">290</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Path to csv file with inputs. Accepted formats: csv.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t291" href="#t291">291</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--input_filename_slide'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t292" href="#t292">292</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Path to csv file with inputs. Accepted formats: csv.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t293" href="#t293">293</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--input_filename_rise'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t294" href="#t294">294</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Path to csv file with inputs. Accepted formats: csv.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t295" href="#t295">295</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--input_filename_tilt'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t296" href="#t296">296</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Path to csv file with inputs. Accepted formats: csv.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t297" href="#t297">297</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--input_filename_roll'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t298" href="#t298">298</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Path to csv file with inputs. Accepted formats: csv.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t299" href="#t299">299</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--input_filename_twist'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t300" href="#t300">300</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Path to csv file with inputs. Accepted formats: csv.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t301" href="#t301">301</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--output_csv_path'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t302" href="#t302">302</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Path to output file. Accepted formats: csv.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t303" href="#t303">303</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--output_jpg_path'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t304" href="#t304">304</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Path to output file. Accepted formats: csv.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t305" href="#t305">305</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t306" href="#t306">306</a></span><span class="t">    <span class="nam">args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">parse_args</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t307" href="#t307">307</a></span><span class="t">    <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="op">=</span> <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="key">or</span> <span class="str">"{}"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t308" href="#t308">308</a></span><span class="t">    <span class="nam">properties</span> <span class="op">=</span> <span class="nam">settings</span><span class="op">.</span><span class="nam">ConfReader</span><span class="op">(</span><span class="nam">config</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">config</span><span class="op">)</span><span class="op">.</span><span class="nam">get_prop_dic</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t309" href="#t309">309</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t310" href="#t310">310</a></span><span class="t">    <span class="nam">interhpcorr</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t311" href="#t311">311</a></span><span class="t">        <span class="nam">input_filename_shift</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_filename_shift</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t312" href="#t312">312</a></span><span class="t">        <span class="nam">input_filename_slide</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_filename_slide</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t313" href="#t313">313</a></span><span class="t">        <span class="nam">input_filename_rise</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_filename_rise</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t314" href="#t314">314</a></span><span class="t">        <span class="nam">input_filename_tilt</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_filename_tilt</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t315" href="#t315">315</a></span><span class="t">        <span class="nam">input_filename_roll</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_filename_roll</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t316" href="#t316">316</a></span><span class="t">        <span class="nam">input_filename_twist</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_filename_twist</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t317" href="#t317">317</a></span><span class="t">        <span class="nam">output_csv_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">output_csv_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t318" href="#t318">318</a></span><span class="t">        <span class="nam">output_jpg_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">output_jpg_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t319" href="#t319">319</a></span><span class="t">        <span class="nam">properties</span><span class="op">=</span><span class="nam">properties</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t320" href="#t320">320</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t321" href="#t321">321</a></span><span class="t"><span class="key">if</span> <span class="nam">__name__</span> <span class="op">==</span> <span class="str">'__main__'</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t322" href="#t322">322</a></span><span class="t">    <span class="nam">main</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t321" href="#t321">321</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t322" href="#t322">322</a></span><span class="t"><span class="key">if</span> <span class="nam">__name__</span> <span class="op">==</span> <span class="str">'__main__'</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t323" href="#t323">323</a></span><span class="t">    <span class="nam">main</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
 </main>
 <footer>
     <div class="content">
@@ -411,7 +412,7 @@ <h2>
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-            created at 2024-05-07 09:06 +0000
+            created at 2024-05-24 09:29 +0000
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@@ -65,7 +65,7 @@ <h2>
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+            created at 2024-05-24 09:29 +0000
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@@ -101,225 +101,226 @@ <h2>
     <p class="pln"><span class="n"><a id="t19" href="#t19">19</a></span><span class="t">    <span class="str">"""</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t20" href="#t20">20</a></span><span class="t"><span class="str">    | biobb_dna InterSequenceCorrelation</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t21" href="#t21">21</a></span><span class="t"><span class="str">    | Calculate correlation between all base pairs of a single sequence and for a single helical parameter.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t22" href="#t22">22</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t23" href="#t23">23</a></span><span class="t"><span class="str">    Args:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t24" href="#t24">24</a></span><span class="t"><span class="str">        input_ser_path (str): Path to .ser file with data for single helical parameter. File type: input. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/correlation/canal_output_roll.ser>`_. Accepted formats: ser (edam:format_2330).</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t25" href="#t25">25</a></span><span class="t"><span class="str">        output_csv_path (str): Path to directory where output is saved. File type: output. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/reference/correlation/inter_seqcorr_roll.csv>`_. Accepted formats: csv (edam:format_3752).</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t26" href="#t26">26</a></span><span class="t"><span class="str">        output_jpg_path (str): Path to .jpg file where output is saved. File type: output. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/reference/correlation/inter_seqcorr_roll.jpg>`_. Accepted formats: jpg (edam:format_3579).</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t27" href="#t27">27</a></span><span class="t"><span class="str">        properties (dict):</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t28" href="#t28">28</a></span><span class="t"><span class="str">            * **sequence** (*str*) - (None) Nucleic acid sequence for the input .ser file. Length of sequence is expected to be the same as the total number of columns in the .ser file, minus the index column (even if later on a subset of columns is selected with the *seqpos* option).</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t29" href="#t29">29</a></span><span class="t"><span class="str">            * **helpar_name** (*str*) - (None) helical parameter name to add to plot title.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t30" href="#t30">30</a></span><span class="t"><span class="str">            * **seqpos** (*list*) - (None) list of sequence positions (columns indices starting by 0) to analyze.  If not specified it will analyse the complete sequence.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t31" href="#t31">31</a></span><span class="t"><span class="str">            * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t32" href="#t32">32</a></span><span class="t"><span class="str">            * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t33" href="#t33">33</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t34" href="#t34">34</a></span><span class="t"><span class="str">    Examples:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t35" href="#t35">35</a></span><span class="t"><span class="str">        This is a use example of how to use the building block from Python::</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t36" href="#t36">36</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t37" href="#t37">37</a></span><span class="t"><span class="str">            from biobb_dna.interbp_correlations.interseqcorr import interseqcorr</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t38" href="#t38">38</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t39" href="#t39">39</a></span><span class="t"><span class="str">            prop = {</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t40" href="#t40">40</a></span><span class="t"><span class="str">                "helpar_name": "helpar",</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t41" href="#t41">41</a></span><span class="t"><span class="str">                "sequence": "CGTAATCG"</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t42" href="#t42">42</a></span><span class="t"><span class="str">            }</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t43" href="#t43">43</a></span><span class="t"><span class="str">            interseqcorr(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t44" href="#t44">44</a></span><span class="t"><span class="str">                input_ser_path='path/to/input/file.ser',</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t45" href="#t45">45</a></span><span class="t"><span class="str">                output_csv_path='path/to/output/file.csv',</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t46" href="#t46">46</a></span><span class="t"><span class="str">                output_jpg_path='path/to/output/plot.jpg',</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t47" href="#t47">47</a></span><span class="t"><span class="str">                properties=prop)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t48" href="#t48">48</a></span><span class="t"><span class="str">    Info:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t49" href="#t49">49</a></span><span class="t"><span class="str">        * wrapped_software:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t50" href="#t50">50</a></span><span class="t"><span class="str">            * name: In house</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t51" href="#t51">51</a></span><span class="t"><span class="str">            * license: Apache-2.0</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t52" href="#t52">52</a></span><span class="t"><span class="str">        * ontology:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t53" href="#t53">53</a></span><span class="t"><span class="str">            * name: EDAM</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t54" href="#t54">54</a></span><span class="t"><span class="str">            * schema: http://edamontology.org/EDAM.owl</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t55" href="#t55">55</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t56" href="#t56">56</a></span><span class="t"><span class="str">    """</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t57" href="#t57">57</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t58" href="#t58">58</a></span><span class="t">    <span class="key">def</span> <span class="nam">__init__</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t59" href="#t59">59</a></span><span class="t">            <span class="nam">self</span><span class="op">,</span> <span class="nam">input_ser_path</span><span class="op">,</span> <span class="nam">output_csv_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t60" href="#t60">60</a></span><span class="t">            <span class="nam">output_jpg_path</span><span class="op">,</span> <span class="nam">properties</span><span class="op">=</span><span class="key">None</span><span class="op">,</span> <span class="op">**</span><span class="nam">kwargs</span><span class="op">)</span> <span class="op">-></span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t61" href="#t61">61</a></span><span class="t">        <span class="nam">properties</span> <span class="op">=</span> <span class="nam">properties</span> <span class="key">or</span> <span class="op">{</span><span class="op">}</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t62" href="#t62">62</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t63" href="#t63">63</a></span><span class="t">        <span class="com"># Call parent class constructor</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t64" href="#t64">64</a></span><span class="t">        <span class="nam">super</span><span class="op">(</span><span class="op">)</span><span class="op">.</span><span class="nam">__init__</span><span class="op">(</span><span class="nam">properties</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t65" href="#t65">65</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">locals_var_dict</span> <span class="op">=</span> <span class="nam">locals</span><span class="op">(</span><span class="op">)</span><span class="op">.</span><span class="nam">copy</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t66" href="#t66">66</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t67" href="#t67">67</a></span><span class="t">        <span class="com"># Input/Output files</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t68" href="#t68">68</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span> <span class="op">=</span> <span class="op">{</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t69" href="#t69">69</a></span><span class="t">            <span class="str">'in'</span><span class="op">:</span> <span class="op">{</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t70" href="#t70">70</a></span><span class="t">                <span class="str">'input_ser_path'</span><span class="op">:</span> <span class="nam">input_ser_path</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t71" href="#t71">71</a></span><span class="t">            <span class="op">}</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t72" href="#t72">72</a></span><span class="t">            <span class="str">'out'</span><span class="op">:</span> <span class="op">{</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t73" href="#t73">73</a></span><span class="t">                <span class="str">'output_csv_path'</span><span class="op">:</span> <span class="nam">output_csv_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t74" href="#t74">74</a></span><span class="t">                <span class="str">'output_jpg_path'</span><span class="op">:</span> <span class="nam">output_jpg_path</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t75" href="#t75">75</a></span><span class="t">            <span class="op">}</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t76" href="#t76">76</a></span><span class="t">        <span class="op">}</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t77" href="#t77">77</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t78" href="#t78">78</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">properties</span> <span class="op">=</span> <span class="nam">properties</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t79" href="#t79">79</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"sequence"</span><span class="op">,</span> <span class="key">None</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t80" href="#t80">80</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"seqpos"</span><span class="op">,</span> <span class="key">None</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t81" href="#t81">81</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">helpar_name</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"helpar_name"</span><span class="op">,</span> <span class="key">None</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t82" href="#t82">82</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t83" href="#t83">83</a></span><span class="t">        <span class="com"># Check the properties</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t84" href="#t84">84</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_properties</span><span class="op">(</span><span class="nam">properties</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t85" href="#t85">85</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_arguments</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t86" href="#t86">86</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t87" href="#t87">87</a></span><span class="t">    <span class="op">@</span><span class="nam">launchlogger</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t88" href="#t88">88</a></span><span class="t">    <span class="key">def</span> <span class="nam">launch</span><span class="op">(</span><span class="nam">self</span><span class="op">)</span> <span class="op">-></span> <span class="nam">int</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t89" href="#t89">89</a></span><span class="t">        <span class="str">"""Execute the :class:`HelParCorrelation &lt;interbp_correlations.interseqcorr.InterSequenceCorrelation>` object."""</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t90" href="#t90">90</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t91" href="#t91">91</a></span><span class="t">        <span class="com"># Setup Biobb</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t92" href="#t92">92</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">check_restart</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t93" href="#t93">93</a></span><span class="t">            <span class="key">return</span> <span class="num">0</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t94" href="#t94">94</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">stage_files</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t95" href="#t95">95</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t96" href="#t96">96</a></span><span class="t">        <span class="com"># check sequence</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t97" href="#t97">97</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span> <span class="key">is</span> <span class="key">None</span> <span class="key">or</span> <span class="nam">len</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span><span class="op">)</span> <span class="op">&lt;</span> <span class="num">2</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t98" href="#t98">98</a></span><span class="t">            <span class="key">raise</span> <span class="nam">ValueError</span><span class="op">(</span><span class="str">"sequence is null or too short!"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t99" href="#t99">99</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t100" href="#t100">100</a></span><span class="t">        <span class="com"># get helical parameter from filename if not specified</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t101" href="#t101">101</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">helpar_name</span> <span class="key">is</span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t102" href="#t102">102</a></span><span class="t">            <span class="key">for</span> <span class="nam">hp</span> <span class="key">in</span> <span class="nam">constants</span><span class="op">.</span><span class="nam">helical_parameters</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t103" href="#t103">103</a></span><span class="t">                <span class="key">if</span> <span class="nam">hp</span><span class="op">.</span><span class="nam">lower</span><span class="op">(</span><span class="op">)</span> <span class="key">in</span> <span class="nam">Path</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t104" href="#t104">104</a></span><span class="t">                        <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'input_ser_path'</span><span class="op">]</span><span class="op">)</span><span class="op">.</span><span class="nam">name</span><span class="op">.</span><span class="nam">lower</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t105" href="#t105">105</a></span><span class="t">                    <span class="nam">self</span><span class="op">.</span><span class="nam">helpar_name</span> <span class="op">=</span> <span class="nam">hp</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t106" href="#t106">106</a></span><span class="t">            <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">helpar_name</span> <span class="key">is</span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t107" href="#t107">107</a></span><span class="t">                <span class="key">raise</span> <span class="nam">ValueError</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t108" href="#t108">108</a></span><span class="t">                    <span class="str">"Helical parameter name can't be inferred from file, "</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t109" href="#t109">109</a></span><span class="t">                    <span class="str">"so it must be specified!"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t110" href="#t110">110</a></span><span class="t">        <span class="key">else</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t111" href="#t111">111</a></span><span class="t">            <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">helpar_name</span> <span class="key">not</span> <span class="key">in</span> <span class="nam">constants</span><span class="op">.</span><span class="nam">helical_parameters</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t112" href="#t112">112</a></span><span class="t">                <span class="key">raise</span> <span class="nam">ValueError</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t113" href="#t113">113</a></span><span class="t">                    <span class="str">"Helical parameter name is invalid! "</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t114" href="#t114">114</a></span><span class="t">                    <span class="str">f"Options: {constants.helical_parameters}"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t115" href="#t115">115</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t116" href="#t116">116</a></span><span class="t">        <span class="com"># get base length and unit from helical parameter name</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t117" href="#t117">117</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">helpar_name</span> <span class="key">in</span> <span class="nam">constants</span><span class="op">.</span><span class="nam">hp_angular</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t118" href="#t118">118</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">method</span> <span class="op">=</span> <span class="str">"pearson"</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t119" href="#t119">119</a></span><span class="t">        <span class="key">else</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t120" href="#t120">120</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">method</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">circular</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t121" href="#t121">121</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t122" href="#t122">122</a></span><span class="t">        <span class="com"># check seqpos</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t123" href="#t123">123</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span> <span class="key">is</span> <span class="key">not</span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t124" href="#t124">124</a></span><span class="t">            <span class="key">if</span> <span class="key">not</span> <span class="op">(</span><span class="nam">isinstance</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">,</span> <span class="nam">list</span><span class="op">)</span> <span class="key">and</span> <span class="nam">len</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">)</span> <span class="op">></span> <span class="num">1</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t125" href="#t125">125</a></span><span class="t">                <span class="key">raise</span> <span class="nam">ValueError</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t126" href="#t126">126</a></span><span class="t">                    <span class="str">"seqpos must be a list of at least two integers"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t127" href="#t127">127</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t128" href="#t128">128</a></span><span class="t">        <span class="com"># Creating temporary folder</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t129" href="#t129">129</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span> <span class="op">=</span> <span class="nam">fu</span><span class="op">.</span><span class="nam">create_unique_dir</span><span class="op">(</span><span class="nam">prefix</span><span class="op">=</span><span class="str">"bpcorrelation_"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t130" href="#t130">130</a></span><span class="t">        <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="str">'Creating %s temporary folder'</span> <span class="op">%</span> <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t131" href="#t131">131</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t132" href="#t132">132</a></span><span class="t">        <span class="com"># read input .ser file</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t133" href="#t133">133</a></span><span class="t">        <span class="nam">ser_data</span> <span class="op">=</span> <span class="nam">read_series</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t134" href="#t134">134</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'input_ser_path'</span><span class="op">]</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t135" href="#t135">135</a></span><span class="t">            <span class="nam">usecols</span><span class="op">=</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t136" href="#t136">136</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span> <span class="key">is</span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t137" href="#t137">137</a></span><span class="t">            <span class="nam">ser_data</span> <span class="op">=</span> <span class="nam">ser_data</span><span class="op">[</span><span class="nam">ser_data</span><span class="op">.</span><span class="nam">columns</span><span class="op">[</span><span class="num">1</span><span class="op">:</span><span class="op">-</span><span class="num">1</span><span class="op">]</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t138" href="#t138">138</a></span><span class="t">            <span class="com"># discard first and last base(pairs) from strands</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t139" href="#t139">139</a></span><span class="t">            <span class="nam">sequence</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span><span class="op">[</span><span class="num">1</span><span class="op">:</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t140" href="#t140">140</a></span><span class="t">            <span class="nam">labels</span> <span class="op">=</span> <span class="op">[</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t141" href="#t141">141</a></span><span class="t">                <span class="str">f"{i+1}_{sequence[i:i+2]}"</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">range</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">ser_data</span><span class="op">.</span><span class="nam">columns</span><span class="op">)</span><span class="op">)</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t142" href="#t142">142</a></span><span class="t">        <span class="key">else</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t143" href="#t143">143</a></span><span class="t">            <span class="nam">labels</span> <span class="op">=</span> <span class="op">[</span><span class="str">f"{i+1}_{self.sequence[i:i+2]}"</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t144" href="#t144">144</a></span><span class="t">        <span class="nam">ser_data</span><span class="op">.</span><span class="nam">columns</span> <span class="op">=</span> <span class="nam">labels</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t145" href="#t145">145</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t146" href="#t146">146</a></span><span class="t">        <span class="com"># make matrix</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t147" href="#t147">147</a></span><span class="t">        <span class="nam">corr_data</span> <span class="op">=</span> <span class="nam">ser_data</span><span class="op">.</span><span class="nam">corr</span><span class="op">(</span><span class="nam">method</span><span class="op">=</span><span class="nam">self</span><span class="op">.</span><span class="nam">method</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t148" href="#t148">148</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t149" href="#t149">149</a></span><span class="t">        <span class="com"># save csv data</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t150" href="#t150">150</a></span><span class="t">        <span class="nam">corr_data</span><span class="op">.</span><span class="nam">to_csv</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">"out"</span><span class="op">]</span><span class="op">[</span><span class="str">"output_csv_path"</span><span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t151" href="#t151">151</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t152" href="#t152">152</a></span><span class="t">        <span class="com"># create heatmap</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t153" href="#t153">153</a></span><span class="t">        <span class="nam">fig</span><span class="op">,</span> <span class="nam">axs</span> <span class="op">=</span> <span class="nam">plt</span><span class="op">.</span><span class="nam">subplots</span><span class="op">(</span><span class="num">1</span><span class="op">,</span> <span class="num">1</span><span class="op">,</span> <span class="nam">dpi</span><span class="op">=</span><span class="num">300</span><span class="op">,</span> <span class="nam">tight_layout</span><span class="op">=</span><span class="key">True</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t154" href="#t154">154</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">pcolor</span><span class="op">(</span><span class="nam">corr_data</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t155" href="#t155">155</a></span><span class="t">        <span class="com"># Loop over data dimensions and create text annotations.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t156" href="#t156">156</a></span><span class="t">        <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">range</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">corr_data</span><span class="op">)</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t157" href="#t157">157</a></span><span class="t">            <span class="key">for</span> <span class="nam">j</span> <span class="key">in</span> <span class="nam">range</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">corr_data</span><span class="op">)</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t158" href="#t158">158</a></span><span class="t">                <span class="nam">axs</span><span class="op">.</span><span class="nam">text</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t159" href="#t159">159</a></span><span class="t">                    <span class="nam">j</span><span class="op">+</span><span class="num">.5</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t160" href="#t160">160</a></span><span class="t">                    <span class="nam">i</span><span class="op">+</span><span class="num">.5</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t161" href="#t161">161</a></span><span class="t">                    <span class="str">f"{corr_data[corr_data.columns[j]].iloc[i]:.2f}"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t162" href="#t162">162</a></span><span class="t">                    <span class="nam">ha</span><span class="op">=</span><span class="str">"center"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t163" href="#t163">163</a></span><span class="t">                    <span class="nam">va</span><span class="op">=</span><span class="str">"center"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t164" href="#t164">164</a></span><span class="t">                    <span class="nam">color</span><span class="op">=</span><span class="str">"w"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t165" href="#t165">165</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_xticks</span><span class="op">(</span><span class="op">[</span><span class="nam">i</span> <span class="op">+</span> <span class="num">0.5</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">range</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">corr_data</span><span class="op">)</span><span class="op">)</span><span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t166" href="#t166">166</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_xticklabels</span><span class="op">(</span><span class="nam">labels</span><span class="op">,</span> <span class="nam">rotation</span><span class="op">=</span><span class="num">90</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t167" href="#t167">167</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_yticks</span><span class="op">(</span><span class="op">[</span><span class="nam">i</span> <span class="op">+</span> <span class="num">0.5</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">range</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">corr_data</span><span class="op">)</span><span class="op">)</span><span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t168" href="#t168">168</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_yticklabels</span><span class="op">(</span><span class="nam">labels</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t169" href="#t169">169</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_title</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t170" href="#t170">170</a></span><span class="t">            <span class="str">"Base Pair Correlation "</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t171" href="#t171">171</a></span><span class="t">            <span class="str">f"for Helical Parameter \'{self.helpar_name}\'"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t172" href="#t172">172</a></span><span class="t">        <span class="nam">fig</span><span class="op">.</span><span class="nam">tight_layout</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t173" href="#t173">173</a></span><span class="t">        <span class="nam">fig</span><span class="op">.</span><span class="nam">savefig</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t174" href="#t174">174</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'out'</span><span class="op">]</span><span class="op">[</span><span class="str">'output_jpg_path'</span><span class="op">]</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t175" href="#t175">175</a></span><span class="t">            <span class="nam">format</span><span class="op">=</span><span class="str">"jpg"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t176" href="#t176">176</a></span><span class="t">        <span class="nam">plt</span><span class="op">.</span><span class="nam">close</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t177" href="#t177">177</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t178" href="#t178">178</a></span><span class="t">        <span class="com"># Remove temporary file(s)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t179" href="#t179">179</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_files</span><span class="op">.</span><span class="nam">extend</span><span class="op">(</span><span class="op">[</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t180" href="#t180">180</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"unique_dir"</span><span class="op">)</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t181" href="#t181">181</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t182" href="#t182">182</a></span><span class="t">        <span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t183" href="#t183">183</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">remove_tmp_files</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t184" href="#t184">184</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t185" href="#t185">185</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_arguments</span><span class="op">(</span><span class="nam">output_files_created</span><span class="op">=</span><span class="key">True</span><span class="op">,</span> <span class="nam">raise_exception</span><span class="op">=</span><span class="key">False</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t186" href="#t186">186</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t187" href="#t187">187</a></span><span class="t">        <span class="key">return</span> <span class="num">0</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t188" href="#t188">188</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t189" href="#t189">189</a></span><span class="t">    <span class="op">@</span><span class="nam">staticmethod</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t190" href="#t190">190</a></span><span class="t">    <span class="key">def</span> <span class="nam">circular</span><span class="op">(</span><span class="nam">x1</span><span class="op">,</span> <span class="nam">x2</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t191" href="#t191">191</a></span><span class="t">        <span class="nam">x1</span> <span class="op">=</span> <span class="nam">x1</span> <span class="op">*</span> <span class="nam">np</span><span class="op">.</span><span class="nam">pi</span> <span class="op">/</span> <span class="num">180</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t192" href="#t192">192</a></span><span class="t">        <span class="nam">x2</span> <span class="op">=</span> <span class="nam">x2</span> <span class="op">*</span> <span class="nam">np</span><span class="op">.</span><span class="nam">pi</span> <span class="op">/</span> <span class="num">180</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t193" href="#t193">193</a></span><span class="t">        <span class="nam">diff_1</span> <span class="op">=</span> <span class="nam">np</span><span class="op">.</span><span class="nam">sin</span><span class="op">(</span><span class="nam">x1</span> <span class="op">-</span> <span class="nam">x1</span><span class="op">.</span><span class="nam">mean</span><span class="op">(</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t194" href="#t194">194</a></span><span class="t">        <span class="nam">diff_2</span> <span class="op">=</span> <span class="nam">np</span><span class="op">.</span><span class="nam">sin</span><span class="op">(</span><span class="nam">x2</span> <span class="op">-</span> <span class="nam">x2</span><span class="op">.</span><span class="nam">mean</span><span class="op">(</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t195" href="#t195">195</a></span><span class="t">        <span class="nam">num</span> <span class="op">=</span> <span class="op">(</span><span class="nam">diff_1</span> <span class="op">*</span> <span class="nam">diff_2</span><span class="op">)</span><span class="op">.</span><span class="nam">sum</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t196" href="#t196">196</a></span><span class="t">        <span class="nam">den</span> <span class="op">=</span> <span class="nam">np</span><span class="op">.</span><span class="nam">sqrt</span><span class="op">(</span><span class="op">(</span><span class="nam">diff_1</span> <span class="op">**</span> <span class="num">2</span><span class="op">)</span><span class="op">.</span><span class="nam">sum</span><span class="op">(</span><span class="op">)</span> <span class="op">*</span> <span class="op">(</span><span class="nam">diff_2</span> <span class="op">**</span> <span class="num">2</span><span class="op">)</span><span class="op">.</span><span class="nam">sum</span><span class="op">(</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t197" href="#t197">197</a></span><span class="t">        <span class="key">return</span> <span class="nam">num</span> <span class="op">/</span> <span class="nam">den</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t198" href="#t198">198</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t22" href="#t22">22</a></span><span class="t"><span class="str">    | Calculate correlation between all base pairs of a single sequence and for a single helical parameter.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t23" href="#t23">23</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t24" href="#t24">24</a></span><span class="t"><span class="str">    Args:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t25" href="#t25">25</a></span><span class="t"><span class="str">        input_ser_path (str): Path to .ser file with data for single helical parameter. File type: input. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/correlation/canal_output_roll.ser>`_. Accepted formats: ser (edam:format_2330).</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t26" href="#t26">26</a></span><span class="t"><span class="str">        output_csv_path (str): Path to directory where output is saved. File type: output. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/reference/correlation/inter_seqcorr_roll.csv>`_. Accepted formats: csv (edam:format_3752).</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t27" href="#t27">27</a></span><span class="t"><span class="str">        output_jpg_path (str): Path to .jpg file where output is saved. File type: output. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/reference/correlation/inter_seqcorr_roll.jpg>`_. Accepted formats: jpg (edam:format_3579).</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t28" href="#t28">28</a></span><span class="t"><span class="str">        properties (dict):</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t29" href="#t29">29</a></span><span class="t"><span class="str">            * **sequence** (*str*) - (None) Nucleic acid sequence for the input .ser file. Length of sequence is expected to be the same as the total number of columns in the .ser file, minus the index column (even if later on a subset of columns is selected with the *seqpos* option).</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t30" href="#t30">30</a></span><span class="t"><span class="str">            * **helpar_name** (*str*) - (None) helical parameter name to add to plot title.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t31" href="#t31">31</a></span><span class="t"><span class="str">            * **seqpos** (*list*) - (None) list of sequence positions (columns indices starting by 0) to analyze.  If not specified it will analyse the complete sequence.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t32" href="#t32">32</a></span><span class="t"><span class="str">            * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t33" href="#t33">33</a></span><span class="t"><span class="str">            * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t34" href="#t34">34</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t35" href="#t35">35</a></span><span class="t"><span class="str">    Examples:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t36" href="#t36">36</a></span><span class="t"><span class="str">        This is a use example of how to use the building block from Python::</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t37" href="#t37">37</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t38" href="#t38">38</a></span><span class="t"><span class="str">            from biobb_dna.interbp_correlations.interseqcorr import interseqcorr</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t39" href="#t39">39</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t40" href="#t40">40</a></span><span class="t"><span class="str">            prop = {</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t41" href="#t41">41</a></span><span class="t"><span class="str">                "helpar_name": "helpar",</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t42" href="#t42">42</a></span><span class="t"><span class="str">                "sequence": "CGTAATCG"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t43" href="#t43">43</a></span><span class="t"><span class="str">            }</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t44" href="#t44">44</a></span><span class="t"><span class="str">            interseqcorr(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t45" href="#t45">45</a></span><span class="t"><span class="str">                input_ser_path='path/to/input/file.ser',</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t46" href="#t46">46</a></span><span class="t"><span class="str">                output_csv_path='path/to/output/file.csv',</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t47" href="#t47">47</a></span><span class="t"><span class="str">                output_jpg_path='path/to/output/plot.jpg',</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t48" href="#t48">48</a></span><span class="t"><span class="str">                properties=prop)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t49" href="#t49">49</a></span><span class="t"><span class="str">    Info:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t50" href="#t50">50</a></span><span class="t"><span class="str">        * wrapped_software:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t51" href="#t51">51</a></span><span class="t"><span class="str">            * name: In house</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t52" href="#t52">52</a></span><span class="t"><span class="str">            * license: Apache-2.0</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t53" href="#t53">53</a></span><span class="t"><span class="str">        * ontology:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t54" href="#t54">54</a></span><span class="t"><span class="str">            * name: EDAM</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t55" href="#t55">55</a></span><span class="t"><span class="str">            * schema: http://edamontology.org/EDAM.owl</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t56" href="#t56">56</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t57" href="#t57">57</a></span><span class="t"><span class="str">    """</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t58" href="#t58">58</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t59" href="#t59">59</a></span><span class="t">    <span class="key">def</span> <span class="nam">__init__</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t60" href="#t60">60</a></span><span class="t">            <span class="nam">self</span><span class="op">,</span> <span class="nam">input_ser_path</span><span class="op">,</span> <span class="nam">output_csv_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t61" href="#t61">61</a></span><span class="t">            <span class="nam">output_jpg_path</span><span class="op">,</span> <span class="nam">properties</span><span class="op">=</span><span class="key">None</span><span class="op">,</span> <span class="op">**</span><span class="nam">kwargs</span><span class="op">)</span> <span class="op">-></span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t62" href="#t62">62</a></span><span class="t">        <span class="nam">properties</span> <span class="op">=</span> <span class="nam">properties</span> <span class="key">or</span> <span class="op">{</span><span class="op">}</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t63" href="#t63">63</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t64" href="#t64">64</a></span><span class="t">        <span class="com"># Call parent class constructor</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t65" href="#t65">65</a></span><span class="t">        <span class="nam">super</span><span class="op">(</span><span class="op">)</span><span class="op">.</span><span class="nam">__init__</span><span class="op">(</span><span class="nam">properties</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t66" href="#t66">66</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">locals_var_dict</span> <span class="op">=</span> <span class="nam">locals</span><span class="op">(</span><span class="op">)</span><span class="op">.</span><span class="nam">copy</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t67" href="#t67">67</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t68" href="#t68">68</a></span><span class="t">        <span class="com"># Input/Output files</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t69" href="#t69">69</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span> <span class="op">=</span> <span class="op">{</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t70" href="#t70">70</a></span><span class="t">            <span class="str">'in'</span><span class="op">:</span> <span class="op">{</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t71" href="#t71">71</a></span><span class="t">                <span class="str">'input_ser_path'</span><span class="op">:</span> <span class="nam">input_ser_path</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t72" href="#t72">72</a></span><span class="t">            <span class="op">}</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t73" href="#t73">73</a></span><span class="t">            <span class="str">'out'</span><span class="op">:</span> <span class="op">{</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t74" href="#t74">74</a></span><span class="t">                <span class="str">'output_csv_path'</span><span class="op">:</span> <span class="nam">output_csv_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t75" href="#t75">75</a></span><span class="t">                <span class="str">'output_jpg_path'</span><span class="op">:</span> <span class="nam">output_jpg_path</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t76" href="#t76">76</a></span><span class="t">            <span class="op">}</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t77" href="#t77">77</a></span><span class="t">        <span class="op">}</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t78" href="#t78">78</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t79" href="#t79">79</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">properties</span> <span class="op">=</span> <span class="nam">properties</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t80" href="#t80">80</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"sequence"</span><span class="op">,</span> <span class="key">None</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t81" href="#t81">81</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"seqpos"</span><span class="op">,</span> <span class="key">None</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t82" href="#t82">82</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">helpar_name</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"helpar_name"</span><span class="op">,</span> <span class="key">None</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t83" href="#t83">83</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t84" href="#t84">84</a></span><span class="t">        <span class="com"># Check the properties</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t85" href="#t85">85</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_properties</span><span class="op">(</span><span class="nam">properties</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t86" href="#t86">86</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_arguments</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t87" href="#t87">87</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t88" href="#t88">88</a></span><span class="t">    <span class="op">@</span><span class="nam">launchlogger</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t89" href="#t89">89</a></span><span class="t">    <span class="key">def</span> <span class="nam">launch</span><span class="op">(</span><span class="nam">self</span><span class="op">)</span> <span class="op">-></span> <span class="nam">int</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t90" href="#t90">90</a></span><span class="t">        <span class="str">"""Execute the :class:`HelParCorrelation &lt;interbp_correlations.interseqcorr.InterSequenceCorrelation>` object."""</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t91" href="#t91">91</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t92" href="#t92">92</a></span><span class="t">        <span class="com"># Setup Biobb</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t93" href="#t93">93</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">check_restart</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t94" href="#t94">94</a></span><span class="t">            <span class="key">return</span> <span class="num">0</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t95" href="#t95">95</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">stage_files</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t96" href="#t96">96</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t97" href="#t97">97</a></span><span class="t">        <span class="com"># check sequence</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t98" href="#t98">98</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span> <span class="key">is</span> <span class="key">None</span> <span class="key">or</span> <span class="nam">len</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span><span class="op">)</span> <span class="op">&lt;</span> <span class="num">2</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t99" href="#t99">99</a></span><span class="t">            <span class="key">raise</span> <span class="nam">ValueError</span><span class="op">(</span><span class="str">"sequence is null or too short!"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t100" href="#t100">100</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t101" href="#t101">101</a></span><span class="t">        <span class="com"># get helical parameter from filename if not specified</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t102" href="#t102">102</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">helpar_name</span> <span class="key">is</span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t103" href="#t103">103</a></span><span class="t">            <span class="key">for</span> <span class="nam">hp</span> <span class="key">in</span> <span class="nam">constants</span><span class="op">.</span><span class="nam">helical_parameters</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t104" href="#t104">104</a></span><span class="t">                <span class="key">if</span> <span class="nam">hp</span><span class="op">.</span><span class="nam">lower</span><span class="op">(</span><span class="op">)</span> <span class="key">in</span> <span class="nam">Path</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t105" href="#t105">105</a></span><span class="t">                        <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'input_ser_path'</span><span class="op">]</span><span class="op">)</span><span class="op">.</span><span class="nam">name</span><span class="op">.</span><span class="nam">lower</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t106" href="#t106">106</a></span><span class="t">                    <span class="nam">self</span><span class="op">.</span><span class="nam">helpar_name</span> <span class="op">=</span> <span class="nam">hp</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t107" href="#t107">107</a></span><span class="t">            <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">helpar_name</span> <span class="key">is</span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t108" href="#t108">108</a></span><span class="t">                <span class="key">raise</span> <span class="nam">ValueError</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t109" href="#t109">109</a></span><span class="t">                    <span class="str">"Helical parameter name can't be inferred from file, "</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t110" href="#t110">110</a></span><span class="t">                    <span class="str">"so it must be specified!"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t111" href="#t111">111</a></span><span class="t">        <span class="key">else</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t112" href="#t112">112</a></span><span class="t">            <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">helpar_name</span> <span class="key">not</span> <span class="key">in</span> <span class="nam">constants</span><span class="op">.</span><span class="nam">helical_parameters</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t113" href="#t113">113</a></span><span class="t">                <span class="key">raise</span> <span class="nam">ValueError</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t114" href="#t114">114</a></span><span class="t">                    <span class="str">"Helical parameter name is invalid! "</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t115" href="#t115">115</a></span><span class="t">                    <span class="str">f"Options: {constants.helical_parameters}"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t116" href="#t116">116</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t117" href="#t117">117</a></span><span class="t">        <span class="com"># get base length and unit from helical parameter name</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t118" href="#t118">118</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">helpar_name</span> <span class="key">in</span> <span class="nam">constants</span><span class="op">.</span><span class="nam">hp_angular</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t119" href="#t119">119</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">method</span> <span class="op">=</span> <span class="str">"pearson"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t120" href="#t120">120</a></span><span class="t">        <span class="key">else</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t121" href="#t121">121</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">method</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">circular</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t122" href="#t122">122</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t123" href="#t123">123</a></span><span class="t">        <span class="com"># check seqpos</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t124" href="#t124">124</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span> <span class="key">is</span> <span class="key">not</span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t125" href="#t125">125</a></span><span class="t">            <span class="key">if</span> <span class="key">not</span> <span class="op">(</span><span class="nam">isinstance</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">,</span> <span class="nam">list</span><span class="op">)</span> <span class="key">and</span> <span class="nam">len</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">)</span> <span class="op">></span> <span class="num">1</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t126" href="#t126">126</a></span><span class="t">                <span class="key">raise</span> <span class="nam">ValueError</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t127" href="#t127">127</a></span><span class="t">                    <span class="str">"seqpos must be a list of at least two integers"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t128" href="#t128">128</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t129" href="#t129">129</a></span><span class="t">        <span class="com"># Creating temporary folder</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t130" href="#t130">130</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span> <span class="op">=</span> <span class="nam">fu</span><span class="op">.</span><span class="nam">create_unique_dir</span><span class="op">(</span><span class="nam">prefix</span><span class="op">=</span><span class="str">"bpcorrelation_"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t131" href="#t131">131</a></span><span class="t">        <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="str">'Creating %s temporary folder'</span> <span class="op">%</span> <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t132" href="#t132">132</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t133" href="#t133">133</a></span><span class="t">        <span class="com"># read input .ser file</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t134" href="#t134">134</a></span><span class="t">        <span class="nam">ser_data</span> <span class="op">=</span> <span class="nam">read_series</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t135" href="#t135">135</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'input_ser_path'</span><span class="op">]</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t136" href="#t136">136</a></span><span class="t">            <span class="nam">usecols</span><span class="op">=</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t137" href="#t137">137</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span> <span class="key">is</span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t138" href="#t138">138</a></span><span class="t">            <span class="nam">ser_data</span> <span class="op">=</span> <span class="nam">ser_data</span><span class="op">[</span><span class="nam">ser_data</span><span class="op">.</span><span class="nam">columns</span><span class="op">[</span><span class="num">1</span><span class="op">:</span><span class="op">-</span><span class="num">1</span><span class="op">]</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t139" href="#t139">139</a></span><span class="t">            <span class="com"># discard first and last base(pairs) from strands</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t140" href="#t140">140</a></span><span class="t">            <span class="nam">sequence</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span><span class="op">[</span><span class="num">1</span><span class="op">:</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t141" href="#t141">141</a></span><span class="t">            <span class="nam">labels</span> <span class="op">=</span> <span class="op">[</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t142" href="#t142">142</a></span><span class="t">                <span class="str">f"{i+1}_{sequence[i:i+2]}"</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">range</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">ser_data</span><span class="op">.</span><span class="nam">columns</span><span class="op">)</span><span class="op">)</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t143" href="#t143">143</a></span><span class="t">        <span class="key">else</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t144" href="#t144">144</a></span><span class="t">            <span class="nam">labels</span> <span class="op">=</span> <span class="op">[</span><span class="str">f"{i+1}_{self.sequence[i:i+2]}"</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t145" href="#t145">145</a></span><span class="t">        <span class="nam">ser_data</span><span class="op">.</span><span class="nam">columns</span> <span class="op">=</span> <span class="nam">labels</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t146" href="#t146">146</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t147" href="#t147">147</a></span><span class="t">        <span class="com"># make matrix</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t148" href="#t148">148</a></span><span class="t">        <span class="nam">corr_data</span> <span class="op">=</span> <span class="nam">ser_data</span><span class="op">.</span><span class="nam">corr</span><span class="op">(</span><span class="nam">method</span><span class="op">=</span><span class="nam">self</span><span class="op">.</span><span class="nam">method</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t149" href="#t149">149</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t150" href="#t150">150</a></span><span class="t">        <span class="com"># save csv data</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t151" href="#t151">151</a></span><span class="t">        <span class="nam">corr_data</span><span class="op">.</span><span class="nam">to_csv</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">"out"</span><span class="op">]</span><span class="op">[</span><span class="str">"output_csv_path"</span><span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t152" href="#t152">152</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t153" href="#t153">153</a></span><span class="t">        <span class="com"># create heatmap</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t154" href="#t154">154</a></span><span class="t">        <span class="nam">fig</span><span class="op">,</span> <span class="nam">axs</span> <span class="op">=</span> <span class="nam">plt</span><span class="op">.</span><span class="nam">subplots</span><span class="op">(</span><span class="num">1</span><span class="op">,</span> <span class="num">1</span><span class="op">,</span> <span class="nam">dpi</span><span class="op">=</span><span class="num">300</span><span class="op">,</span> <span class="nam">tight_layout</span><span class="op">=</span><span class="key">True</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t155" href="#t155">155</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">pcolor</span><span class="op">(</span><span class="nam">corr_data</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t156" href="#t156">156</a></span><span class="t">        <span class="com"># Loop over data dimensions and create text annotations.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t157" href="#t157">157</a></span><span class="t">        <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">range</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">corr_data</span><span class="op">)</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t158" href="#t158">158</a></span><span class="t">            <span class="key">for</span> <span class="nam">j</span> <span class="key">in</span> <span class="nam">range</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">corr_data</span><span class="op">)</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t159" href="#t159">159</a></span><span class="t">                <span class="nam">axs</span><span class="op">.</span><span class="nam">text</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t160" href="#t160">160</a></span><span class="t">                    <span class="nam">j</span><span class="op">+</span><span class="num">.5</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t161" href="#t161">161</a></span><span class="t">                    <span class="nam">i</span><span class="op">+</span><span class="num">.5</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t162" href="#t162">162</a></span><span class="t">                    <span class="str">f"{corr_data[corr_data.columns[j]].iloc[i]:.2f}"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t163" href="#t163">163</a></span><span class="t">                    <span class="nam">ha</span><span class="op">=</span><span class="str">"center"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t164" href="#t164">164</a></span><span class="t">                    <span class="nam">va</span><span class="op">=</span><span class="str">"center"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t165" href="#t165">165</a></span><span class="t">                    <span class="nam">color</span><span class="op">=</span><span class="str">"w"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t166" href="#t166">166</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_xticks</span><span class="op">(</span><span class="op">[</span><span class="nam">i</span> <span class="op">+</span> <span class="num">0.5</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">range</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">corr_data</span><span class="op">)</span><span class="op">)</span><span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t167" href="#t167">167</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_xticklabels</span><span class="op">(</span><span class="nam">labels</span><span class="op">,</span> <span class="nam">rotation</span><span class="op">=</span><span class="num">90</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t168" href="#t168">168</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_yticks</span><span class="op">(</span><span class="op">[</span><span class="nam">i</span> <span class="op">+</span> <span class="num">0.5</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">range</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">corr_data</span><span class="op">)</span><span class="op">)</span><span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t169" href="#t169">169</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_yticklabels</span><span class="op">(</span><span class="nam">labels</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t170" href="#t170">170</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_title</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t171" href="#t171">171</a></span><span class="t">            <span class="str">"Base Pair Correlation "</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t172" href="#t172">172</a></span><span class="t">            <span class="str">f"for Helical Parameter \'{self.helpar_name}\'"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t173" href="#t173">173</a></span><span class="t">        <span class="nam">fig</span><span class="op">.</span><span class="nam">tight_layout</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t174" href="#t174">174</a></span><span class="t">        <span class="nam">fig</span><span class="op">.</span><span class="nam">savefig</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t175" href="#t175">175</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'out'</span><span class="op">]</span><span class="op">[</span><span class="str">'output_jpg_path'</span><span class="op">]</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t176" href="#t176">176</a></span><span class="t">            <span class="nam">format</span><span class="op">=</span><span class="str">"jpg"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t177" href="#t177">177</a></span><span class="t">        <span class="nam">plt</span><span class="op">.</span><span class="nam">close</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t178" href="#t178">178</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t179" href="#t179">179</a></span><span class="t">        <span class="com"># Remove temporary file(s)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t180" href="#t180">180</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_files</span><span class="op">.</span><span class="nam">extend</span><span class="op">(</span><span class="op">[</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t181" href="#t181">181</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"unique_dir"</span><span class="op">)</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t182" href="#t182">182</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t183" href="#t183">183</a></span><span class="t">        <span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t184" href="#t184">184</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">remove_tmp_files</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t185" href="#t185">185</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t186" href="#t186">186</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_arguments</span><span class="op">(</span><span class="nam">output_files_created</span><span class="op">=</span><span class="key">True</span><span class="op">,</span> <span class="nam">raise_exception</span><span class="op">=</span><span class="key">False</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t187" href="#t187">187</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t188" href="#t188">188</a></span><span class="t">        <span class="key">return</span> <span class="num">0</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t189" href="#t189">189</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t190" href="#t190">190</a></span><span class="t">    <span class="op">@</span><span class="nam">staticmethod</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t191" href="#t191">191</a></span><span class="t">    <span class="key">def</span> <span class="nam">circular</span><span class="op">(</span><span class="nam">x1</span><span class="op">,</span> <span class="nam">x2</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t192" href="#t192">192</a></span><span class="t">        <span class="nam">x1</span> <span class="op">=</span> <span class="nam">x1</span> <span class="op">*</span> <span class="nam">np</span><span class="op">.</span><span class="nam">pi</span> <span class="op">/</span> <span class="num">180</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t193" href="#t193">193</a></span><span class="t">        <span class="nam">x2</span> <span class="op">=</span> <span class="nam">x2</span> <span class="op">*</span> <span class="nam">np</span><span class="op">.</span><span class="nam">pi</span> <span class="op">/</span> <span class="num">180</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t194" href="#t194">194</a></span><span class="t">        <span class="nam">diff_1</span> <span class="op">=</span> <span class="nam">np</span><span class="op">.</span><span class="nam">sin</span><span class="op">(</span><span class="nam">x1</span> <span class="op">-</span> <span class="nam">x1</span><span class="op">.</span><span class="nam">mean</span><span class="op">(</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t195" href="#t195">195</a></span><span class="t">        <span class="nam">diff_2</span> <span class="op">=</span> <span class="nam">np</span><span class="op">.</span><span class="nam">sin</span><span class="op">(</span><span class="nam">x2</span> <span class="op">-</span> <span class="nam">x2</span><span class="op">.</span><span class="nam">mean</span><span class="op">(</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t196" href="#t196">196</a></span><span class="t">        <span class="nam">num</span> <span class="op">=</span> <span class="op">(</span><span class="nam">diff_1</span> <span class="op">*</span> <span class="nam">diff_2</span><span class="op">)</span><span class="op">.</span><span class="nam">sum</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t197" href="#t197">197</a></span><span class="t">        <span class="nam">den</span> <span class="op">=</span> <span class="nam">np</span><span class="op">.</span><span class="nam">sqrt</span><span class="op">(</span><span class="op">(</span><span class="nam">diff_1</span> <span class="op">**</span> <span class="num">2</span><span class="op">)</span><span class="op">.</span><span class="nam">sum</span><span class="op">(</span><span class="op">)</span> <span class="op">*</span> <span class="op">(</span><span class="nam">diff_2</span> <span class="op">**</span> <span class="num">2</span><span class="op">)</span><span class="op">.</span><span class="nam">sum</span><span class="op">(</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t198" href="#t198">198</a></span><span class="t">        <span class="key">return</span> <span class="nam">num</span> <span class="op">/</span> <span class="nam">den</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t199" href="#t199">199</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t200" href="#t200">200</a></span><span class="t"><span class="key">def</span> <span class="nam">interseqcorr</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t201" href="#t201">201</a></span><span class="t">        <span class="nam">input_ser_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t202" href="#t202">202</a></span><span class="t">        <span class="nam">output_csv_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span> <span class="nam">output_jpg_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t203" href="#t203">203</a></span><span class="t">        <span class="nam">properties</span><span class="op">:</span> <span class="nam">dict</span> <span class="op">=</span> <span class="key">None</span><span class="op">,</span> <span class="op">**</span><span class="nam">kwargs</span><span class="op">)</span> <span class="op">-></span> <span class="nam">int</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t204" href="#t204">204</a></span><span class="t">    <span class="str">"""Create :class:`HelParCorrelation &lt;interbp_correlations.interseqcorr.InterSequenceCorrelation>` class and</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t205" href="#t205">205</a></span><span class="t"><span class="str">    execute the :meth:`launch() &lt;interbp_correlations.interseqcorr.InterSequenceCorrelation.launch>` method."""</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t206" href="#t206">206</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t207" href="#t207">207</a></span><span class="t">    <span class="key">return</span> <span class="nam">InterSequenceCorrelation</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t208" href="#t208">208</a></span><span class="t">        <span class="nam">input_ser_path</span><span class="op">=</span><span class="nam">input_ser_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t209" href="#t209">209</a></span><span class="t">        <span class="nam">output_csv_path</span><span class="op">=</span><span class="nam">output_csv_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t210" href="#t210">210</a></span><span class="t">        <span class="nam">output_jpg_path</span><span class="op">=</span><span class="nam">output_jpg_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t211" href="#t211">211</a></span><span class="t">        <span class="nam">properties</span><span class="op">=</span><span class="nam">properties</span><span class="op">,</span> <span class="op">**</span><span class="nam">kwargs</span><span class="op">)</span><span class="op">.</span><span class="nam">launch</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t212" href="#t212">212</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t200" href="#t200">200</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t201" href="#t201">201</a></span><span class="t"><span class="key">def</span> <span class="nam">interseqcorr</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t202" href="#t202">202</a></span><span class="t">        <span class="nam">input_ser_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t203" href="#t203">203</a></span><span class="t">        <span class="nam">output_csv_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span> <span class="nam">output_jpg_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t204" href="#t204">204</a></span><span class="t">        <span class="nam">properties</span><span class="op">:</span> <span class="nam">dict</span> <span class="op">=</span> <span class="key">None</span><span class="op">,</span> <span class="op">**</span><span class="nam">kwargs</span><span class="op">)</span> <span class="op">-></span> <span class="nam">int</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t205" href="#t205">205</a></span><span class="t">    <span class="str">"""Create :class:`HelParCorrelation &lt;interbp_correlations.interseqcorr.InterSequenceCorrelation>` class and</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t206" href="#t206">206</a></span><span class="t"><span class="str">    execute the :meth:`launch() &lt;interbp_correlations.interseqcorr.InterSequenceCorrelation.launch>` method."""</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t207" href="#t207">207</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t208" href="#t208">208</a></span><span class="t">    <span class="key">return</span> <span class="nam">InterSequenceCorrelation</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t209" href="#t209">209</a></span><span class="t">        <span class="nam">input_ser_path</span><span class="op">=</span><span class="nam">input_ser_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t210" href="#t210">210</a></span><span class="t">        <span class="nam">output_csv_path</span><span class="op">=</span><span class="nam">output_csv_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t211" href="#t211">211</a></span><span class="t">        <span class="nam">output_jpg_path</span><span class="op">=</span><span class="nam">output_jpg_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t212" href="#t212">212</a></span><span class="t">        <span class="nam">properties</span><span class="op">=</span><span class="nam">properties</span><span class="op">,</span> <span class="op">**</span><span class="nam">kwargs</span><span class="op">)</span><span class="op">.</span><span class="nam">launch</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t213" href="#t213">213</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t214" href="#t214">214</a></span><span class="t"><span class="key">def</span> <span class="nam">main</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t215" href="#t215">215</a></span><span class="t">    <span class="str">"""Command line execution of this building block. Please check the command line documentation."""</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t216" href="#t216">216</a></span><span class="t">    <span class="nam">parser</span> <span class="op">=</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">ArgumentParser</span><span class="op">(</span><span class="nam">description</span><span class="op">=</span><span class="str">'Load .ser file from Canal output and calculate correlation between base pairs of the corresponding sequence.'</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t217" href="#t217">217</a></span><span class="t">                                     <span class="nam">formatter_class</span><span class="op">=</span><span class="key">lambda</span> <span class="nam">prog</span><span class="op">:</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">RawTextHelpFormatter</span><span class="op">(</span><span class="nam">prog</span><span class="op">,</span> <span class="nam">width</span><span class="op">=</span><span class="num">99999</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t218" href="#t218">218</a></span><span class="t">    <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--config'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">False</span><span class="op">,</span> <span class="nam">help</span><span class="op">=</span><span class="str">'Configuration file'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t219" href="#t219">219</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t220" href="#t220">220</a></span><span class="t">    <span class="nam">required_args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument_group</span><span class="op">(</span><span class="str">'required arguments'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t221" href="#t221">221</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--input_ser_path'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t222" href="#t222">222</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Path to ser file with inputs. Accepted formats: ser.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t223" href="#t223">223</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--output_csv_path'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t224" href="#t224">224</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Path to output file. Accepted formats: csv.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t225" href="#t225">225</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--output_jpg_path'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t226" href="#t226">226</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Path to output plot. Accepted formats: jpg.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t227" href="#t227">227</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t228" href="#t228">228</a></span><span class="t">    <span class="nam">args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">parse_args</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t229" href="#t229">229</a></span><span class="t">    <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="op">=</span> <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="key">or</span> <span class="str">"{}"</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t230" href="#t230">230</a></span><span class="t">    <span class="nam">properties</span> <span class="op">=</span> <span class="nam">settings</span><span class="op">.</span><span class="nam">ConfReader</span><span class="op">(</span><span class="nam">config</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">config</span><span class="op">)</span><span class="op">.</span><span class="nam">get_prop_dic</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t231" href="#t231">231</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t232" href="#t232">232</a></span><span class="t">    <span class="nam">interseqcorr</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t233" href="#t233">233</a></span><span class="t">        <span class="nam">input_ser_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_ser_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t234" href="#t234">234</a></span><span class="t">        <span class="nam">output_csv_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">output_csv_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t235" href="#t235">235</a></span><span class="t">        <span class="nam">output_jpg_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">output_jpg_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t236" href="#t236">236</a></span><span class="t">        <span class="nam">properties</span><span class="op">=</span><span class="nam">properties</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t237" href="#t237">237</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t214" href="#t214">214</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t215" href="#t215">215</a></span><span class="t"><span class="key">def</span> <span class="nam">main</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t216" href="#t216">216</a></span><span class="t">    <span class="str">"""Command line execution of this building block. Please check the command line documentation."""</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t217" href="#t217">217</a></span><span class="t">    <span class="nam">parser</span> <span class="op">=</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">ArgumentParser</span><span class="op">(</span><span class="nam">description</span><span class="op">=</span><span class="str">'Load .ser file from Canal output and calculate correlation between base pairs of the corresponding sequence.'</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t218" href="#t218">218</a></span><span class="t">                                     <span class="nam">formatter_class</span><span class="op">=</span><span class="key">lambda</span> <span class="nam">prog</span><span class="op">:</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">RawTextHelpFormatter</span><span class="op">(</span><span class="nam">prog</span><span class="op">,</span> <span class="nam">width</span><span class="op">=</span><span class="num">99999</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t219" href="#t219">219</a></span><span class="t">    <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--config'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">False</span><span class="op">,</span> <span class="nam">help</span><span class="op">=</span><span class="str">'Configuration file'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t220" href="#t220">220</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t221" href="#t221">221</a></span><span class="t">    <span class="nam">required_args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument_group</span><span class="op">(</span><span class="str">'required arguments'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t222" href="#t222">222</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--input_ser_path'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t223" href="#t223">223</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Path to ser file with inputs. Accepted formats: ser.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t224" href="#t224">224</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--output_csv_path'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t225" href="#t225">225</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Path to output file. Accepted formats: csv.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t226" href="#t226">226</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--output_jpg_path'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t227" href="#t227">227</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Path to output plot. Accepted formats: jpg.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t228" href="#t228">228</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t229" href="#t229">229</a></span><span class="t">    <span class="nam">args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">parse_args</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t230" href="#t230">230</a></span><span class="t">    <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="op">=</span> <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="key">or</span> <span class="str">"{}"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t231" href="#t231">231</a></span><span class="t">    <span class="nam">properties</span> <span class="op">=</span> <span class="nam">settings</span><span class="op">.</span><span class="nam">ConfReader</span><span class="op">(</span><span class="nam">config</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">config</span><span class="op">)</span><span class="op">.</span><span class="nam">get_prop_dic</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t232" href="#t232">232</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t233" href="#t233">233</a></span><span class="t">    <span class="nam">interseqcorr</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t234" href="#t234">234</a></span><span class="t">        <span class="nam">input_ser_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_ser_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t235" href="#t235">235</a></span><span class="t">        <span class="nam">output_csv_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">output_csv_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t236" href="#t236">236</a></span><span class="t">        <span class="nam">output_jpg_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">output_jpg_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t237" href="#t237">237</a></span><span class="t">        <span class="nam">properties</span><span class="op">=</span><span class="nam">properties</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t238" href="#t238">238</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t239" href="#t239">239</a></span><span class="t"><span class="key">if</span> <span class="nam">__name__</span> <span class="op">==</span> <span class="str">'__main__'</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t240" href="#t240">240</a></span><span class="t">    <span class="nam">main</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t239" href="#t239">239</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t240" href="#t240">240</a></span><span class="t"><span class="key">if</span> <span class="nam">__name__</span> <span class="op">==</span> <span class="str">'__main__'</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t241" href="#t241">241</a></span><span class="t">    <span class="nam">main</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
 </main>
 <footer>
     <div class="content">
@@ -329,7 +330,7 @@ <h2>
             <a class="nav" href="z_64e03be4370b7ecc___init___py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.5.1">coverage.py v7.5.1</a>,
-            created at 2024-05-07 09:06 +0000
+            created at 2024-05-24 09:29 +0000
         </p>
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 </footer>
diff --git a/coverage/z_957b841f7413f0a1___init___py.html b/coverage/z_957b841f7413f0a1___init___py.html
index efe71e04..0c3ae7ce 100644
--- a/coverage/z_957b841f7413f0a1___init___py.html
+++ b/coverage/z_957b841f7413f0a1___init___py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_020f76a90aa51c7b_test_bipopulations_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
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-            created at 2024-05-07 09:06 +0000
+            created at 2024-05-24 09:29 +0000
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         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -89,7 +89,7 @@ <h2>
             <a class="nav" href="z_020f76a90aa51c7b_test_bipopulations_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.5.1">coverage.py v7.5.1</a>,
-            created at 2024-05-07 09:06 +0000
+            created at 2024-05-24 09:29 +0000
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 </footer>
diff --git a/coverage/z_97f47455ed834d2d_test_correlation_py.html b/coverage/z_97f47455ed834d2d_test_correlation_py.html
index d63b7c53..9d599663 100644
--- a/coverage/z_97f47455ed834d2d_test_correlation_py.html
+++ b/coverage/z_97f47455ed834d2d_test_correlation_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_8030ef0ea5bfd6aa_test_canal_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
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-            created at 2024-05-07 09:06 +0000
+            created at 2024-05-24 09:29 +0000
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         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -207,7 +207,7 @@ <h2>
             <a class="nav" href="z_8030ef0ea5bfd6aa_test_canal_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
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-            created at 2024-05-07 09:06 +0000
+            created at 2024-05-24 09:29 +0000
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index e273fef5..5df94620 100644
--- a/coverage/z_9de9475b0a6fab52___init___py.html
+++ b/coverage/z_9de9475b0a6fab52___init___py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_9de9475b0a6fab52_average_stiffness_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
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-            created at 2024-05-07 09:06 +0000
+            created at 2024-05-24 09:29 +0000
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@@ -102,226 +102,227 @@ <h2>
     <p class="pln"><span class="n"><a id="t20" href="#t20">20</a></span><span class="t">    <span class="str">"""</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t21" href="#t21">21</a></span><span class="t"><span class="str">    | biobb_dna AverageStiffness</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t22" href="#t22">22</a></span><span class="t"><span class="str">    | Calculate average stiffness constants for each base pair of a trajectory's series.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t23" href="#t23">23</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t24" href="#t24">24</a></span><span class="t"><span class="str">    Args:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t25" href="#t25">25</a></span><span class="t"><span class="str">        input_ser_path (str): Path to .ser file for helical parameter. File is expected to be a table, with the first column being an index and the rest the helical parameter values for each base/basepair. File type: input. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/stiffness/canal_output_roll.ser>`_. Accepted formats: ser (edam:format_2330).</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t26" href="#t26">26</a></span><span class="t"><span class="str">        output_csv_path (str): Path to .csv file where output is saved. File type: output. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/reference/stiffness/stiffavg_roll.csv>`_. Accepted formats: csv (edam:format_3752).</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t27" href="#t27">27</a></span><span class="t"><span class="str">        output_jpg_path (str): Path to .jpg file where output is saved. File type: output. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/reference/stiffness/stiffavg_roll.jpg>`_. Accepted formats: jpg (edam:format_3579).</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t28" href="#t28">28</a></span><span class="t"><span class="str">        properties (dict):</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t29" href="#t29">29</a></span><span class="t"><span class="str">            * **KT** (*float*) - (0.592186827) Value of Boltzmann temperature factor.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t30" href="#t30">30</a></span><span class="t"><span class="str">            * **sequence** (*str*) - (None) Nucleic acid sequence corresponding to the input .ser file. Length of sequence is expected to be the same as the total number of columns in the .ser file, minus the index column (even if later on a subset of columns is selected with the *usecols* option).</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t31" href="#t31">31</a></span><span class="t"><span class="str">            * **helpar_name** (*str*) - (None) helical parameter name.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t32" href="#t32">32</a></span><span class="t"><span class="str">            * **seqpos** (*list*) - (None) list of sequence positions (columns indices starting by 0) to analyze.  If not specified it will analyse the complete sequence.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t33" href="#t33">33</a></span><span class="t"><span class="str">            * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t34" href="#t34">34</a></span><span class="t"><span class="str">            * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t35" href="#t35">35</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t36" href="#t36">36</a></span><span class="t"><span class="str">    Examples:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t37" href="#t37">37</a></span><span class="t"><span class="str">        This is a use example of how to use the building block from Python::</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t38" href="#t38">38</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t39" href="#t39">39</a></span><span class="t"><span class="str">            from biobb_dna.stiffness.average_stiffness import average_stiffness</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t40" href="#t40">40</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t41" href="#t41">41</a></span><span class="t"><span class="str">            prop = {</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t42" href="#t42">42</a></span><span class="t"><span class="str">                'helpar_name': 'twist',</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t43" href="#t43">43</a></span><span class="t"><span class="str">                'sequence': 'GCAT',</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t44" href="#t44">44</a></span><span class="t"><span class="str">            }</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t45" href="#t45">45</a></span><span class="t"><span class="str">            average_stiffness(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t46" href="#t46">46</a></span><span class="t"><span class="str">                input_ser_path='/path/to/twist.ser',</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t47" href="#t47">47</a></span><span class="t"><span class="str">                output_csv_path='/path/to/table/output.csv',</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t48" href="#t48">48</a></span><span class="t"><span class="str">                output_jpg_path='/path/to/table/output.jpg',</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t49" href="#t49">49</a></span><span class="t"><span class="str">                properties=prop)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t50" href="#t50">50</a></span><span class="t"><span class="str">    Info:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t51" href="#t51">51</a></span><span class="t"><span class="str">        * wrapped_software:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t52" href="#t52">52</a></span><span class="t"><span class="str">            * name: In house</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t53" href="#t53">53</a></span><span class="t"><span class="str">            * license: Apache-2.0</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t54" href="#t54">54</a></span><span class="t"><span class="str">        * ontology:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t55" href="#t55">55</a></span><span class="t"><span class="str">            * name: EDAM</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t56" href="#t56">56</a></span><span class="t"><span class="str">            * schema: http://edamontology.org/EDAM.owl</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t57" href="#t57">57</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t58" href="#t58">58</a></span><span class="t"><span class="str">    """</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t59" href="#t59">59</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t60" href="#t60">60</a></span><span class="t">    <span class="key">def</span> <span class="nam">__init__</span><span class="op">(</span><span class="nam">self</span><span class="op">,</span> <span class="nam">input_ser_path</span><span class="op">,</span> <span class="nam">output_csv_path</span><span class="op">,</span> <span class="nam">output_jpg_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t61" href="#t61">61</a></span><span class="t">                 <span class="nam">properties</span><span class="op">=</span><span class="key">None</span><span class="op">,</span> <span class="op">**</span><span class="nam">kwargs</span><span class="op">)</span> <span class="op">-></span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t62" href="#t62">62</a></span><span class="t">        <span class="nam">properties</span> <span class="op">=</span> <span class="nam">properties</span> <span class="key">or</span> <span class="op">{</span><span class="op">}</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t63" href="#t63">63</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t64" href="#t64">64</a></span><span class="t">        <span class="com"># Call parent class constructor</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t65" href="#t65">65</a></span><span class="t">        <span class="nam">super</span><span class="op">(</span><span class="op">)</span><span class="op">.</span><span class="nam">__init__</span><span class="op">(</span><span class="nam">properties</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t66" href="#t66">66</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">locals_var_dict</span> <span class="op">=</span> <span class="nam">locals</span><span class="op">(</span><span class="op">)</span><span class="op">.</span><span class="nam">copy</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t67" href="#t67">67</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t68" href="#t68">68</a></span><span class="t">        <span class="com"># Input/Output files</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t69" href="#t69">69</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span> <span class="op">=</span> <span class="op">{</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t70" href="#t70">70</a></span><span class="t">            <span class="str">'in'</span><span class="op">:</span> <span class="op">{</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t71" href="#t71">71</a></span><span class="t">                <span class="str">'input_ser_path'</span><span class="op">:</span> <span class="nam">input_ser_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t72" href="#t72">72</a></span><span class="t">            <span class="op">}</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t73" href="#t73">73</a></span><span class="t">            <span class="str">'out'</span><span class="op">:</span> <span class="op">{</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t74" href="#t74">74</a></span><span class="t">                <span class="str">'output_csv_path'</span><span class="op">:</span> <span class="nam">output_csv_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t75" href="#t75">75</a></span><span class="t">                <span class="str">'output_jpg_path'</span><span class="op">:</span> <span class="nam">output_jpg_path</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t76" href="#t76">76</a></span><span class="t">            <span class="op">}</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t77" href="#t77">77</a></span><span class="t">        <span class="op">}</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t78" href="#t78">78</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t79" href="#t79">79</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">properties</span> <span class="op">=</span> <span class="nam">properties</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t80" href="#t80">80</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"sequence"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t81" href="#t81">81</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">KT</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t82" href="#t82">82</a></span><span class="t">            <span class="str">"KT"</span><span class="op">,</span> <span class="num">0.592186827</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t83" href="#t83">83</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"seqpos"</span><span class="op">,</span> <span class="key">None</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t84" href="#t84">84</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">helpar_name</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"helpar_name"</span><span class="op">,</span> <span class="key">None</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t85" href="#t85">85</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t86" href="#t86">86</a></span><span class="t">        <span class="com"># Check the properties</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t87" href="#t87">87</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_properties</span><span class="op">(</span><span class="nam">properties</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t88" href="#t88">88</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_arguments</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t89" href="#t89">89</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t90" href="#t90">90</a></span><span class="t">    <span class="op">@</span><span class="nam">launchlogger</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t91" href="#t91">91</a></span><span class="t">    <span class="key">def</span> <span class="nam">launch</span><span class="op">(</span><span class="nam">self</span><span class="op">)</span> <span class="op">-></span> <span class="nam">int</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t92" href="#t92">92</a></span><span class="t">        <span class="str">"""Execute the :class:`AverageStiffness &lt;stiffness.average_stiffness.AverageStiffness>` object."""</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t93" href="#t93">93</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t94" href="#t94">94</a></span><span class="t">        <span class="com"># Setup Biobb</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t95" href="#t95">95</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">check_restart</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t96" href="#t96">96</a></span><span class="t">            <span class="key">return</span> <span class="num">0</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t97" href="#t97">97</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">stage_files</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t98" href="#t98">98</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t99" href="#t99">99</a></span><span class="t">        <span class="com"># check sequence</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t100" href="#t100">100</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span> <span class="key">is</span> <span class="key">None</span> <span class="key">or</span> <span class="nam">len</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span><span class="op">)</span> <span class="op">&lt;</span> <span class="num">2</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t101" href="#t101">101</a></span><span class="t">            <span class="key">raise</span> <span class="nam">ValueError</span><span class="op">(</span><span class="str">"sequence is null or too short!"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t102" href="#t102">102</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t103" href="#t103">103</a></span><span class="t">        <span class="com"># get helical parameter from filename if not specified</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t104" href="#t104">104</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">helpar_name</span> <span class="key">is</span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t105" href="#t105">105</a></span><span class="t">            <span class="key">for</span> <span class="nam">hp</span> <span class="key">in</span> <span class="nam">constants</span><span class="op">.</span><span class="nam">helical_parameters</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t106" href="#t106">106</a></span><span class="t">                <span class="key">if</span> <span class="nam">hp</span><span class="op">.</span><span class="nam">lower</span><span class="op">(</span><span class="op">)</span> <span class="key">in</span> <span class="nam">Path</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t107" href="#t107">107</a></span><span class="t">                        <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'input_ser_path'</span><span class="op">]</span><span class="op">)</span><span class="op">.</span><span class="nam">name</span><span class="op">.</span><span class="nam">lower</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t108" href="#t108">108</a></span><span class="t">                    <span class="nam">self</span><span class="op">.</span><span class="nam">helpar_name</span> <span class="op">=</span> <span class="nam">hp</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t109" href="#t109">109</a></span><span class="t">            <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">helpar_name</span> <span class="key">is</span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t110" href="#t110">110</a></span><span class="t">                <span class="key">raise</span> <span class="nam">ValueError</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t111" href="#t111">111</a></span><span class="t">                    <span class="str">"Helical parameter name can't be inferred from file, "</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t112" href="#t112">112</a></span><span class="t">                    <span class="str">"so it must be specified!"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t113" href="#t113">113</a></span><span class="t">        <span class="key">else</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t114" href="#t114">114</a></span><span class="t">            <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">helpar_name</span> <span class="key">not</span> <span class="key">in</span> <span class="nam">constants</span><span class="op">.</span><span class="nam">helical_parameters</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t115" href="#t115">115</a></span><span class="t">                <span class="key">raise</span> <span class="nam">ValueError</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t116" href="#t116">116</a></span><span class="t">                    <span class="str">"Helical parameter name is invalid! "</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t117" href="#t117">117</a></span><span class="t">                    <span class="str">f"Options: {constants.helical_parameters}"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t118" href="#t118">118</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t119" href="#t119">119</a></span><span class="t">        <span class="com"># get base length and unit from helical parameter name</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t120" href="#t120">120</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">helpar_name</span><span class="op">.</span><span class="nam">lower</span><span class="op">(</span><span class="op">)</span> <span class="key">in</span> <span class="op">[</span><span class="str">"roll"</span><span class="op">,</span> <span class="str">"tilt"</span><span class="op">,</span> <span class="str">"twist"</span><span class="op">]</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t121" href="#t121">121</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">hp_unit</span> <span class="op">=</span> <span class="str">"kcal/(mol*degree&#178;)"</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t122" href="#t122">122</a></span><span class="t">            <span class="nam">scale</span> <span class="op">=</span> <span class="num">1</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t123" href="#t123">123</a></span><span class="t">        <span class="key">else</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t124" href="#t124">124</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">hp_unit</span> <span class="op">=</span> <span class="str">"kcal/(mol*&#197;&#178;)"</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t125" href="#t125">125</a></span><span class="t">            <span class="nam">scale</span> <span class="op">=</span> <span class="num">10.6</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t126" href="#t126">126</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t127" href="#t127">127</a></span><span class="t">        <span class="com"># check seqpos</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t128" href="#t128">128</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span> <span class="key">is</span> <span class="key">not</span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t129" href="#t129">129</a></span><span class="t">            <span class="key">if</span> <span class="op">(</span><span class="nam">max</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">)</span> <span class="op">></span> <span class="nam">len</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span><span class="op">)</span> <span class="op">-</span> <span class="num">2</span><span class="op">)</span> <span class="key">or</span> <span class="op">(</span><span class="nam">min</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">)</span> <span class="op">&lt;</span> <span class="num">1</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t130" href="#t130">130</a></span><span class="t">                <span class="key">raise</span> <span class="nam">ValueError</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t131" href="#t131">131</a></span><span class="t">                    <span class="str">f"seqpos values must be between 1 and {len(self.sequence) - 2}"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t132" href="#t132">132</a></span><span class="t">            <span class="key">if</span> <span class="key">not</span> <span class="op">(</span><span class="nam">isinstance</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">,</span> <span class="nam">list</span><span class="op">)</span> <span class="key">and</span> <span class="nam">len</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">)</span> <span class="op">></span> <span class="num">1</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t133" href="#t133">133</a></span><span class="t">                <span class="key">raise</span> <span class="nam">ValueError</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t134" href="#t134">134</a></span><span class="t">                    <span class="str">"seqpos must be a list of at least two integers"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t135" href="#t135">135</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t136" href="#t136">136</a></span><span class="t">        <span class="com"># Creating temporary folder</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t137" href="#t137">137</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span> <span class="op">=</span> <span class="nam">fu</span><span class="op">.</span><span class="nam">create_unique_dir</span><span class="op">(</span><span class="nam">prefix</span><span class="op">=</span><span class="str">"avgstiffness_"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t138" href="#t138">138</a></span><span class="t">        <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="str">'Creating %s temporary folder'</span> <span class="op">%</span> <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t139" href="#t139">139</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t140" href="#t140">140</a></span><span class="t">        <span class="com"># Copy input_file_path1 to temporary folder</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t141" href="#t141">141</a></span><span class="t">        <span class="nam">shutil</span><span class="op">.</span><span class="nam">copy</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'input_ser_path'</span><span class="op">]</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t142" href="#t142">142</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t143" href="#t143">143</a></span><span class="t">        <span class="com"># read input .ser file</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t144" href="#t144">144</a></span><span class="t">        <span class="nam">ser_data</span> <span class="op">=</span> <span class="nam">read_series</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t145" href="#t145">145</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'input_ser_path'</span><span class="op">]</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t146" href="#t146">146</a></span><span class="t">            <span class="nam">usecols</span><span class="op">=</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t147" href="#t147">147</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span> <span class="key">is</span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t148" href="#t148">148</a></span><span class="t">            <span class="nam">ser_data</span> <span class="op">=</span> <span class="nam">ser_data</span><span class="op">[</span><span class="nam">ser_data</span><span class="op">.</span><span class="nam">columns</span><span class="op">[</span><span class="num">1</span><span class="op">:</span><span class="op">-</span><span class="num">1</span><span class="op">]</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t149" href="#t149">149</a></span><span class="t">            <span class="com"># discard first and last base(pairs) from sequence</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t150" href="#t150">150</a></span><span class="t">            <span class="nam">sequence</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span><span class="op">[</span><span class="num">1</span><span class="op">:</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t151" href="#t151">151</a></span><span class="t">            <span class="nam">xlabels</span> <span class="op">=</span> <span class="op">[</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t152" href="#t152">152</a></span><span class="t">                <span class="str">f"{sequence[i:i+2]}"</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t153" href="#t153">153</a></span><span class="t">                <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">range</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">ser_data</span><span class="op">.</span><span class="nam">columns</span><span class="op">)</span><span class="op">)</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t154" href="#t154">154</a></span><span class="t">        <span class="key">else</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t155" href="#t155">155</a></span><span class="t">            <span class="nam">sequence</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t156" href="#t156">156</a></span><span class="t">            <span class="nam">xlabels</span> <span class="op">=</span> <span class="op">[</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t157" href="#t157">157</a></span><span class="t">                <span class="str">f"{sequence[i:i+2]}"</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t158" href="#t158">158</a></span><span class="t">                <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t159" href="#t159">159</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t160" href="#t160">160</a></span><span class="t">        <span class="com"># calculate average stiffness</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t161" href="#t161">161</a></span><span class="t">        <span class="nam">cov</span> <span class="op">=</span> <span class="nam">ser_data</span><span class="op">.</span><span class="nam">cov</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t162" href="#t162">162</a></span><span class="t">        <span class="nam">stiff</span> <span class="op">=</span> <span class="nam">np</span><span class="op">.</span><span class="nam">linalg</span><span class="op">.</span><span class="nam">inv</span><span class="op">(</span><span class="nam">cov</span><span class="op">)</span> <span class="op">*</span> <span class="nam">self</span><span class="op">.</span><span class="nam">KT</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t163" href="#t163">163</a></span><span class="t">        <span class="nam">avg_stiffness</span> <span class="op">=</span> <span class="nam">np</span><span class="op">.</span><span class="nam">diag</span><span class="op">(</span><span class="nam">stiff</span><span class="op">)</span> <span class="op">*</span> <span class="nam">scale</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t164" href="#t164">164</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t165" href="#t165">165</a></span><span class="t">        <span class="com"># save plot</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t166" href="#t166">166</a></span><span class="t">        <span class="nam">fig</span><span class="op">,</span> <span class="nam">axs</span> <span class="op">=</span> <span class="nam">plt</span><span class="op">.</span><span class="nam">subplots</span><span class="op">(</span><span class="num">1</span><span class="op">,</span> <span class="num">1</span><span class="op">,</span> <span class="nam">dpi</span><span class="op">=</span><span class="num">300</span><span class="op">,</span> <span class="nam">tight_layout</span><span class="op">=</span><span class="key">True</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t167" href="#t167">167</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">plot</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t168" href="#t168">168</a></span><span class="t">            <span class="nam">range</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">xlabels</span><span class="op">)</span><span class="op">)</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t169" href="#t169">169</a></span><span class="t">            <span class="nam">avg_stiffness</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t170" href="#t170">170</a></span><span class="t">            <span class="str">"-o"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t171" href="#t171">171</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_xticks</span><span class="op">(</span><span class="nam">range</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">xlabels</span><span class="op">)</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t172" href="#t172">172</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_xticklabels</span><span class="op">(</span><span class="nam">xlabels</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t173" href="#t173">173</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_xlabel</span><span class="op">(</span><span class="str">"Sequence Base Pair"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t174" href="#t174">174</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_ylabel</span><span class="op">(</span><span class="str">f"{self.helpar_name.capitalize()} ({self.hp_unit})"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t175" href="#t175">175</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_title</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t176" href="#t176">176</a></span><span class="t">            <span class="str">"Base Pair Helical Parameter Stiffness: "</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t177" href="#t177">177</a></span><span class="t">            <span class="str">f"{self.helpar_name.capitalize()}"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t178" href="#t178">178</a></span><span class="t">        <span class="nam">fig</span><span class="op">.</span><span class="nam">savefig</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t179" href="#t179">179</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'out'</span><span class="op">]</span><span class="op">[</span><span class="str">'output_jpg_path'</span><span class="op">]</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t180" href="#t180">180</a></span><span class="t">            <span class="nam">format</span><span class="op">=</span><span class="str">"jpg"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t181" href="#t181">181</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t182" href="#t182">182</a></span><span class="t">        <span class="com"># save table</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t183" href="#t183">183</a></span><span class="t">        <span class="nam">dataset</span> <span class="op">=</span> <span class="nam">pd</span><span class="op">.</span><span class="nam">DataFrame</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t184" href="#t184">184</a></span><span class="t">            <span class="nam">data</span><span class="op">=</span><span class="nam">avg_stiffness</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t185" href="#t185">185</a></span><span class="t">            <span class="nam">index</span><span class="op">=</span><span class="nam">xlabels</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t186" href="#t186">186</a></span><span class="t">            <span class="nam">columns</span><span class="op">=</span><span class="op">[</span><span class="str">f"{self.helpar_name}_stiffness"</span><span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t187" href="#t187">187</a></span><span class="t">        <span class="nam">dataset</span><span class="op">.</span><span class="nam">to_csv</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'out'</span><span class="op">]</span><span class="op">[</span><span class="str">'output_csv_path'</span><span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t188" href="#t188">188</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t189" href="#t189">189</a></span><span class="t">        <span class="nam">plt</span><span class="op">.</span><span class="nam">close</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t190" href="#t190">190</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t191" href="#t191">191</a></span><span class="t">        <span class="com"># Remove temporary file(s)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t192" href="#t192">192</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_files</span><span class="op">.</span><span class="nam">extend</span><span class="op">(</span><span class="op">[</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t193" href="#t193">193</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"unique_dir"</span><span class="op">)</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t194" href="#t194">194</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t195" href="#t195">195</a></span><span class="t">        <span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t196" href="#t196">196</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">remove_tmp_files</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t197" href="#t197">197</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t198" href="#t198">198</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_arguments</span><span class="op">(</span><span class="nam">output_files_created</span><span class="op">=</span><span class="key">True</span><span class="op">,</span> <span class="nam">raise_exception</span><span class="op">=</span><span class="key">False</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t199" href="#t199">199</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t200" href="#t200">200</a></span><span class="t">        <span class="key">return</span> <span class="num">0</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t201" href="#t201">201</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t23" href="#t23">23</a></span><span class="t"><span class="str">    | Calculate the average stiffness constants for each base pair of a trajectory's series. The input is a .ser file with the helical parameter values for each base/basepair. The output is a .csv file with the average stiffness constants for each base pair and a .jpg file with a plot of the average stiffness constants for each base pair.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t24" href="#t24">24</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t25" href="#t25">25</a></span><span class="t"><span class="str">    Args:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t26" href="#t26">26</a></span><span class="t"><span class="str">        input_ser_path (str): Path to .ser file for helical parameter. File is expected to be a table, with the first column being an index and the rest the helical parameter values for each base/basepair. File type: input. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/stiffness/canal_output_roll.ser>`_. Accepted formats: ser (edam:format_2330).</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t27" href="#t27">27</a></span><span class="t"><span class="str">        output_csv_path (str): Path to .csv file where output is saved. File type: output. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/reference/stiffness/stiffavg_roll.csv>`_. Accepted formats: csv (edam:format_3752).</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t28" href="#t28">28</a></span><span class="t"><span class="str">        output_jpg_path (str): Path to .jpg file where output is saved. File type: output. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/reference/stiffness/stiffavg_roll.jpg>`_. Accepted formats: jpg (edam:format_3579).</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t29" href="#t29">29</a></span><span class="t"><span class="str">        properties (dict):</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t30" href="#t30">30</a></span><span class="t"><span class="str">            * **KT** (*float*) - (0.592186827) Value of Boltzmann temperature factor.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t31" href="#t31">31</a></span><span class="t"><span class="str">            * **sequence** (*str*) - (None) Nucleic acid sequence corresponding to the input .ser file. Length of sequence is expected to be the same as the total number of columns in the .ser file, minus the index column (even if later on a subset of columns is selected with the *usecols* option).</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t32" href="#t32">32</a></span><span class="t"><span class="str">            * **helpar_name** (*str*) - (None) helical parameter name.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t33" href="#t33">33</a></span><span class="t"><span class="str">            * **seqpos** (*list*) - (None) list of sequence positions (columns indices starting by 0) to analyze.  If not specified it will analyse the complete sequence.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t34" href="#t34">34</a></span><span class="t"><span class="str">            * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t35" href="#t35">35</a></span><span class="t"><span class="str">            * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t36" href="#t36">36</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t37" href="#t37">37</a></span><span class="t"><span class="str">    Examples:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t38" href="#t38">38</a></span><span class="t"><span class="str">        This is a use example of how to use the building block from Python::</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t39" href="#t39">39</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t40" href="#t40">40</a></span><span class="t"><span class="str">            from biobb_dna.stiffness.average_stiffness import average_stiffness</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t41" href="#t41">41</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t42" href="#t42">42</a></span><span class="t"><span class="str">            prop = {</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t43" href="#t43">43</a></span><span class="t"><span class="str">                'helpar_name': 'twist',</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t44" href="#t44">44</a></span><span class="t"><span class="str">                'sequence': 'GCAT',</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t45" href="#t45">45</a></span><span class="t"><span class="str">            }</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t46" href="#t46">46</a></span><span class="t"><span class="str">            average_stiffness(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t47" href="#t47">47</a></span><span class="t"><span class="str">                input_ser_path='/path/to/twist.ser',</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t48" href="#t48">48</a></span><span class="t"><span class="str">                output_csv_path='/path/to/table/output.csv',</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t49" href="#t49">49</a></span><span class="t"><span class="str">                output_jpg_path='/path/to/table/output.jpg',</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t50" href="#t50">50</a></span><span class="t"><span class="str">                properties=prop)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t51" href="#t51">51</a></span><span class="t"><span class="str">    Info:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t52" href="#t52">52</a></span><span class="t"><span class="str">        * wrapped_software:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t53" href="#t53">53</a></span><span class="t"><span class="str">            * name: In house</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t54" href="#t54">54</a></span><span class="t"><span class="str">            * license: Apache-2.0</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t55" href="#t55">55</a></span><span class="t"><span class="str">        * ontology:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t56" href="#t56">56</a></span><span class="t"><span class="str">            * name: EDAM</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t57" href="#t57">57</a></span><span class="t"><span class="str">            * schema: http://edamontology.org/EDAM.owl</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t58" href="#t58">58</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t59" href="#t59">59</a></span><span class="t"><span class="str">    """</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t60" href="#t60">60</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t61" href="#t61">61</a></span><span class="t">    <span class="key">def</span> <span class="nam">__init__</span><span class="op">(</span><span class="nam">self</span><span class="op">,</span> <span class="nam">input_ser_path</span><span class="op">,</span> <span class="nam">output_csv_path</span><span class="op">,</span> <span class="nam">output_jpg_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t62" href="#t62">62</a></span><span class="t">                 <span class="nam">properties</span><span class="op">=</span><span class="key">None</span><span class="op">,</span> <span class="op">**</span><span class="nam">kwargs</span><span class="op">)</span> <span class="op">-></span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t63" href="#t63">63</a></span><span class="t">        <span class="nam">properties</span> <span class="op">=</span> <span class="nam">properties</span> <span class="key">or</span> <span class="op">{</span><span class="op">}</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t64" href="#t64">64</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t65" href="#t65">65</a></span><span class="t">        <span class="com"># Call parent class constructor</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t66" href="#t66">66</a></span><span class="t">        <span class="nam">super</span><span class="op">(</span><span class="op">)</span><span class="op">.</span><span class="nam">__init__</span><span class="op">(</span><span class="nam">properties</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t67" href="#t67">67</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">locals_var_dict</span> <span class="op">=</span> <span class="nam">locals</span><span class="op">(</span><span class="op">)</span><span class="op">.</span><span class="nam">copy</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t68" href="#t68">68</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t69" href="#t69">69</a></span><span class="t">        <span class="com"># Input/Output files</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t70" href="#t70">70</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span> <span class="op">=</span> <span class="op">{</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t71" href="#t71">71</a></span><span class="t">            <span class="str">'in'</span><span class="op">:</span> <span class="op">{</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t72" href="#t72">72</a></span><span class="t">                <span class="str">'input_ser_path'</span><span class="op">:</span> <span class="nam">input_ser_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t73" href="#t73">73</a></span><span class="t">            <span class="op">}</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t74" href="#t74">74</a></span><span class="t">            <span class="str">'out'</span><span class="op">:</span> <span class="op">{</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t75" href="#t75">75</a></span><span class="t">                <span class="str">'output_csv_path'</span><span class="op">:</span> <span class="nam">output_csv_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t76" href="#t76">76</a></span><span class="t">                <span class="str">'output_jpg_path'</span><span class="op">:</span> <span class="nam">output_jpg_path</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t77" href="#t77">77</a></span><span class="t">            <span class="op">}</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t78" href="#t78">78</a></span><span class="t">        <span class="op">}</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t79" href="#t79">79</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t80" href="#t80">80</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">properties</span> <span class="op">=</span> <span class="nam">properties</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t81" href="#t81">81</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"sequence"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t82" href="#t82">82</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">KT</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t83" href="#t83">83</a></span><span class="t">            <span class="str">"KT"</span><span class="op">,</span> <span class="num">0.592186827</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t84" href="#t84">84</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"seqpos"</span><span class="op">,</span> <span class="key">None</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t85" href="#t85">85</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">helpar_name</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"helpar_name"</span><span class="op">,</span> <span class="key">None</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t86" href="#t86">86</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t87" href="#t87">87</a></span><span class="t">        <span class="com"># Check the properties</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t88" href="#t88">88</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_properties</span><span class="op">(</span><span class="nam">properties</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t89" href="#t89">89</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_arguments</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t90" href="#t90">90</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t91" href="#t91">91</a></span><span class="t">    <span class="op">@</span><span class="nam">launchlogger</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t92" href="#t92">92</a></span><span class="t">    <span class="key">def</span> <span class="nam">launch</span><span class="op">(</span><span class="nam">self</span><span class="op">)</span> <span class="op">-></span> <span class="nam">int</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t93" href="#t93">93</a></span><span class="t">        <span class="str">"""Execute the :class:`AverageStiffness &lt;stiffness.average_stiffness.AverageStiffness>` object."""</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t94" href="#t94">94</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t95" href="#t95">95</a></span><span class="t">        <span class="com"># Setup Biobb</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t96" href="#t96">96</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">check_restart</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t97" href="#t97">97</a></span><span class="t">            <span class="key">return</span> <span class="num">0</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t98" href="#t98">98</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">stage_files</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t99" href="#t99">99</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t100" href="#t100">100</a></span><span class="t">        <span class="com"># check sequence</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t101" href="#t101">101</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span> <span class="key">is</span> <span class="key">None</span> <span class="key">or</span> <span class="nam">len</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span><span class="op">)</span> <span class="op">&lt;</span> <span class="num">2</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t102" href="#t102">102</a></span><span class="t">            <span class="key">raise</span> <span class="nam">ValueError</span><span class="op">(</span><span class="str">"sequence is null or too short!"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t103" href="#t103">103</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t104" href="#t104">104</a></span><span class="t">        <span class="com"># get helical parameter from filename if not specified</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t105" href="#t105">105</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">helpar_name</span> <span class="key">is</span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t106" href="#t106">106</a></span><span class="t">            <span class="key">for</span> <span class="nam">hp</span> <span class="key">in</span> <span class="nam">constants</span><span class="op">.</span><span class="nam">helical_parameters</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t107" href="#t107">107</a></span><span class="t">                <span class="key">if</span> <span class="nam">hp</span><span class="op">.</span><span class="nam">lower</span><span class="op">(</span><span class="op">)</span> <span class="key">in</span> <span class="nam">Path</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t108" href="#t108">108</a></span><span class="t">                        <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'input_ser_path'</span><span class="op">]</span><span class="op">)</span><span class="op">.</span><span class="nam">name</span><span class="op">.</span><span class="nam">lower</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t109" href="#t109">109</a></span><span class="t">                    <span class="nam">self</span><span class="op">.</span><span class="nam">helpar_name</span> <span class="op">=</span> <span class="nam">hp</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t110" href="#t110">110</a></span><span class="t">            <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">helpar_name</span> <span class="key">is</span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t111" href="#t111">111</a></span><span class="t">                <span class="key">raise</span> <span class="nam">ValueError</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t112" href="#t112">112</a></span><span class="t">                    <span class="str">"Helical parameter name can't be inferred from file, "</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t113" href="#t113">113</a></span><span class="t">                    <span class="str">"so it must be specified!"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t114" href="#t114">114</a></span><span class="t">        <span class="key">else</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t115" href="#t115">115</a></span><span class="t">            <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">helpar_name</span> <span class="key">not</span> <span class="key">in</span> <span class="nam">constants</span><span class="op">.</span><span class="nam">helical_parameters</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t116" href="#t116">116</a></span><span class="t">                <span class="key">raise</span> <span class="nam">ValueError</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t117" href="#t117">117</a></span><span class="t">                    <span class="str">"Helical parameter name is invalid! "</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t118" href="#t118">118</a></span><span class="t">                    <span class="str">f"Options: {constants.helical_parameters}"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t119" href="#t119">119</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t120" href="#t120">120</a></span><span class="t">        <span class="com"># get base length and unit from helical parameter name</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t121" href="#t121">121</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">helpar_name</span><span class="op">.</span><span class="nam">lower</span><span class="op">(</span><span class="op">)</span> <span class="key">in</span> <span class="op">[</span><span class="str">"roll"</span><span class="op">,</span> <span class="str">"tilt"</span><span class="op">,</span> <span class="str">"twist"</span><span class="op">]</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t122" href="#t122">122</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">hp_unit</span> <span class="op">=</span> <span class="str">"kcal/(mol*degree&#178;)"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t123" href="#t123">123</a></span><span class="t">            <span class="nam">scale</span> <span class="op">=</span> <span class="num">1</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t124" href="#t124">124</a></span><span class="t">        <span class="key">else</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t125" href="#t125">125</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">hp_unit</span> <span class="op">=</span> <span class="str">"kcal/(mol*&#197;&#178;)"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t126" href="#t126">126</a></span><span class="t">            <span class="nam">scale</span> <span class="op">=</span> <span class="num">10.6</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t127" href="#t127">127</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t128" href="#t128">128</a></span><span class="t">        <span class="com"># check seqpos</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t129" href="#t129">129</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span> <span class="key">is</span> <span class="key">not</span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t130" href="#t130">130</a></span><span class="t">            <span class="key">if</span> <span class="op">(</span><span class="nam">max</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">)</span> <span class="op">></span> <span class="nam">len</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span><span class="op">)</span> <span class="op">-</span> <span class="num">2</span><span class="op">)</span> <span class="key">or</span> <span class="op">(</span><span class="nam">min</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">)</span> <span class="op">&lt;</span> <span class="num">1</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t131" href="#t131">131</a></span><span class="t">                <span class="key">raise</span> <span class="nam">ValueError</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t132" href="#t132">132</a></span><span class="t">                    <span class="str">f"seqpos values must be between 1 and {len(self.sequence) - 2}"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t133" href="#t133">133</a></span><span class="t">            <span class="key">if</span> <span class="key">not</span> <span class="op">(</span><span class="nam">isinstance</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">,</span> <span class="nam">list</span><span class="op">)</span> <span class="key">and</span> <span class="nam">len</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">)</span> <span class="op">></span> <span class="num">1</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t134" href="#t134">134</a></span><span class="t">                <span class="key">raise</span> <span class="nam">ValueError</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t135" href="#t135">135</a></span><span class="t">                    <span class="str">"seqpos must be a list of at least two integers"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t136" href="#t136">136</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t137" href="#t137">137</a></span><span class="t">        <span class="com"># Creating temporary folder</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t138" href="#t138">138</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span> <span class="op">=</span> <span class="nam">fu</span><span class="op">.</span><span class="nam">create_unique_dir</span><span class="op">(</span><span class="nam">prefix</span><span class="op">=</span><span class="str">"avgstiffness_"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t139" href="#t139">139</a></span><span class="t">        <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="str">'Creating %s temporary folder'</span> <span class="op">%</span> <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t140" href="#t140">140</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t141" href="#t141">141</a></span><span class="t">        <span class="com"># Copy input_file_path1 to temporary folder</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t142" href="#t142">142</a></span><span class="t">        <span class="nam">shutil</span><span class="op">.</span><span class="nam">copy</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'input_ser_path'</span><span class="op">]</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t143" href="#t143">143</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t144" href="#t144">144</a></span><span class="t">        <span class="com"># read input .ser file</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t145" href="#t145">145</a></span><span class="t">        <span class="nam">ser_data</span> <span class="op">=</span> <span class="nam">read_series</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t146" href="#t146">146</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'input_ser_path'</span><span class="op">]</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t147" href="#t147">147</a></span><span class="t">            <span class="nam">usecols</span><span class="op">=</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t148" href="#t148">148</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span> <span class="key">is</span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t149" href="#t149">149</a></span><span class="t">            <span class="nam">ser_data</span> <span class="op">=</span> <span class="nam">ser_data</span><span class="op">[</span><span class="nam">ser_data</span><span class="op">.</span><span class="nam">columns</span><span class="op">[</span><span class="num">1</span><span class="op">:</span><span class="op">-</span><span class="num">1</span><span class="op">]</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t150" href="#t150">150</a></span><span class="t">            <span class="com"># discard first and last base(pairs) from sequence</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t151" href="#t151">151</a></span><span class="t">            <span class="nam">sequence</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span><span class="op">[</span><span class="num">1</span><span class="op">:</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t152" href="#t152">152</a></span><span class="t">            <span class="nam">xlabels</span> <span class="op">=</span> <span class="op">[</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t153" href="#t153">153</a></span><span class="t">                <span class="str">f"{sequence[i:i+2]}"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t154" href="#t154">154</a></span><span class="t">                <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">range</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">ser_data</span><span class="op">.</span><span class="nam">columns</span><span class="op">)</span><span class="op">)</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t155" href="#t155">155</a></span><span class="t">        <span class="key">else</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t156" href="#t156">156</a></span><span class="t">            <span class="nam">sequence</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t157" href="#t157">157</a></span><span class="t">            <span class="nam">xlabels</span> <span class="op">=</span> <span class="op">[</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t158" href="#t158">158</a></span><span class="t">                <span class="str">f"{sequence[i:i+2]}"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t159" href="#t159">159</a></span><span class="t">                <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t160" href="#t160">160</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t161" href="#t161">161</a></span><span class="t">        <span class="com"># calculate average stiffness</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t162" href="#t162">162</a></span><span class="t">        <span class="nam">cov</span> <span class="op">=</span> <span class="nam">ser_data</span><span class="op">.</span><span class="nam">cov</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t163" href="#t163">163</a></span><span class="t">        <span class="nam">stiff</span> <span class="op">=</span> <span class="nam">np</span><span class="op">.</span><span class="nam">linalg</span><span class="op">.</span><span class="nam">inv</span><span class="op">(</span><span class="nam">cov</span><span class="op">)</span> <span class="op">*</span> <span class="nam">self</span><span class="op">.</span><span class="nam">KT</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t164" href="#t164">164</a></span><span class="t">        <span class="nam">avg_stiffness</span> <span class="op">=</span> <span class="nam">np</span><span class="op">.</span><span class="nam">diag</span><span class="op">(</span><span class="nam">stiff</span><span class="op">)</span> <span class="op">*</span> <span class="nam">scale</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t165" href="#t165">165</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t166" href="#t166">166</a></span><span class="t">        <span class="com"># save plot</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t167" href="#t167">167</a></span><span class="t">        <span class="nam">fig</span><span class="op">,</span> <span class="nam">axs</span> <span class="op">=</span> <span class="nam">plt</span><span class="op">.</span><span class="nam">subplots</span><span class="op">(</span><span class="num">1</span><span class="op">,</span> <span class="num">1</span><span class="op">,</span> <span class="nam">dpi</span><span class="op">=</span><span class="num">300</span><span class="op">,</span> <span class="nam">tight_layout</span><span class="op">=</span><span class="key">True</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t168" href="#t168">168</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">plot</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t169" href="#t169">169</a></span><span class="t">            <span class="nam">range</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">xlabels</span><span class="op">)</span><span class="op">)</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t170" href="#t170">170</a></span><span class="t">            <span class="nam">avg_stiffness</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t171" href="#t171">171</a></span><span class="t">            <span class="str">"-o"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t172" href="#t172">172</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_xticks</span><span class="op">(</span><span class="nam">range</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">xlabels</span><span class="op">)</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t173" href="#t173">173</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_xticklabels</span><span class="op">(</span><span class="nam">xlabels</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t174" href="#t174">174</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_xlabel</span><span class="op">(</span><span class="str">"Sequence Base Pair"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t175" href="#t175">175</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_ylabel</span><span class="op">(</span><span class="str">f"{self.helpar_name.capitalize()} ({self.hp_unit})"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t176" href="#t176">176</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_title</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t177" href="#t177">177</a></span><span class="t">            <span class="str">"Base Pair Helical Parameter Stiffness: "</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t178" href="#t178">178</a></span><span class="t">            <span class="str">f"{self.helpar_name.capitalize()}"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t179" href="#t179">179</a></span><span class="t">        <span class="nam">fig</span><span class="op">.</span><span class="nam">savefig</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t180" href="#t180">180</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'out'</span><span class="op">]</span><span class="op">[</span><span class="str">'output_jpg_path'</span><span class="op">]</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t181" href="#t181">181</a></span><span class="t">            <span class="nam">format</span><span class="op">=</span><span class="str">"jpg"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t182" href="#t182">182</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t183" href="#t183">183</a></span><span class="t">        <span class="com"># save table</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t184" href="#t184">184</a></span><span class="t">        <span class="nam">dataset</span> <span class="op">=</span> <span class="nam">pd</span><span class="op">.</span><span class="nam">DataFrame</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t185" href="#t185">185</a></span><span class="t">            <span class="nam">data</span><span class="op">=</span><span class="nam">avg_stiffness</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t186" href="#t186">186</a></span><span class="t">            <span class="nam">index</span><span class="op">=</span><span class="nam">xlabels</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t187" href="#t187">187</a></span><span class="t">            <span class="nam">columns</span><span class="op">=</span><span class="op">[</span><span class="str">f"{self.helpar_name}_stiffness"</span><span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t188" href="#t188">188</a></span><span class="t">        <span class="nam">dataset</span><span class="op">.</span><span class="nam">to_csv</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'out'</span><span class="op">]</span><span class="op">[</span><span class="str">'output_csv_path'</span><span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t189" href="#t189">189</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t190" href="#t190">190</a></span><span class="t">        <span class="nam">plt</span><span class="op">.</span><span class="nam">close</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t191" href="#t191">191</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t192" href="#t192">192</a></span><span class="t">        <span class="com"># Remove temporary file(s)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t193" href="#t193">193</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_files</span><span class="op">.</span><span class="nam">extend</span><span class="op">(</span><span class="op">[</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t194" href="#t194">194</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"unique_dir"</span><span class="op">)</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t195" href="#t195">195</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t196" href="#t196">196</a></span><span class="t">        <span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t197" href="#t197">197</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">remove_tmp_files</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t198" href="#t198">198</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t199" href="#t199">199</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_arguments</span><span class="op">(</span><span class="nam">output_files_created</span><span class="op">=</span><span class="key">True</span><span class="op">,</span> <span class="nam">raise_exception</span><span class="op">=</span><span class="key">False</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t200" href="#t200">200</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t201" href="#t201">201</a></span><span class="t">        <span class="key">return</span> <span class="num">0</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t202" href="#t202">202</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t203" href="#t203">203</a></span><span class="t"><span class="key">def</span> <span class="nam">average_stiffness</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t204" href="#t204">204</a></span><span class="t">        <span class="nam">input_ser_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span> <span class="nam">output_csv_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span> <span class="nam">output_jpg_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t205" href="#t205">205</a></span><span class="t">        <span class="nam">properties</span><span class="op">:</span> <span class="nam">dict</span> <span class="op">=</span> <span class="key">None</span><span class="op">,</span> <span class="op">**</span><span class="nam">kwargs</span><span class="op">)</span> <span class="op">-></span> <span class="nam">int</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t206" href="#t206">206</a></span><span class="t">    <span class="str">"""Create :class:`AverageStiffness &lt;stiffness.average_stiffness.AverageStiffness>` class and</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t207" href="#t207">207</a></span><span class="t"><span class="str">    execute the :meth:`launch() &lt;stiffness.average_stiffness.AverageStiffness.launch>` method."""</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t208" href="#t208">208</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t209" href="#t209">209</a></span><span class="t">    <span class="key">return</span> <span class="nam">AverageStiffness</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t210" href="#t210">210</a></span><span class="t">        <span class="nam">input_ser_path</span><span class="op">=</span><span class="nam">input_ser_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t211" href="#t211">211</a></span><span class="t">        <span class="nam">output_csv_path</span><span class="op">=</span><span class="nam">output_csv_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t212" href="#t212">212</a></span><span class="t">        <span class="nam">output_jpg_path</span><span class="op">=</span><span class="nam">output_jpg_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t213" href="#t213">213</a></span><span class="t">        <span class="nam">properties</span><span class="op">=</span><span class="nam">properties</span><span class="op">,</span> <span class="op">**</span><span class="nam">kwargs</span><span class="op">)</span><span class="op">.</span><span class="nam">launch</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t214" href="#t214">214</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t203" href="#t203">203</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t204" href="#t204">204</a></span><span class="t"><span class="key">def</span> <span class="nam">average_stiffness</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t205" href="#t205">205</a></span><span class="t">        <span class="nam">input_ser_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span> <span class="nam">output_csv_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span> <span class="nam">output_jpg_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t206" href="#t206">206</a></span><span class="t">        <span class="nam">properties</span><span class="op">:</span> <span class="nam">dict</span> <span class="op">=</span> <span class="key">None</span><span class="op">,</span> <span class="op">**</span><span class="nam">kwargs</span><span class="op">)</span> <span class="op">-></span> <span class="nam">int</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t207" href="#t207">207</a></span><span class="t">    <span class="str">"""Create :class:`AverageStiffness &lt;stiffness.average_stiffness.AverageStiffness>` class and</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t208" href="#t208">208</a></span><span class="t"><span class="str">    execute the :meth:`launch() &lt;stiffness.average_stiffness.AverageStiffness.launch>` method."""</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t209" href="#t209">209</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t210" href="#t210">210</a></span><span class="t">    <span class="key">return</span> <span class="nam">AverageStiffness</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t211" href="#t211">211</a></span><span class="t">        <span class="nam">input_ser_path</span><span class="op">=</span><span class="nam">input_ser_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t212" href="#t212">212</a></span><span class="t">        <span class="nam">output_csv_path</span><span class="op">=</span><span class="nam">output_csv_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t213" href="#t213">213</a></span><span class="t">        <span class="nam">output_jpg_path</span><span class="op">=</span><span class="nam">output_jpg_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t214" href="#t214">214</a></span><span class="t">        <span class="nam">properties</span><span class="op">=</span><span class="nam">properties</span><span class="op">,</span> <span class="op">**</span><span class="nam">kwargs</span><span class="op">)</span><span class="op">.</span><span class="nam">launch</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t215" href="#t215">215</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t216" href="#t216">216</a></span><span class="t"><span class="key">def</span> <span class="nam">main</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t217" href="#t217">217</a></span><span class="t">    <span class="str">"""Command line execution of this building block. Please check the command line documentation."""</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t218" href="#t218">218</a></span><span class="t">    <span class="nam">parser</span> <span class="op">=</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">ArgumentParser</span><span class="op">(</span><span class="nam">description</span><span class="op">=</span><span class="str">'Calculate average stiffness constants for each base pair of a trajectory\'s series.'</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t219" href="#t219">219</a></span><span class="t">                                     <span class="nam">formatter_class</span><span class="op">=</span><span class="key">lambda</span> <span class="nam">prog</span><span class="op">:</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">RawTextHelpFormatter</span><span class="op">(</span><span class="nam">prog</span><span class="op">,</span> <span class="nam">width</span><span class="op">=</span><span class="num">99999</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t220" href="#t220">220</a></span><span class="t">    <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--config'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">False</span><span class="op">,</span> <span class="nam">help</span><span class="op">=</span><span class="str">'Configuration file'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t221" href="#t221">221</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t222" href="#t222">222</a></span><span class="t">    <span class="nam">required_args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument_group</span><span class="op">(</span><span class="str">'required arguments'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t223" href="#t223">223</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--input_ser_path'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t224" href="#t224">224</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Helical parameter input ser file path. Accepted formats: ser.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t225" href="#t225">225</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--output_csv_path'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t226" href="#t226">226</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Path to output csv file. Accepted formats: csv.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t227" href="#t227">227</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--output_jpg_path'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t228" href="#t228">228</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Path to output jpg file. Accepted formats: jpg.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t229" href="#t229">229</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t230" href="#t230">230</a></span><span class="t">    <span class="nam">args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">parse_args</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t231" href="#t231">231</a></span><span class="t">    <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="op">=</span> <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="key">or</span> <span class="str">"{}"</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t232" href="#t232">232</a></span><span class="t">    <span class="nam">properties</span> <span class="op">=</span> <span class="nam">settings</span><span class="op">.</span><span class="nam">ConfReader</span><span class="op">(</span><span class="nam">config</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">config</span><span class="op">)</span><span class="op">.</span><span class="nam">get_prop_dic</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t233" href="#t233">233</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t234" href="#t234">234</a></span><span class="t">    <span class="nam">average_stiffness</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t235" href="#t235">235</a></span><span class="t">        <span class="nam">input_ser_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_ser_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t236" href="#t236">236</a></span><span class="t">        <span class="nam">output_csv_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">output_csv_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t237" href="#t237">237</a></span><span class="t">        <span class="nam">output_jpg_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">output_jpg_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t238" href="#t238">238</a></span><span class="t">        <span class="nam">properties</span><span class="op">=</span><span class="nam">properties</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t239" href="#t239">239</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t216" href="#t216">216</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t217" href="#t217">217</a></span><span class="t"><span class="key">def</span> <span class="nam">main</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t218" href="#t218">218</a></span><span class="t">    <span class="str">"""Command line execution of this building block. Please check the command line documentation."""</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t219" href="#t219">219</a></span><span class="t">    <span class="nam">parser</span> <span class="op">=</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">ArgumentParser</span><span class="op">(</span><span class="nam">description</span><span class="op">=</span><span class="str">'Calculate average stiffness constants for each base pair of a trajectory\'s series.'</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t220" href="#t220">220</a></span><span class="t">                                     <span class="nam">formatter_class</span><span class="op">=</span><span class="key">lambda</span> <span class="nam">prog</span><span class="op">:</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">RawTextHelpFormatter</span><span class="op">(</span><span class="nam">prog</span><span class="op">,</span> <span class="nam">width</span><span class="op">=</span><span class="num">99999</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t221" href="#t221">221</a></span><span class="t">    <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--config'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">False</span><span class="op">,</span> <span class="nam">help</span><span class="op">=</span><span class="str">'Configuration file'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t222" href="#t222">222</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t223" href="#t223">223</a></span><span class="t">    <span class="nam">required_args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument_group</span><span class="op">(</span><span class="str">'required arguments'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t224" href="#t224">224</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--input_ser_path'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t225" href="#t225">225</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Helical parameter input ser file path. Accepted formats: ser.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t226" href="#t226">226</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--output_csv_path'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t227" href="#t227">227</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Path to output csv file. Accepted formats: csv.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t228" href="#t228">228</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--output_jpg_path'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t229" href="#t229">229</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Path to output jpg file. Accepted formats: jpg.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t230" href="#t230">230</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t231" href="#t231">231</a></span><span class="t">    <span class="nam">args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">parse_args</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t232" href="#t232">232</a></span><span class="t">    <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="op">=</span> <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="key">or</span> <span class="str">"{}"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t233" href="#t233">233</a></span><span class="t">    <span class="nam">properties</span> <span class="op">=</span> <span class="nam">settings</span><span class="op">.</span><span class="nam">ConfReader</span><span class="op">(</span><span class="nam">config</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">config</span><span class="op">)</span><span class="op">.</span><span class="nam">get_prop_dic</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t234" href="#t234">234</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t235" href="#t235">235</a></span><span class="t">    <span class="nam">average_stiffness</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t236" href="#t236">236</a></span><span class="t">        <span class="nam">input_ser_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_ser_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t237" href="#t237">237</a></span><span class="t">        <span class="nam">output_csv_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">output_csv_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t238" href="#t238">238</a></span><span class="t">        <span class="nam">output_jpg_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">output_jpg_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t239" href="#t239">239</a></span><span class="t">        <span class="nam">properties</span><span class="op">=</span><span class="nam">properties</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t240" href="#t240">240</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t241" href="#t241">241</a></span><span class="t"><span class="key">if</span> <span class="nam">__name__</span> <span class="op">==</span> <span class="str">'__main__'</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t242" href="#t242">242</a></span><span class="t">    <span class="nam">main</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t241" href="#t241">241</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t242" href="#t242">242</a></span><span class="t"><span class="key">if</span> <span class="nam">__name__</span> <span class="op">==</span> <span class="str">'__main__'</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t243" href="#t243">243</a></span><span class="t">    <span class="nam">main</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
 </main>
 <footer>
     <div class="content">
@@ -331,7 +332,7 @@ <h2>
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             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.5.1">coverage.py v7.5.1</a>,
-            created at 2024-05-07 09:06 +0000
+            created at 2024-05-24 09:29 +0000
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--- a/coverage/z_9de9475b0a6fab52_basepair_stiffness_py.html
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             <a id="nextFileLink" class="nav" href="z_957b841f7413f0a1___init___py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.5.1">coverage.py v7.5.1</a>,
-            created at 2024-05-07 09:06 +0000
+            created at 2024-05-24 09:29 +0000
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@@ -101,239 +101,240 @@ <h2>
     <p class="pln"><span class="n"><a id="t19" href="#t19">19</a></span><span class="t">    <span class="str">"""</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t20" href="#t20">20</a></span><span class="t"><span class="str">    | biobb_dna BPStiffness</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t21" href="#t21">21</a></span><span class="t"><span class="str">    | Calculate stiffness constants matrix between all six helical parameters for a single base pair step.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t22" href="#t22">22</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t23" href="#t23">23</a></span><span class="t"><span class="str">    Args:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t24" href="#t24">24</a></span><span class="t"><span class="str">        input_filename_shift (str): Path to csv file with data for helical parameter 'shift'. File type: input. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/stiffness/series_shift_AA.csv>`_. Accepted formats: csv (edam:format_3752)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t25" href="#t25">25</a></span><span class="t"><span class="str">        input_filename_slide (str): Path to csv file with data for helical parameter 'slide'. File type: input. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/stiffness/series_slide_AA.csv>`_. Accepted formats: csv (edam:format_3752)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t26" href="#t26">26</a></span><span class="t"><span class="str">        input_filename_rise (str): Path to csv file with data for helical parameter 'rise'. File type: input. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/stiffness/series_rise_AA.csv>`_. Accepted formats: csv (edam:format_3752)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t27" href="#t27">27</a></span><span class="t"><span class="str">        input_filename_tilt (str): Path to csv file with data for helical parameter 'tilt'. File type: input. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/stiffness/series_tilt_AA.csv>`_. Accepted formats: csv (edam:format_3752)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t28" href="#t28">28</a></span><span class="t"><span class="str">        input_filename_roll (str): Path to csv file with data for helical parameter 'roll'. File type: input. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/stiffness/series_roll_AA.csv>`_. Accepted formats: csv (edam:format_3752)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t29" href="#t29">29</a></span><span class="t"><span class="str">        input_filename_twist (str): Path to csv file with data for helical parameter 'twist'. File type: input. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/stiffness/series_twist_AA.csv>`_. Accepted formats: csv (edam:format_3752)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t30" href="#t30">30</a></span><span class="t"><span class="str">        output_csv_path (str): Path to directory where stiffness matrix file is saved as a csv file. File type: output. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/reference/stiffness/stiffbp_ref.csv>`_. Accepted formats: csv (edam:format_3752)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t31" href="#t31">31</a></span><span class="t"><span class="str">        output_jpg_path (str): Path to directory where stiffness heatmap image is saved as a jpg file. File type: output. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/reference/stiffness/stiffbp_ref.jpg>`_. Accepted formats: jpg (edam:format_3579)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t32" href="#t32">32</a></span><span class="t"><span class="str">        properties (dict):</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t33" href="#t33">33</a></span><span class="t"><span class="str">            * **KT** (*float*) - (0.592186827) Value of Boltzmann temperature factor.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t34" href="#t34">34</a></span><span class="t"><span class="str">            * **scaling** (*list*) - ([1, 1, 1, 10.6, 10.6, 10.6]) Values by which to scale stiffness. Positions correspond to helical parameters in the order: shift, slide, rise, tilt, roll, twist.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t35" href="#t35">35</a></span><span class="t"><span class="str">            * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t36" href="#t36">36</a></span><span class="t"><span class="str">            * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t37" href="#t37">37</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t38" href="#t38">38</a></span><span class="t"><span class="str">    Examples:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t39" href="#t39">39</a></span><span class="t"><span class="str">        This is a use example of how to use the building block from Python::</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t40" href="#t40">40</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t41" href="#t41">41</a></span><span class="t"><span class="str">            from biobb_dna.stiffness.basepair_stiffness import basepair_stiffness</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t42" href="#t42">42</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t43" href="#t43">43</a></span><span class="t"><span class="str">            prop = {</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t44" href="#t44">44</a></span><span class="t"><span class="str">                'KT': 0.592186827,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t45" href="#t45">45</a></span><span class="t"><span class="str">                'scaling': [1, 1, 1, 10.6, 10.6, 10.6]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t46" href="#t46">46</a></span><span class="t"><span class="str">            }</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t47" href="#t47">47</a></span><span class="t"><span class="str">            basepair_stiffness(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t48" href="#t48">48</a></span><span class="t"><span class="str">                input_filename_shift='path/to/basepair/shift.csv',</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t49" href="#t49">49</a></span><span class="t"><span class="str">                input_filename_slide='path/to/basepair/slide.csv',</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t50" href="#t50">50</a></span><span class="t"><span class="str">                input_filename_rise='path/to/basepair/rise.csv',</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t51" href="#t51">51</a></span><span class="t"><span class="str">                input_filename_tilt='path/to/basepair/tilt.csv',</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t52" href="#t52">52</a></span><span class="t"><span class="str">                input_filename_roll='path/to/basepair/roll.csv',</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t53" href="#t53">53</a></span><span class="t"><span class="str">                input_filename_twist='path/to/basepair/twist.csv',</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t54" href="#t54">54</a></span><span class="t"><span class="str">                output_csv_path='path/to/output/file.csv',</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t55" href="#t55">55</a></span><span class="t"><span class="str">                output_jpg_path='path/to/output/plot.jpg',</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t56" href="#t56">56</a></span><span class="t"><span class="str">                properties=prop)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t57" href="#t57">57</a></span><span class="t"><span class="str">    Info:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t58" href="#t58">58</a></span><span class="t"><span class="str">        * wrapped_software:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t59" href="#t59">59</a></span><span class="t"><span class="str">            * name: In house</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t60" href="#t60">60</a></span><span class="t"><span class="str">            * license: Apache-2.0</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t61" href="#t61">61</a></span><span class="t"><span class="str">        * ontology:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t62" href="#t62">62</a></span><span class="t"><span class="str">            * name: EDAM</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t63" href="#t63">63</a></span><span class="t"><span class="str">            * schema: http://edamontology.org/EDAM.owl</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t64" href="#t64">64</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t65" href="#t65">65</a></span><span class="t"><span class="str">    """</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t66" href="#t66">66</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t67" href="#t67">67</a></span><span class="t">    <span class="key">def</span> <span class="nam">__init__</span><span class="op">(</span><span class="nam">self</span><span class="op">,</span> <span class="nam">input_filename_shift</span><span class="op">,</span> <span class="nam">input_filename_slide</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t68" href="#t68">68</a></span><span class="t">                 <span class="nam">input_filename_rise</span><span class="op">,</span> <span class="nam">input_filename_tilt</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t69" href="#t69">69</a></span><span class="t">                 <span class="nam">input_filename_roll</span><span class="op">,</span> <span class="nam">input_filename_twist</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t70" href="#t70">70</a></span><span class="t">                 <span class="nam">output_csv_path</span><span class="op">,</span> <span class="nam">output_jpg_path</span><span class="op">,</span> <span class="nam">properties</span><span class="op">=</span><span class="key">None</span><span class="op">,</span> <span class="op">**</span><span class="nam">kwargs</span><span class="op">)</span> <span class="op">-></span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t71" href="#t71">71</a></span><span class="t">        <span class="nam">properties</span> <span class="op">=</span> <span class="nam">properties</span> <span class="key">or</span> <span class="op">{</span><span class="op">}</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t72" href="#t72">72</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t73" href="#t73">73</a></span><span class="t">        <span class="com"># Call parent class constructor</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t74" href="#t74">74</a></span><span class="t">        <span class="nam">super</span><span class="op">(</span><span class="op">)</span><span class="op">.</span><span class="nam">__init__</span><span class="op">(</span><span class="nam">properties</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t75" href="#t75">75</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">locals_var_dict</span> <span class="op">=</span> <span class="nam">locals</span><span class="op">(</span><span class="op">)</span><span class="op">.</span><span class="nam">copy</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t76" href="#t76">76</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t77" href="#t77">77</a></span><span class="t">        <span class="com"># Input/Output files</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t78" href="#t78">78</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span> <span class="op">=</span> <span class="op">{</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t79" href="#t79">79</a></span><span class="t">            <span class="str">'in'</span><span class="op">:</span> <span class="op">{</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t80" href="#t80">80</a></span><span class="t">                <span class="str">'input_filename_shift'</span><span class="op">:</span> <span class="nam">input_filename_shift</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t81" href="#t81">81</a></span><span class="t">                <span class="str">'input_filename_slide'</span><span class="op">:</span> <span class="nam">input_filename_slide</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t82" href="#t82">82</a></span><span class="t">                <span class="str">'input_filename_rise'</span><span class="op">:</span> <span class="nam">input_filename_rise</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t83" href="#t83">83</a></span><span class="t">                <span class="str">'input_filename_tilt'</span><span class="op">:</span> <span class="nam">input_filename_tilt</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t84" href="#t84">84</a></span><span class="t">                <span class="str">'input_filename_roll'</span><span class="op">:</span> <span class="nam">input_filename_roll</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t85" href="#t85">85</a></span><span class="t">                <span class="str">'input_filename_twist'</span><span class="op">:</span> <span class="nam">input_filename_twist</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t86" href="#t86">86</a></span><span class="t">            <span class="op">}</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t87" href="#t87">87</a></span><span class="t">            <span class="str">'out'</span><span class="op">:</span> <span class="op">{</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t88" href="#t88">88</a></span><span class="t">                <span class="str">'output_csv_path'</span><span class="op">:</span> <span class="nam">output_csv_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t89" href="#t89">89</a></span><span class="t">                <span class="str">'output_jpg_path'</span><span class="op">:</span> <span class="nam">output_jpg_path</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t90" href="#t90">90</a></span><span class="t">            <span class="op">}</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t91" href="#t91">91</a></span><span class="t">        <span class="op">}</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t92" href="#t92">92</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t93" href="#t93">93</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">properties</span> <span class="op">=</span> <span class="nam">properties</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t94" href="#t94">94</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">KT</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t95" href="#t95">95</a></span><span class="t">            <span class="str">"KT"</span><span class="op">,</span> <span class="num">0.592186827</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t96" href="#t96">96</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">scaling</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t97" href="#t97">97</a></span><span class="t">            <span class="str">"scaling"</span><span class="op">,</span> <span class="op">[</span><span class="num">1</span><span class="op">,</span> <span class="num">1</span><span class="op">,</span> <span class="num">1</span><span class="op">,</span> <span class="num">10.6</span><span class="op">,</span> <span class="num">10.6</span><span class="op">,</span> <span class="num">10.6</span><span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t98" href="#t98">98</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t99" href="#t99">99</a></span><span class="t">        <span class="com"># Check the properties</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t100" href="#t100">100</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_properties</span><span class="op">(</span><span class="nam">properties</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t101" href="#t101">101</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_arguments</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t102" href="#t102">102</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t103" href="#t103">103</a></span><span class="t">    <span class="op">@</span><span class="nam">launchlogger</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t104" href="#t104">104</a></span><span class="t">    <span class="key">def</span> <span class="nam">launch</span><span class="op">(</span><span class="nam">self</span><span class="op">)</span> <span class="op">-></span> <span class="nam">int</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t105" href="#t105">105</a></span><span class="t">        <span class="str">"""Execute the :class:`BPStiffness &lt;stiffness.basepair_stiffness.BPStiffness>` object."""</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t106" href="#t106">106</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t107" href="#t107">107</a></span><span class="t">        <span class="com"># Setup Biobb</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t108" href="#t108">108</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">check_restart</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t109" href="#t109">109</a></span><span class="t">            <span class="key">return</span> <span class="num">0</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t110" href="#t110">110</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">stage_files</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t111" href="#t111">111</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t112" href="#t112">112</a></span><span class="t">        <span class="com"># Creating temporary folder</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t113" href="#t113">113</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span> <span class="op">=</span> <span class="nam">fu</span><span class="op">.</span><span class="nam">create_unique_dir</span><span class="op">(</span><span class="nam">prefix</span><span class="op">=</span><span class="str">"bp_stiffness_"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t114" href="#t114">114</a></span><span class="t">        <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="str">'Creating %s temporary folder'</span> <span class="op">%</span> <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t115" href="#t115">115</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t116" href="#t116">116</a></span><span class="t">        <span class="com"># read input</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t117" href="#t117">117</a></span><span class="t">        <span class="nam">shift</span> <span class="op">=</span> <span class="nam">load_data</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t118" href="#t118">118</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">"in"</span><span class="op">]</span><span class="op">[</span><span class="str">"input_filename_shift"</span><span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t119" href="#t119">119</a></span><span class="t">        <span class="nam">slide</span> <span class="op">=</span> <span class="nam">load_data</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t120" href="#t120">120</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">"in"</span><span class="op">]</span><span class="op">[</span><span class="str">"input_filename_slide"</span><span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t121" href="#t121">121</a></span><span class="t">        <span class="nam">rise</span> <span class="op">=</span> <span class="nam">load_data</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t122" href="#t122">122</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">"in"</span><span class="op">]</span><span class="op">[</span><span class="str">"input_filename_rise"</span><span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t123" href="#t123">123</a></span><span class="t">        <span class="nam">tilt</span> <span class="op">=</span> <span class="nam">load_data</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t124" href="#t124">124</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">"in"</span><span class="op">]</span><span class="op">[</span><span class="str">"input_filename_tilt"</span><span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t125" href="#t125">125</a></span><span class="t">        <span class="nam">roll</span> <span class="op">=</span> <span class="nam">load_data</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t126" href="#t126">126</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">"in"</span><span class="op">]</span><span class="op">[</span><span class="str">"input_filename_roll"</span><span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t127" href="#t127">127</a></span><span class="t">        <span class="nam">twist</span> <span class="op">=</span> <span class="nam">load_data</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t128" href="#t128">128</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">"in"</span><span class="op">]</span><span class="op">[</span><span class="str">"input_filename_twist"</span><span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t129" href="#t129">129</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t130" href="#t130">130</a></span><span class="t">        <span class="com"># build matrix cols_arr from helpar input data files</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t131" href="#t131">131</a></span><span class="t">        <span class="nam">coordinates</span> <span class="op">=</span> <span class="op">[</span><span class="str">"shift"</span><span class="op">,</span> <span class="str">"slide"</span><span class="op">,</span> <span class="str">"rise"</span><span class="op">,</span> <span class="str">"tilt"</span><span class="op">,</span> <span class="str">"roll"</span><span class="op">,</span> <span class="str">"twist"</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t132" href="#t132">132</a></span><span class="t">        <span class="nam">basepairname</span> <span class="op">=</span> <span class="nam">shift</span><span class="op">.</span><span class="nam">columns</span><span class="op">[</span><span class="num">0</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t133" href="#t133">133</a></span><span class="t">        <span class="nam">helpar_matrix</span> <span class="op">=</span> <span class="nam">pd</span><span class="op">.</span><span class="nam">concat</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t134" href="#t134">134</a></span><span class="t">            <span class="op">[</span><span class="nam">shift</span><span class="op">,</span> <span class="nam">slide</span><span class="op">,</span> <span class="nam">rise</span><span class="op">,</span> <span class="nam">tilt</span><span class="op">,</span> <span class="nam">roll</span><span class="op">,</span> <span class="nam">twist</span><span class="op">]</span><span class="op">,</span> <span class="nam">axis</span><span class="op">=</span><span class="num">1</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t135" href="#t135">135</a></span><span class="t">        <span class="nam">helpar_matrix</span><span class="op">.</span><span class="nam">columns</span> <span class="op">=</span> <span class="nam">coordinates</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t136" href="#t136">136</a></span><span class="t">        <span class="com"># covariance</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t137" href="#t137">137</a></span><span class="t">        <span class="nam">cov_df</span> <span class="op">=</span> <span class="nam">helpar_matrix</span><span class="op">.</span><span class="nam">cov</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t138" href="#t138">138</a></span><span class="t">        <span class="com"># stiffness</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t139" href="#t139">139</a></span><span class="t">        <span class="nam">stiff</span> <span class="op">=</span> <span class="nam">np</span><span class="op">.</span><span class="nam">linalg</span><span class="op">.</span><span class="nam">inv</span><span class="op">(</span><span class="nam">cov_df</span><span class="op">)</span> <span class="op">*</span> <span class="nam">self</span><span class="op">.</span><span class="nam">KT</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t140" href="#t140">140</a></span><span class="t">        <span class="nam">stiff_diag</span> <span class="op">=</span> <span class="nam">stiff</span> <span class="op">*</span> <span class="nam">np</span><span class="op">.</span><span class="nam">array</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">scaling</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t141" href="#t141">141</a></span><span class="t">        <span class="nam">stiff_df</span> <span class="op">=</span> <span class="nam">pd</span><span class="op">.</span><span class="nam">DataFrame</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t142" href="#t142">142</a></span><span class="t">            <span class="nam">stiff_diag</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t143" href="#t143">143</a></span><span class="t">            <span class="nam">columns</span><span class="op">=</span><span class="nam">cov_df</span><span class="op">.</span><span class="nam">columns</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t144" href="#t144">144</a></span><span class="t">            <span class="nam">index</span><span class="op">=</span><span class="nam">cov_df</span><span class="op">.</span><span class="nam">index</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t145" href="#t145">145</a></span><span class="t">        <span class="nam">stiff_df</span><span class="op">.</span><span class="nam">index</span><span class="op">.</span><span class="nam">name</span> <span class="op">=</span> <span class="nam">basepairname</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t146" href="#t146">146</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t147" href="#t147">147</a></span><span class="t">        <span class="com"># save csv data</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t148" href="#t148">148</a></span><span class="t">        <span class="nam">stiff_df</span><span class="op">.</span><span class="nam">to_csv</span><span class="op">(</span><span class="nam">Path</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">"out"</span><span class="op">]</span><span class="op">[</span><span class="str">"output_csv_path"</span><span class="op">]</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t149" href="#t149">149</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t150" href="#t150">150</a></span><span class="t">        <span class="com"># create heatmap</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t151" href="#t151">151</a></span><span class="t">        <span class="nam">fig</span><span class="op">,</span> <span class="nam">axs</span> <span class="op">=</span> <span class="nam">plt</span><span class="op">.</span><span class="nam">subplots</span><span class="op">(</span><span class="num">1</span><span class="op">,</span> <span class="num">1</span><span class="op">,</span> <span class="nam">dpi</span><span class="op">=</span><span class="num">300</span><span class="op">,</span> <span class="nam">tight_layout</span><span class="op">=</span><span class="key">True</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t152" href="#t152">152</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">pcolor</span><span class="op">(</span><span class="nam">stiff_df</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t153" href="#t153">153</a></span><span class="t">        <span class="com"># Loop over data dimensions and create text annotations.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t154" href="#t154">154</a></span><span class="t">        <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">range</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">stiff_df</span><span class="op">)</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t155" href="#t155">155</a></span><span class="t">            <span class="key">for</span> <span class="nam">j</span> <span class="key">in</span> <span class="nam">range</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">stiff_df</span><span class="op">)</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t156" href="#t156">156</a></span><span class="t">                <span class="nam">axs</span><span class="op">.</span><span class="nam">text</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t157" href="#t157">157</a></span><span class="t">                    <span class="nam">j</span><span class="op">+</span><span class="num">.5</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t158" href="#t158">158</a></span><span class="t">                    <span class="nam">i</span><span class="op">+</span><span class="num">.5</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t159" href="#t159">159</a></span><span class="t">                    <span class="str">f"{stiff_df[coordinates[j]].loc[coordinates[i]]:.2f}"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t160" href="#t160">160</a></span><span class="t">                    <span class="nam">ha</span><span class="op">=</span><span class="str">"center"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t161" href="#t161">161</a></span><span class="t">                    <span class="nam">va</span><span class="op">=</span><span class="str">"center"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t162" href="#t162">162</a></span><span class="t">                    <span class="nam">color</span><span class="op">=</span><span class="str">"w"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t163" href="#t163">163</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">text</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t164" href="#t164">164</a></span><span class="t">            <span class="num">0</span><span class="op">,</span> <span class="op">-</span><span class="num">1.35</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t165" href="#t165">165</a></span><span class="t">            <span class="str">"Units:\n"</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t166" href="#t166">166</a></span><span class="t">            <span class="str">"Diagonal Shift/Slide/Rise in kcal/(mol*&#197;&#178;), Diagonal Tilt/Roll/Twist in kcal/(mol*degree&#178;)\n"</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t167" href="#t167">167</a></span><span class="t">            <span class="str">"Out of Diagonal: Shift/Slide/Rise in kcal/(mol*&#197;), Out of Diagonal Tilt/Roll/Twist in kcal/(mol*degree)"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t168" href="#t168">168</a></span><span class="t">            <span class="nam">fontsize</span><span class="op">=</span><span class="num">6</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t169" href="#t169">169</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_xticks</span><span class="op">(</span><span class="op">[</span><span class="nam">i</span> <span class="op">+</span> <span class="num">0.5</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">range</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">stiff_df</span><span class="op">)</span><span class="op">)</span><span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t170" href="#t170">170</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_xticklabels</span><span class="op">(</span><span class="nam">stiff_df</span><span class="op">.</span><span class="nam">columns</span><span class="op">,</span> <span class="nam">rotation</span><span class="op">=</span><span class="num">90</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t171" href="#t171">171</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_yticks</span><span class="op">(</span><span class="op">[</span><span class="nam">i</span><span class="op">+</span><span class="num">0.5</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">range</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">stiff_df</span><span class="op">)</span><span class="op">)</span><span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t172" href="#t172">172</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_yticklabels</span><span class="op">(</span><span class="nam">stiff_df</span><span class="op">.</span><span class="nam">index</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t173" href="#t173">173</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_title</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t174" href="#t174">174</a></span><span class="t">            <span class="str">f"Stiffness Constants for Base Pair Step \'{basepairname}\'"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t175" href="#t175">175</a></span><span class="t">        <span class="nam">fig</span><span class="op">.</span><span class="nam">tight_layout</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t176" href="#t176">176</a></span><span class="t">        <span class="nam">fig</span><span class="op">.</span><span class="nam">savefig</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t177" href="#t177">177</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'out'</span><span class="op">]</span><span class="op">[</span><span class="str">'output_jpg_path'</span><span class="op">]</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t178" href="#t178">178</a></span><span class="t">            <span class="nam">format</span><span class="op">=</span><span class="str">"jpg"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t179" href="#t179">179</a></span><span class="t">        <span class="nam">plt</span><span class="op">.</span><span class="nam">close</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t180" href="#t180">180</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t181" href="#t181">181</a></span><span class="t">        <span class="com"># Remove temporary file(s)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t182" href="#t182">182</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_files</span><span class="op">.</span><span class="nam">extend</span><span class="op">(</span><span class="op">[</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t183" href="#t183">183</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"unique_dir"</span><span class="op">)</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t184" href="#t184">184</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t185" href="#t185">185</a></span><span class="t">        <span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t186" href="#t186">186</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">remove_tmp_files</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t187" href="#t187">187</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t188" href="#t188">188</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_arguments</span><span class="op">(</span><span class="nam">output_files_created</span><span class="op">=</span><span class="key">True</span><span class="op">,</span> <span class="nam">raise_exception</span><span class="op">=</span><span class="key">False</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t189" href="#t189">189</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t190" href="#t190">190</a></span><span class="t">        <span class="key">return</span> <span class="num">0</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t191" href="#t191">191</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t22" href="#t22">22</a></span><span class="t"><span class="str">    | Calculate stiffness constants matrix between all six helical parameters for a single base pair step.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t23" href="#t23">23</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t24" href="#t24">24</a></span><span class="t"><span class="str">    Args:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t25" href="#t25">25</a></span><span class="t"><span class="str">        input_filename_shift (str): Path to csv file with data for helical parameter 'shift'. File type: input. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/stiffness/series_shift_AA.csv>`_. Accepted formats: csv (edam:format_3752)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t26" href="#t26">26</a></span><span class="t"><span class="str">        input_filename_slide (str): Path to csv file with data for helical parameter 'slide'. File type: input. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/stiffness/series_slide_AA.csv>`_. Accepted formats: csv (edam:format_3752)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t27" href="#t27">27</a></span><span class="t"><span class="str">        input_filename_rise (str): Path to csv file with data for helical parameter 'rise'. File type: input. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/stiffness/series_rise_AA.csv>`_. Accepted formats: csv (edam:format_3752)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t28" href="#t28">28</a></span><span class="t"><span class="str">        input_filename_tilt (str): Path to csv file with data for helical parameter 'tilt'. File type: input. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/stiffness/series_tilt_AA.csv>`_. Accepted formats: csv (edam:format_3752)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t29" href="#t29">29</a></span><span class="t"><span class="str">        input_filename_roll (str): Path to csv file with data for helical parameter 'roll'. File type: input. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/stiffness/series_roll_AA.csv>`_. Accepted formats: csv (edam:format_3752)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t30" href="#t30">30</a></span><span class="t"><span class="str">        input_filename_twist (str): Path to csv file with data for helical parameter 'twist'. File type: input. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/stiffness/series_twist_AA.csv>`_. Accepted formats: csv (edam:format_3752)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t31" href="#t31">31</a></span><span class="t"><span class="str">        output_csv_path (str): Path to directory where stiffness matrix file is saved as a csv file. File type: output. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/reference/stiffness/stiffbp_ref.csv>`_. Accepted formats: csv (edam:format_3752)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t32" href="#t32">32</a></span><span class="t"><span class="str">        output_jpg_path (str): Path to directory where stiffness heatmap image is saved as a jpg file. File type: output. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/reference/stiffness/stiffbp_ref.jpg>`_. Accepted formats: jpg (edam:format_3579)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t33" href="#t33">33</a></span><span class="t"><span class="str">        properties (dict):</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t34" href="#t34">34</a></span><span class="t"><span class="str">            * **KT** (*float*) - (0.592186827) Value of Boltzmann temperature factor.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t35" href="#t35">35</a></span><span class="t"><span class="str">            * **scaling** (*list*) - ([1, 1, 1, 10.6, 10.6, 10.6]) Values by which to scale stiffness. Positions correspond to helical parameters in the order: shift, slide, rise, tilt, roll, twist.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t36" href="#t36">36</a></span><span class="t"><span class="str">            * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t37" href="#t37">37</a></span><span class="t"><span class="str">            * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t38" href="#t38">38</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t39" href="#t39">39</a></span><span class="t"><span class="str">    Examples:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t40" href="#t40">40</a></span><span class="t"><span class="str">        This is a use example of how to use the building block from Python::</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t41" href="#t41">41</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t42" href="#t42">42</a></span><span class="t"><span class="str">            from biobb_dna.stiffness.basepair_stiffness import basepair_stiffness</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t43" href="#t43">43</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t44" href="#t44">44</a></span><span class="t"><span class="str">            prop = {</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t45" href="#t45">45</a></span><span class="t"><span class="str">                'KT': 0.592186827,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t46" href="#t46">46</a></span><span class="t"><span class="str">                'scaling': [1, 1, 1, 10.6, 10.6, 10.6]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t47" href="#t47">47</a></span><span class="t"><span class="str">            }</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t48" href="#t48">48</a></span><span class="t"><span class="str">            basepair_stiffness(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t49" href="#t49">49</a></span><span class="t"><span class="str">                input_filename_shift='path/to/basepair/shift.csv',</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t50" href="#t50">50</a></span><span class="t"><span class="str">                input_filename_slide='path/to/basepair/slide.csv',</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t51" href="#t51">51</a></span><span class="t"><span class="str">                input_filename_rise='path/to/basepair/rise.csv',</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t52" href="#t52">52</a></span><span class="t"><span class="str">                input_filename_tilt='path/to/basepair/tilt.csv',</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t53" href="#t53">53</a></span><span class="t"><span class="str">                input_filename_roll='path/to/basepair/roll.csv',</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t54" href="#t54">54</a></span><span class="t"><span class="str">                input_filename_twist='path/to/basepair/twist.csv',</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t55" href="#t55">55</a></span><span class="t"><span class="str">                output_csv_path='path/to/output/file.csv',</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t56" href="#t56">56</a></span><span class="t"><span class="str">                output_jpg_path='path/to/output/plot.jpg',</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t57" href="#t57">57</a></span><span class="t"><span class="str">                properties=prop)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t58" href="#t58">58</a></span><span class="t"><span class="str">    Info:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t59" href="#t59">59</a></span><span class="t"><span class="str">        * wrapped_software:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t60" href="#t60">60</a></span><span class="t"><span class="str">            * name: In house</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t61" href="#t61">61</a></span><span class="t"><span class="str">            * license: Apache-2.0</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t62" href="#t62">62</a></span><span class="t"><span class="str">        * ontology:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t63" href="#t63">63</a></span><span class="t"><span class="str">            * name: EDAM</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t64" href="#t64">64</a></span><span class="t"><span class="str">            * schema: http://edamontology.org/EDAM.owl</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t65" href="#t65">65</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t66" href="#t66">66</a></span><span class="t"><span class="str">    """</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t67" href="#t67">67</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t68" href="#t68">68</a></span><span class="t">    <span class="key">def</span> <span class="nam">__init__</span><span class="op">(</span><span class="nam">self</span><span class="op">,</span> <span class="nam">input_filename_shift</span><span class="op">,</span> <span class="nam">input_filename_slide</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t69" href="#t69">69</a></span><span class="t">                 <span class="nam">input_filename_rise</span><span class="op">,</span> <span class="nam">input_filename_tilt</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t70" href="#t70">70</a></span><span class="t">                 <span class="nam">input_filename_roll</span><span class="op">,</span> <span class="nam">input_filename_twist</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t71" href="#t71">71</a></span><span class="t">                 <span class="nam">output_csv_path</span><span class="op">,</span> <span class="nam">output_jpg_path</span><span class="op">,</span> <span class="nam">properties</span><span class="op">=</span><span class="key">None</span><span class="op">,</span> <span class="op">**</span><span class="nam">kwargs</span><span class="op">)</span> <span class="op">-></span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t72" href="#t72">72</a></span><span class="t">        <span class="nam">properties</span> <span class="op">=</span> <span class="nam">properties</span> <span class="key">or</span> <span class="op">{</span><span class="op">}</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t73" href="#t73">73</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t74" href="#t74">74</a></span><span class="t">        <span class="com"># Call parent class constructor</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t75" href="#t75">75</a></span><span class="t">        <span class="nam">super</span><span class="op">(</span><span class="op">)</span><span class="op">.</span><span class="nam">__init__</span><span class="op">(</span><span class="nam">properties</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t76" href="#t76">76</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">locals_var_dict</span> <span class="op">=</span> <span class="nam">locals</span><span class="op">(</span><span class="op">)</span><span class="op">.</span><span class="nam">copy</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t77" href="#t77">77</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t78" href="#t78">78</a></span><span class="t">        <span class="com"># Input/Output files</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t79" href="#t79">79</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span> <span class="op">=</span> <span class="op">{</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t80" href="#t80">80</a></span><span class="t">            <span class="str">'in'</span><span class="op">:</span> <span class="op">{</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t81" href="#t81">81</a></span><span class="t">                <span class="str">'input_filename_shift'</span><span class="op">:</span> <span class="nam">input_filename_shift</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t82" href="#t82">82</a></span><span class="t">                <span class="str">'input_filename_slide'</span><span class="op">:</span> <span class="nam">input_filename_slide</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t83" href="#t83">83</a></span><span class="t">                <span class="str">'input_filename_rise'</span><span class="op">:</span> <span class="nam">input_filename_rise</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t84" href="#t84">84</a></span><span class="t">                <span class="str">'input_filename_tilt'</span><span class="op">:</span> <span class="nam">input_filename_tilt</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t85" href="#t85">85</a></span><span class="t">                <span class="str">'input_filename_roll'</span><span class="op">:</span> <span class="nam">input_filename_roll</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t86" href="#t86">86</a></span><span class="t">                <span class="str">'input_filename_twist'</span><span class="op">:</span> <span class="nam">input_filename_twist</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t87" href="#t87">87</a></span><span class="t">            <span class="op">}</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t88" href="#t88">88</a></span><span class="t">            <span class="str">'out'</span><span class="op">:</span> <span class="op">{</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t89" href="#t89">89</a></span><span class="t">                <span class="str">'output_csv_path'</span><span class="op">:</span> <span class="nam">output_csv_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t90" href="#t90">90</a></span><span class="t">                <span class="str">'output_jpg_path'</span><span class="op">:</span> <span class="nam">output_jpg_path</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t91" href="#t91">91</a></span><span class="t">            <span class="op">}</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t92" href="#t92">92</a></span><span class="t">        <span class="op">}</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t93" href="#t93">93</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t94" href="#t94">94</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">properties</span> <span class="op">=</span> <span class="nam">properties</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t95" href="#t95">95</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">KT</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t96" href="#t96">96</a></span><span class="t">            <span class="str">"KT"</span><span class="op">,</span> <span class="num">0.592186827</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t97" href="#t97">97</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">scaling</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t98" href="#t98">98</a></span><span class="t">            <span class="str">"scaling"</span><span class="op">,</span> <span class="op">[</span><span class="num">1</span><span class="op">,</span> <span class="num">1</span><span class="op">,</span> <span class="num">1</span><span class="op">,</span> <span class="num">10.6</span><span class="op">,</span> <span class="num">10.6</span><span class="op">,</span> <span class="num">10.6</span><span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t99" href="#t99">99</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t100" href="#t100">100</a></span><span class="t">        <span class="com"># Check the properties</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t101" href="#t101">101</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_properties</span><span class="op">(</span><span class="nam">properties</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t102" href="#t102">102</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_arguments</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t103" href="#t103">103</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t104" href="#t104">104</a></span><span class="t">    <span class="op">@</span><span class="nam">launchlogger</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t105" href="#t105">105</a></span><span class="t">    <span class="key">def</span> <span class="nam">launch</span><span class="op">(</span><span class="nam">self</span><span class="op">)</span> <span class="op">-></span> <span class="nam">int</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t106" href="#t106">106</a></span><span class="t">        <span class="str">"""Execute the :class:`BPStiffness &lt;stiffness.basepair_stiffness.BPStiffness>` object."""</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t107" href="#t107">107</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t108" href="#t108">108</a></span><span class="t">        <span class="com"># Setup Biobb</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t109" href="#t109">109</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">check_restart</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t110" href="#t110">110</a></span><span class="t">            <span class="key">return</span> <span class="num">0</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t111" href="#t111">111</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">stage_files</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t112" href="#t112">112</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t113" href="#t113">113</a></span><span class="t">        <span class="com"># Creating temporary folder</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t114" href="#t114">114</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span> <span class="op">=</span> <span class="nam">fu</span><span class="op">.</span><span class="nam">create_unique_dir</span><span class="op">(</span><span class="nam">prefix</span><span class="op">=</span><span class="str">"bp_stiffness_"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t115" href="#t115">115</a></span><span class="t">        <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="str">'Creating %s temporary folder'</span> <span class="op">%</span> <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t116" href="#t116">116</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t117" href="#t117">117</a></span><span class="t">        <span class="com"># read input</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t118" href="#t118">118</a></span><span class="t">        <span class="nam">shift</span> <span class="op">=</span> <span class="nam">load_data</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t119" href="#t119">119</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">"in"</span><span class="op">]</span><span class="op">[</span><span class="str">"input_filename_shift"</span><span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t120" href="#t120">120</a></span><span class="t">        <span class="nam">slide</span> <span class="op">=</span> <span class="nam">load_data</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t121" href="#t121">121</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">"in"</span><span class="op">]</span><span class="op">[</span><span class="str">"input_filename_slide"</span><span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t122" href="#t122">122</a></span><span class="t">        <span class="nam">rise</span> <span class="op">=</span> <span class="nam">load_data</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t123" href="#t123">123</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">"in"</span><span class="op">]</span><span class="op">[</span><span class="str">"input_filename_rise"</span><span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t124" href="#t124">124</a></span><span class="t">        <span class="nam">tilt</span> <span class="op">=</span> <span class="nam">load_data</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t125" href="#t125">125</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">"in"</span><span class="op">]</span><span class="op">[</span><span class="str">"input_filename_tilt"</span><span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t126" href="#t126">126</a></span><span class="t">        <span class="nam">roll</span> <span class="op">=</span> <span class="nam">load_data</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t127" href="#t127">127</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">"in"</span><span class="op">]</span><span class="op">[</span><span class="str">"input_filename_roll"</span><span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t128" href="#t128">128</a></span><span class="t">        <span class="nam">twist</span> <span class="op">=</span> <span class="nam">load_data</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t129" href="#t129">129</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">"in"</span><span class="op">]</span><span class="op">[</span><span class="str">"input_filename_twist"</span><span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t130" href="#t130">130</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t131" href="#t131">131</a></span><span class="t">        <span class="com"># build matrix cols_arr from helpar input data files</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t132" href="#t132">132</a></span><span class="t">        <span class="nam">coordinates</span> <span class="op">=</span> <span class="op">[</span><span class="str">"shift"</span><span class="op">,</span> <span class="str">"slide"</span><span class="op">,</span> <span class="str">"rise"</span><span class="op">,</span> <span class="str">"tilt"</span><span class="op">,</span> <span class="str">"roll"</span><span class="op">,</span> <span class="str">"twist"</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t133" href="#t133">133</a></span><span class="t">        <span class="nam">basepairname</span> <span class="op">=</span> <span class="nam">shift</span><span class="op">.</span><span class="nam">columns</span><span class="op">[</span><span class="num">0</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t134" href="#t134">134</a></span><span class="t">        <span class="nam">helpar_matrix</span> <span class="op">=</span> <span class="nam">pd</span><span class="op">.</span><span class="nam">concat</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t135" href="#t135">135</a></span><span class="t">            <span class="op">[</span><span class="nam">shift</span><span class="op">,</span> <span class="nam">slide</span><span class="op">,</span> <span class="nam">rise</span><span class="op">,</span> <span class="nam">tilt</span><span class="op">,</span> <span class="nam">roll</span><span class="op">,</span> <span class="nam">twist</span><span class="op">]</span><span class="op">,</span> <span class="nam">axis</span><span class="op">=</span><span class="num">1</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t136" href="#t136">136</a></span><span class="t">        <span class="nam">helpar_matrix</span><span class="op">.</span><span class="nam">columns</span> <span class="op">=</span> <span class="nam">coordinates</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t137" href="#t137">137</a></span><span class="t">        <span class="com"># covariance</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t138" href="#t138">138</a></span><span class="t">        <span class="nam">cov_df</span> <span class="op">=</span> <span class="nam">helpar_matrix</span><span class="op">.</span><span class="nam">cov</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t139" href="#t139">139</a></span><span class="t">        <span class="com"># stiffness</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t140" href="#t140">140</a></span><span class="t">        <span class="nam">stiff</span> <span class="op">=</span> <span class="nam">np</span><span class="op">.</span><span class="nam">linalg</span><span class="op">.</span><span class="nam">inv</span><span class="op">(</span><span class="nam">cov_df</span><span class="op">)</span> <span class="op">*</span> <span class="nam">self</span><span class="op">.</span><span class="nam">KT</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t141" href="#t141">141</a></span><span class="t">        <span class="nam">stiff_diag</span> <span class="op">=</span> <span class="nam">stiff</span> <span class="op">*</span> <span class="nam">np</span><span class="op">.</span><span class="nam">array</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">scaling</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t142" href="#t142">142</a></span><span class="t">        <span class="nam">stiff_df</span> <span class="op">=</span> <span class="nam">pd</span><span class="op">.</span><span class="nam">DataFrame</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t143" href="#t143">143</a></span><span class="t">            <span class="nam">stiff_diag</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t144" href="#t144">144</a></span><span class="t">            <span class="nam">columns</span><span class="op">=</span><span class="nam">cov_df</span><span class="op">.</span><span class="nam">columns</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t145" href="#t145">145</a></span><span class="t">            <span class="nam">index</span><span class="op">=</span><span class="nam">cov_df</span><span class="op">.</span><span class="nam">index</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t146" href="#t146">146</a></span><span class="t">        <span class="nam">stiff_df</span><span class="op">.</span><span class="nam">index</span><span class="op">.</span><span class="nam">name</span> <span class="op">=</span> <span class="nam">basepairname</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t147" href="#t147">147</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t148" href="#t148">148</a></span><span class="t">        <span class="com"># save csv data</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t149" href="#t149">149</a></span><span class="t">        <span class="nam">stiff_df</span><span class="op">.</span><span class="nam">to_csv</span><span class="op">(</span><span class="nam">Path</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">"out"</span><span class="op">]</span><span class="op">[</span><span class="str">"output_csv_path"</span><span class="op">]</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t150" href="#t150">150</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t151" href="#t151">151</a></span><span class="t">        <span class="com"># create heatmap</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t152" href="#t152">152</a></span><span class="t">        <span class="nam">fig</span><span class="op">,</span> <span class="nam">axs</span> <span class="op">=</span> <span class="nam">plt</span><span class="op">.</span><span class="nam">subplots</span><span class="op">(</span><span class="num">1</span><span class="op">,</span> <span class="num">1</span><span class="op">,</span> <span class="nam">dpi</span><span class="op">=</span><span class="num">300</span><span class="op">,</span> <span class="nam">tight_layout</span><span class="op">=</span><span class="key">True</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t153" href="#t153">153</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">pcolor</span><span class="op">(</span><span class="nam">stiff_df</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t154" href="#t154">154</a></span><span class="t">        <span class="com"># Loop over data dimensions and create text annotations.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t155" href="#t155">155</a></span><span class="t">        <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">range</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">stiff_df</span><span class="op">)</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t156" href="#t156">156</a></span><span class="t">            <span class="key">for</span> <span class="nam">j</span> <span class="key">in</span> <span class="nam">range</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">stiff_df</span><span class="op">)</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t157" href="#t157">157</a></span><span class="t">                <span class="nam">axs</span><span class="op">.</span><span class="nam">text</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t158" href="#t158">158</a></span><span class="t">                    <span class="nam">j</span><span class="op">+</span><span class="num">.5</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t159" href="#t159">159</a></span><span class="t">                    <span class="nam">i</span><span class="op">+</span><span class="num">.5</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t160" href="#t160">160</a></span><span class="t">                    <span class="str">f"{stiff_df[coordinates[j]].loc[coordinates[i]]:.2f}"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t161" href="#t161">161</a></span><span class="t">                    <span class="nam">ha</span><span class="op">=</span><span class="str">"center"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t162" href="#t162">162</a></span><span class="t">                    <span class="nam">va</span><span class="op">=</span><span class="str">"center"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t163" href="#t163">163</a></span><span class="t">                    <span class="nam">color</span><span class="op">=</span><span class="str">"w"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t164" href="#t164">164</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">text</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t165" href="#t165">165</a></span><span class="t">            <span class="num">0</span><span class="op">,</span> <span class="op">-</span><span class="num">1.35</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t166" href="#t166">166</a></span><span class="t">            <span class="str">"Units:\n"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t167" href="#t167">167</a></span><span class="t">            <span class="str">"Diagonal Shift/Slide/Rise in kcal/(mol*&#197;&#178;), Diagonal Tilt/Roll/Twist in kcal/(mol*degree&#178;)\n"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t168" href="#t168">168</a></span><span class="t">            <span class="str">"Out of Diagonal: Shift/Slide/Rise in kcal/(mol*&#197;), Out of Diagonal Tilt/Roll/Twist in kcal/(mol*degree)"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t169" href="#t169">169</a></span><span class="t">            <span class="nam">fontsize</span><span class="op">=</span><span class="num">6</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t170" href="#t170">170</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_xticks</span><span class="op">(</span><span class="op">[</span><span class="nam">i</span> <span class="op">+</span> <span class="num">0.5</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">range</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">stiff_df</span><span class="op">)</span><span class="op">)</span><span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t171" href="#t171">171</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_xticklabels</span><span class="op">(</span><span class="nam">stiff_df</span><span class="op">.</span><span class="nam">columns</span><span class="op">,</span> <span class="nam">rotation</span><span class="op">=</span><span class="num">90</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t172" href="#t172">172</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_yticks</span><span class="op">(</span><span class="op">[</span><span class="nam">i</span><span class="op">+</span><span class="num">0.5</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">range</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">stiff_df</span><span class="op">)</span><span class="op">)</span><span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t173" href="#t173">173</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_yticklabels</span><span class="op">(</span><span class="nam">stiff_df</span><span class="op">.</span><span class="nam">index</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t174" href="#t174">174</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_title</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t175" href="#t175">175</a></span><span class="t">            <span class="str">f"Stiffness Constants for Base Pair Step \'{basepairname}\'"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t176" href="#t176">176</a></span><span class="t">        <span class="nam">fig</span><span class="op">.</span><span class="nam">tight_layout</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t177" href="#t177">177</a></span><span class="t">        <span class="nam">fig</span><span class="op">.</span><span class="nam">savefig</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t178" href="#t178">178</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">'out'</span><span class="op">]</span><span class="op">[</span><span class="str">'output_jpg_path'</span><span class="op">]</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t179" href="#t179">179</a></span><span class="t">            <span class="nam">format</span><span class="op">=</span><span class="str">"jpg"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t180" href="#t180">180</a></span><span class="t">        <span class="nam">plt</span><span class="op">.</span><span class="nam">close</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t181" href="#t181">181</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t182" href="#t182">182</a></span><span class="t">        <span class="com"># Remove temporary file(s)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t183" href="#t183">183</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_files</span><span class="op">.</span><span class="nam">extend</span><span class="op">(</span><span class="op">[</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t184" href="#t184">184</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"unique_dir"</span><span class="op">)</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t185" href="#t185">185</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_folder</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t186" href="#t186">186</a></span><span class="t">        <span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t187" href="#t187">187</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">remove_tmp_files</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t188" href="#t188">188</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t189" href="#t189">189</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_arguments</span><span class="op">(</span><span class="nam">output_files_created</span><span class="op">=</span><span class="key">True</span><span class="op">,</span> <span class="nam">raise_exception</span><span class="op">=</span><span class="key">False</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t190" href="#t190">190</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t191" href="#t191">191</a></span><span class="t">        <span class="key">return</span> <span class="num">0</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t192" href="#t192">192</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t193" href="#t193">193</a></span><span class="t"><span class="key">def</span> <span class="nam">basepair_stiffness</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t194" href="#t194">194</a></span><span class="t">        <span class="nam">input_filename_shift</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span> <span class="nam">input_filename_slide</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t195" href="#t195">195</a></span><span class="t">        <span class="nam">input_filename_rise</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span> <span class="nam">input_filename_tilt</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t196" href="#t196">196</a></span><span class="t">        <span class="nam">input_filename_roll</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span> <span class="nam">input_filename_twist</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t197" href="#t197">197</a></span><span class="t">        <span class="nam">output_csv_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span> <span class="nam">output_jpg_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span> <span class="nam">properties</span><span class="op">:</span> <span class="nam">dict</span> <span class="op">=</span> <span class="key">None</span><span class="op">,</span> <span class="op">**</span><span class="nam">kwargs</span><span class="op">)</span> <span class="op">-></span> <span class="nam">int</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t198" href="#t198">198</a></span><span class="t">    <span class="str">"""Create :class:`BPStiffness &lt;stiffness.basepair_stiffness.BPStiffness>` class and</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t199" href="#t199">199</a></span><span class="t"><span class="str">    execute the :meth:`launch() &lt;stiffness.basepair_stiffness.BPStiffness.BPStiffness.launch>` method."""</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t200" href="#t200">200</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t201" href="#t201">201</a></span><span class="t">    <span class="key">return</span> <span class="nam">BPStiffness</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t202" href="#t202">202</a></span><span class="t">        <span class="nam">input_filename_shift</span><span class="op">=</span><span class="nam">input_filename_shift</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t203" href="#t203">203</a></span><span class="t">        <span class="nam">input_filename_slide</span><span class="op">=</span><span class="nam">input_filename_slide</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t204" href="#t204">204</a></span><span class="t">        <span class="nam">input_filename_rise</span><span class="op">=</span><span class="nam">input_filename_rise</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t205" href="#t205">205</a></span><span class="t">        <span class="nam">input_filename_tilt</span><span class="op">=</span><span class="nam">input_filename_tilt</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t206" href="#t206">206</a></span><span class="t">        <span class="nam">input_filename_roll</span><span class="op">=</span><span class="nam">input_filename_roll</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t207" href="#t207">207</a></span><span class="t">        <span class="nam">input_filename_twist</span><span class="op">=</span><span class="nam">input_filename_twist</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t208" href="#t208">208</a></span><span class="t">        <span class="nam">output_csv_path</span><span class="op">=</span><span class="nam">output_csv_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t209" href="#t209">209</a></span><span class="t">        <span class="nam">output_jpg_path</span><span class="op">=</span><span class="nam">output_jpg_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t210" href="#t210">210</a></span><span class="t">        <span class="nam">properties</span><span class="op">=</span><span class="nam">properties</span><span class="op">,</span> <span class="op">**</span><span class="nam">kwargs</span><span class="op">)</span><span class="op">.</span><span class="nam">launch</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t211" href="#t211">211</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t193" href="#t193">193</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t194" href="#t194">194</a></span><span class="t"><span class="key">def</span> <span class="nam">basepair_stiffness</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t195" href="#t195">195</a></span><span class="t">        <span class="nam">input_filename_shift</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span> <span class="nam">input_filename_slide</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t196" href="#t196">196</a></span><span class="t">        <span class="nam">input_filename_rise</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span> <span class="nam">input_filename_tilt</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t197" href="#t197">197</a></span><span class="t">        <span class="nam">input_filename_roll</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span> <span class="nam">input_filename_twist</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t198" href="#t198">198</a></span><span class="t">        <span class="nam">output_csv_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span> <span class="nam">output_jpg_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span> <span class="nam">properties</span><span class="op">:</span> <span class="nam">dict</span> <span class="op">=</span> <span class="key">None</span><span class="op">,</span> <span class="op">**</span><span class="nam">kwargs</span><span class="op">)</span> <span class="op">-></span> <span class="nam">int</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t199" href="#t199">199</a></span><span class="t">    <span class="str">"""Create :class:`BPStiffness &lt;stiffness.basepair_stiffness.BPStiffness>` class and</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t200" href="#t200">200</a></span><span class="t"><span class="str">    execute the :meth:`launch() &lt;stiffness.basepair_stiffness.BPStiffness.BPStiffness.launch>` method."""</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t201" href="#t201">201</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t202" href="#t202">202</a></span><span class="t">    <span class="key">return</span> <span class="nam">BPStiffness</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t203" href="#t203">203</a></span><span class="t">        <span class="nam">input_filename_shift</span><span class="op">=</span><span class="nam">input_filename_shift</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t204" href="#t204">204</a></span><span class="t">        <span class="nam">input_filename_slide</span><span class="op">=</span><span class="nam">input_filename_slide</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t205" href="#t205">205</a></span><span class="t">        <span class="nam">input_filename_rise</span><span class="op">=</span><span class="nam">input_filename_rise</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t206" href="#t206">206</a></span><span class="t">        <span class="nam">input_filename_tilt</span><span class="op">=</span><span class="nam">input_filename_tilt</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t207" href="#t207">207</a></span><span class="t">        <span class="nam">input_filename_roll</span><span class="op">=</span><span class="nam">input_filename_roll</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t208" href="#t208">208</a></span><span class="t">        <span class="nam">input_filename_twist</span><span class="op">=</span><span class="nam">input_filename_twist</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t209" href="#t209">209</a></span><span class="t">        <span class="nam">output_csv_path</span><span class="op">=</span><span class="nam">output_csv_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t210" href="#t210">210</a></span><span class="t">        <span class="nam">output_jpg_path</span><span class="op">=</span><span class="nam">output_jpg_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t211" href="#t211">211</a></span><span class="t">        <span class="nam">properties</span><span class="op">=</span><span class="nam">properties</span><span class="op">,</span> <span class="op">**</span><span class="nam">kwargs</span><span class="op">)</span><span class="op">.</span><span class="nam">launch</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t212" href="#t212">212</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t213" href="#t213">213</a></span><span class="t"><span class="key">def</span> <span class="nam">main</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t214" href="#t214">214</a></span><span class="t">    <span class="str">"""Command line execution of this building block. Please check the command line documentation."""</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t215" href="#t215">215</a></span><span class="t">    <span class="nam">parser</span> <span class="op">=</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">ArgumentParser</span><span class="op">(</span><span class="nam">description</span><span class="op">=</span><span class="str">'Calculate stiffness constants matrix between all six helical parameters for a single base pair step.'</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t216" href="#t216">216</a></span><span class="t">                                     <span class="nam">formatter_class</span><span class="op">=</span><span class="key">lambda</span> <span class="nam">prog</span><span class="op">:</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">RawTextHelpFormatter</span><span class="op">(</span><span class="nam">prog</span><span class="op">,</span> <span class="nam">width</span><span class="op">=</span><span class="num">99999</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t217" href="#t217">217</a></span><span class="t">    <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--config'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">False</span><span class="op">,</span> <span class="nam">help</span><span class="op">=</span><span class="str">'Configuration file'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t218" href="#t218">218</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t219" href="#t219">219</a></span><span class="t">    <span class="nam">required_args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument_group</span><span class="op">(</span><span class="str">'required arguments'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t220" href="#t220">220</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--input_filename_shift'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t221" href="#t221">221</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Path to csv file with shift inputs. Accepted formats: csv.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t222" href="#t222">222</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--input_filename_slide'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t223" href="#t223">223</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Path to csv file with slide inputs. Accepted formats: csv.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t224" href="#t224">224</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--input_filename_rise'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t225" href="#t225">225</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Path to csv file with rise inputs. Accepted formats: csv.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t226" href="#t226">226</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--input_filename_tilt'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t227" href="#t227">227</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Path to csv file with tilt inputs. Accepted formats: csv.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t228" href="#t228">228</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--input_filename_roll'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t229" href="#t229">229</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Path to csv file with roll inputs. Accepted formats: csv.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t230" href="#t230">230</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--input_filename_twist'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t231" href="#t231">231</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Path to csv file with twist inputs. Accepted formats: csv.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t232" href="#t232">232</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--output_csv_path'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t233" href="#t233">233</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Path to output covariance data file. Accepted formats: csv.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t234" href="#t234">234</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--output_jpg_path'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t235" href="#t235">235</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Path to output covariance data file. Accepted formats: csv.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t236" href="#t236">236</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t237" href="#t237">237</a></span><span class="t">    <span class="nam">args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">parse_args</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t238" href="#t238">238</a></span><span class="t">    <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="op">=</span> <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="key">or</span> <span class="str">"{}"</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t239" href="#t239">239</a></span><span class="t">    <span class="nam">properties</span> <span class="op">=</span> <span class="nam">settings</span><span class="op">.</span><span class="nam">ConfReader</span><span class="op">(</span><span class="nam">config</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">config</span><span class="op">)</span><span class="op">.</span><span class="nam">get_prop_dic</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t240" href="#t240">240</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t241" href="#t241">241</a></span><span class="t">    <span class="nam">basepair_stiffness</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t242" href="#t242">242</a></span><span class="t">        <span class="nam">input_filename_shift</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_filename_shift</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t243" href="#t243">243</a></span><span class="t">        <span class="nam">input_filename_slide</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_filename_slide</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t244" href="#t244">244</a></span><span class="t">        <span class="nam">input_filename_rise</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_filename_rise</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t245" href="#t245">245</a></span><span class="t">        <span class="nam">input_filename_tilt</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_filename_tilt</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t246" href="#t246">246</a></span><span class="t">        <span class="nam">input_filename_roll</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_filename_roll</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t247" href="#t247">247</a></span><span class="t">        <span class="nam">input_filename_twist</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_filename_twist</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t248" href="#t248">248</a></span><span class="t">        <span class="nam">output_csv_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">output_csv_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t249" href="#t249">249</a></span><span class="t">        <span class="nam">output_jpg_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">output_jpg_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t250" href="#t250">250</a></span><span class="t">        <span class="nam">properties</span><span class="op">=</span><span class="nam">properties</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t251" href="#t251">251</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t213" href="#t213">213</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t214" href="#t214">214</a></span><span class="t"><span class="key">def</span> <span class="nam">main</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t215" href="#t215">215</a></span><span class="t">    <span class="str">"""Command line execution of this building block. Please check the command line documentation."""</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t216" href="#t216">216</a></span><span class="t">    <span class="nam">parser</span> <span class="op">=</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">ArgumentParser</span><span class="op">(</span><span class="nam">description</span><span class="op">=</span><span class="str">'Calculate stiffness constants matrix between all six helical parameters for a single base pair step.'</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t217" href="#t217">217</a></span><span class="t">                                     <span class="nam">formatter_class</span><span class="op">=</span><span class="key">lambda</span> <span class="nam">prog</span><span class="op">:</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">RawTextHelpFormatter</span><span class="op">(</span><span class="nam">prog</span><span class="op">,</span> <span class="nam">width</span><span class="op">=</span><span class="num">99999</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t218" href="#t218">218</a></span><span class="t">    <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--config'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">False</span><span class="op">,</span> <span class="nam">help</span><span class="op">=</span><span class="str">'Configuration file'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t219" href="#t219">219</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t220" href="#t220">220</a></span><span class="t">    <span class="nam">required_args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument_group</span><span class="op">(</span><span class="str">'required arguments'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t221" href="#t221">221</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--input_filename_shift'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t222" href="#t222">222</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Path to csv file with shift inputs. Accepted formats: csv.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t223" href="#t223">223</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--input_filename_slide'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t224" href="#t224">224</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Path to csv file with slide inputs. Accepted formats: csv.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t225" href="#t225">225</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--input_filename_rise'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t226" href="#t226">226</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Path to csv file with rise inputs. Accepted formats: csv.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t227" href="#t227">227</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--input_filename_tilt'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t228" href="#t228">228</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Path to csv file with tilt inputs. Accepted formats: csv.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t229" href="#t229">229</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--input_filename_roll'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t230" href="#t230">230</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Path to csv file with roll inputs. Accepted formats: csv.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t231" href="#t231">231</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--input_filename_twist'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t232" href="#t232">232</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Path to csv file with twist inputs. Accepted formats: csv.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t233" href="#t233">233</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--output_csv_path'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t234" href="#t234">234</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Path to output covariance data file. Accepted formats: csv.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t235" href="#t235">235</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--output_jpg_path'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t236" href="#t236">236</a></span><span class="t">                               <span class="nam">help</span><span class="op">=</span><span class="str">'Path to output covariance data file. Accepted formats: csv.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t237" href="#t237">237</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t238" href="#t238">238</a></span><span class="t">    <span class="nam">args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">parse_args</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t239" href="#t239">239</a></span><span class="t">    <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="op">=</span> <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="key">or</span> <span class="str">"{}"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t240" href="#t240">240</a></span><span class="t">    <span class="nam">properties</span> <span class="op">=</span> <span class="nam">settings</span><span class="op">.</span><span class="nam">ConfReader</span><span class="op">(</span><span class="nam">config</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">config</span><span class="op">)</span><span class="op">.</span><span class="nam">get_prop_dic</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t241" href="#t241">241</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t242" href="#t242">242</a></span><span class="t">    <span class="nam">basepair_stiffness</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t243" href="#t243">243</a></span><span class="t">        <span class="nam">input_filename_shift</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_filename_shift</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t244" href="#t244">244</a></span><span class="t">        <span class="nam">input_filename_slide</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_filename_slide</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t245" href="#t245">245</a></span><span class="t">        <span class="nam">input_filename_rise</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_filename_rise</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t246" href="#t246">246</a></span><span class="t">        <span class="nam">input_filename_tilt</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_filename_tilt</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t247" href="#t247">247</a></span><span class="t">        <span class="nam">input_filename_roll</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_filename_roll</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t248" href="#t248">248</a></span><span class="t">        <span class="nam">input_filename_twist</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_filename_twist</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t249" href="#t249">249</a></span><span class="t">        <span class="nam">output_csv_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">output_csv_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t250" href="#t250">250</a></span><span class="t">        <span class="nam">output_jpg_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">output_jpg_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t251" href="#t251">251</a></span><span class="t">        <span class="nam">properties</span><span class="op">=</span><span class="nam">properties</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t252" href="#t252">252</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t253" href="#t253">253</a></span><span class="t"><span class="key">if</span> <span class="nam">__name__</span> <span class="op">==</span> <span class="str">'__main__'</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t254" href="#t254">254</a></span><span class="t">    <span class="nam">main</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t253" href="#t253">253</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t254" href="#t254">254</a></span><span class="t"><span class="key">if</span> <span class="nam">__name__</span> <span class="op">==</span> <span class="str">'__main__'</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t255" href="#t255">255</a></span><span class="t">    <span class="nam">main</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
 </main>
 <footer>
     <div class="content">
@@ -343,7 +344,7 @@ <h2>
             <a class="nav" href="z_957b841f7413f0a1___init___py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.5.1">coverage.py v7.5.1</a>,
-            created at 2024-05-07 09:06 +0000
+            created at 2024-05-24 09:29 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_cda7f8e8576a7189_test_stiffness_py.html b/coverage/z_cda7f8e8576a7189_test_stiffness_py.html
index ed32787d..eca8cf90 100644
--- a/coverage/z_cda7f8e8576a7189_test_stiffness_py.html
+++ b/coverage/z_cda7f8e8576a7189_test_stiffness_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_833b0317e3c43dca___init___py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.5.1">coverage.py v7.5.1</a>,
-            created at 2024-05-07 09:06 +0000
+            created at 2024-05-24 09:29 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -129,7 +129,7 @@ <h2>
             <a class="nav" href="z_833b0317e3c43dca___init___py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.5.1">coverage.py v7.5.1</a>,
-            created at 2024-05-07 09:06 +0000
+            created at 2024-05-24 09:29 +0000
         </p>
     </div>
 </footer>
diff --git a/flake8/index.html b/flake8/index.html
index fed78b7a..1cf38968 100644
--- a/flake8/index.html
+++ b/flake8/index.html
@@ -9,7 +9,7 @@
       <div id="masthead" class="sev-4"></div>
       <div id="page">
           <h1>flake8 violations</h1>
-         <p id="versions">Generated on 2024-05-07 09:05
+         <p id="versions">Generated on 2024-05-24 09:29
             with Installed plugins: flake8-html: 0.4.3, mccabe: 0.7.0, pycodestyle: 2.11.1, pyflakes: 3.2.0
          </p>
          <ul id="index">
diff --git a/junit/junit.xml b/junit/junit.xml
index 8990aec2..1d603f5c 100644
--- a/junit/junit.xml
+++ b/junit/junit.xml
@@ -1 +1 @@
-<?xml version="1.0" encoding="utf-8"?><testsuites><testsuite name="pytest" errors="0" failures="0" skipped="0" tests="17" time="25.968" timestamp="2024-05-07T09:06:00.061031" hostname="biobb-runners"><testcase classname="biobb_dna.test.unitests.test_backbone.test_bipopulations.TestBIPopulations" name="test_bipopulations" time="0.626" /><testcase classname="biobb_dna.test.unitests.test_backbone.test_canonical_alpha_gamma.TestCanonicalAlphaGamma" name="test_canonicalag" time="0.524" /><testcase classname="biobb_dna.test.unitests.test_backbone.test_puckering.TestPuckering" name="test_puckering" time="0.627" /><testcase classname="biobb_dna.test.unitests.test_correlation.test_correlation.TestInterHelparCorrelation" name="test_helparcorrelation" time="0.339" /><testcase classname="biobb_dna.test.unitests.test_correlation.test_correlation.TestInterSequenceCorrelation" name="test_sequencecorrelation" time="0.415" /><testcase classname="biobb_dna.test.unitests.test_correlation.test_correlation.TestInterBasepairCorrelation" name="test_basepaircorrelation" time="0.932" /><testcase classname="biobb_dna.test.unitests.test_correlation.test_correlation.TestIntraHelparCorrelation" name="test_helparcorrelation" time="0.871" /><testcase classname="biobb_dna.test.unitests.test_correlation.test_correlation.TestIntraSequenceCorrelation" name="test_sequencecorrelation" time="0.421" /><testcase classname="biobb_dna.test.unitests.test_correlation.test_correlation.TestIntraBasepairCorrelation" name="test_basepaircorrelation" time="1.003" /><testcase classname="biobb_dna.test.unitests.test_curvesplus.test_canal.TestCanal" name="test_canal" time="3.475" /><testcase classname="biobb_dna.test.unitests.test_curvesplus.test_canion.TestCanal" name="test_canion" time="0.735" /><testcase classname="biobb_dna.test.unitests.test_curvesplus.test_curves.TestCurves" name="test_curves" time="7.838" /><testcase classname="biobb_dna.test.unitests.test_dna.test_averages.TestAverages" name="test_helparaverages" time="0.322" /><testcase classname="biobb_dna.test.unitests.test_dna.test_bimodality.TestBimodality" name="test_helparbimodality" time="0.711" /><testcase classname="biobb_dna.test.unitests.test_dna.test_timeseries.TestTimeSeries" name="test_helpartimeseries" time="4.469" /><testcase classname="biobb_dna.test.unitests.test_stiffness.test_stiffness.TestAvgStiffness" name="test_averagestiffness" time="0.313" /><testcase classname="biobb_dna.test.unitests.test_stiffness.test_stiffness.TestBasePairStiffness" name="test_basepairstiffness" time="0.363" /></testsuite></testsuites>
\ No newline at end of file
+<?xml version="1.0" encoding="utf-8"?><testsuites><testsuite name="pytest" errors="0" failures="0" skipped="0" tests="17" time="21.039" timestamp="2024-05-24T09:29:31.647819" hostname="biobb-runners"><testcase classname="biobb_dna.test.unitests.test_backbone.test_bipopulations.TestBIPopulations" name="test_bipopulations" time="0.578" /><testcase classname="biobb_dna.test.unitests.test_backbone.test_canonical_alpha_gamma.TestCanonicalAlphaGamma" name="test_canonicalag" time="0.529" /><testcase classname="biobb_dna.test.unitests.test_backbone.test_puckering.TestPuckering" name="test_puckering" time="0.693" /><testcase classname="biobb_dna.test.unitests.test_correlation.test_correlation.TestInterHelparCorrelation" name="test_helparcorrelation" time="0.356" /><testcase classname="biobb_dna.test.unitests.test_correlation.test_correlation.TestInterSequenceCorrelation" name="test_sequencecorrelation" time="0.514" /><testcase classname="biobb_dna.test.unitests.test_correlation.test_correlation.TestInterBasepairCorrelation" name="test_basepaircorrelation" time="1.009" /><testcase classname="biobb_dna.test.unitests.test_correlation.test_correlation.TestIntraHelparCorrelation" name="test_helparcorrelation" time="0.352" /><testcase classname="biobb_dna.test.unitests.test_correlation.test_correlation.TestIntraSequenceCorrelation" name="test_sequencecorrelation" time="0.413" /><testcase classname="biobb_dna.test.unitests.test_correlation.test_correlation.TestIntraBasepairCorrelation" name="test_basepaircorrelation" time="1.064" /><testcase classname="biobb_dna.test.unitests.test_curvesplus.test_canal.TestCanal" name="test_canal" time="3.706" /><testcase classname="biobb_dna.test.unitests.test_curvesplus.test_canion.TestCanal" name="test_canion" time="0.723" /><testcase classname="biobb_dna.test.unitests.test_curvesplus.test_curves.TestCurves" name="test_curves" time="6.687" /><testcase classname="biobb_dna.test.unitests.test_dna.test_averages.TestAverages" name="test_helparaverages" time="0.378" /><testcase classname="biobb_dna.test.unitests.test_dna.test_bimodality.TestBimodality" name="test_helparbimodality" time="0.551" /><testcase classname="biobb_dna.test.unitests.test_dna.test_timeseries.TestTimeSeries" name="test_helpartimeseries" time="1.077" /><testcase classname="biobb_dna.test.unitests.test_stiffness.test_stiffness.TestAvgStiffness" name="test_averagestiffness" time="0.317" /><testcase classname="biobb_dna.test.unitests.test_stiffness.test_stiffness.TestBasePairStiffness" name="test_basepairstiffness" time="0.328" /></testsuite></testsuites>
\ No newline at end of file
diff --git a/junit/report.html b/junit/report.html
index 400e69b0..902c9211 100644
--- a/junit/report.html
+++ b/junit/report.html
@@ -7,7 +7,7 @@
   </head>
   <body>
     <h1 id="title">report.html</h1>
-    <p>Report generated on 07-May-2024 at 09:06:26 by <a href="https://pypi.python.org/pypi/pytest-html">pytest-html</a>
+    <p>Report generated on 24-May-2024 at 09:29:52 by <a href="https://pypi.python.org/pypi/pytest-html">pytest-html</a>
         v4.1.1</p>
     <div id="environment-header">
       <h2>Environment</h2>
@@ -61,7 +61,7 @@ <h2>Environment</h2>
         <h2>Summary</h2>
         <div class="additional-summary prefix">
         </div>
-        <p class="run-count">17 tests took 00:00:24.</p>
+        <p class="run-count">17 tests took 00:00:19.</p>
         <p class="filter">(Un)check the boxes to filter the results.</p>
         <div class="summary__reload">
           <div class="summary__reload__button hidden" onclick="location.reload()">
@@ -108,7 +108,7 @@ <h2>Summary</h2>
     </table>
   </body>
   <footer>
-    <div id="data-container" data-jsonblob="{&#34;environment&#34;: {&#34;Python&#34;: &#34;3.9.19&#34;, &#34;Platform&#34;: &#34;Linux-5.4.0-159-generic-x86_64-with-glibc2.31&#34;, &#34;Packages&#34;: {&#34;pytest&#34;: &#34;8.2.0&#34;, &#34;pluggy&#34;: &#34;1.5.0&#34;}, &#34;Plugins&#34;: {&#34;metadata&#34;: &#34;3.1.1&#34;, &#34;html&#34;: &#34;4.1.1&#34;, &#34;cov&#34;: &#34;5.0.0&#34;}, &#34;CI&#34;: &#34;true&#34;}, &#34;tests&#34;: {&#34;biobb_dna/test/unitests/test_backbone/test_bipopulations.py::TestBIPopulations::test_bipopulations&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_dna/test/unitests/test_backbone/test_bipopulations.py::TestBIPopulations::test_bipopulations&#34;, &#34;duration&#34;: &#34;626 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_dna/test/unitests/test_backbone/test_bipopulations.py::TestBIPopulations::test_bipopulations&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;626 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-05-07 09:06:01,757 [MainThread  ] [INFO ]  Executing biobb_dna.backbone.bipopulations Version: 4.1.0\n2024-05-07 09:06:01,758 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/backbone/canal_output_epsilC.ser to /tmp/biobb/unitests_20/bipopulations/f5c68d01-a632-453d-9208-cb16012bcc37\n2024-05-07 09:06:01,759 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/backbone/canal_output_epsilW.ser to /tmp/biobb/unitests_20/bipopulations/f5c68d01-a632-453d-9208-cb16012bcc37\n2024-05-07 09:06:01,759 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/backbone/canal_output_zetaC.ser to /tmp/biobb/unitests_20/bipopulations/f5c68d01-a632-453d-9208-cb16012bcc37\n2024-05-07 09:06:01,760 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/backbone/canal_output_zetaW.ser to /tmp/biobb/unitests_20/bipopulations/f5c68d01-a632-453d-9208-cb16012bcc37\n2024-05-07 09:06:01,760 [MainThread  ] [INFO ]  Creating backbone_ee0bf04e-d20e-4e04-b93c-7b83e86777e5 temporary folder\n2024-05-07 09:06:02,257 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_20/bipopulations/f5c68d01-a632-453d-9208-cb16012bcc37&amp;#x27;, &amp;#x27;backbone_ee0bf04e-d20e-4e04-b93c-7b83e86777e5&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_20/bipopulations/bipop.csv\nChecking if empty file: /tmp/biobb/unitests_20/bipopulations/bipop.jpg\nComparing images of both files:\n     IMAGE_A: /tmp/biobb/unitests_20/bipopulations/bipop.jpg\n     IMAGE_B: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/reference/backbone/bipop_ref.jpg\n     IMAGE_A HASH: ff8981818181c9ff SIZE: 64 bits\n     IMAGE_B HASH: ff8981818181c9ff SIZE: 64 bits\n     TOLERANCE: 1.0%, ABS TOLERANCE: 1 bits, DIFFERENCE: 0 bits\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_20/bipopulations/bipopulations_log.out:file_utils.py:390 Executing biobb_dna.backbone.bipopulations Version: 4.1.0\nINFO     /tmp/biobb/unitests_20/bipopulations/bipopulations_log.out:file_utils.py:390 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/backbone/canal_output_epsilC.ser to /tmp/biobb/unitests_20/bipopulations/f5c68d01-a632-453d-9208-cb16012bcc37\nINFO     /tmp/biobb/unitests_20/bipopulations/bipopulations_log.out:file_utils.py:390 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/backbone/canal_output_epsilW.ser to /tmp/biobb/unitests_20/bipopulations/f5c68d01-a632-453d-9208-cb16012bcc37\nINFO     /tmp/biobb/unitests_20/bipopulations/bipopulations_log.out:file_utils.py:390 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/backbone/canal_output_zetaC.ser to /tmp/biobb/unitests_20/bipopulations/f5c68d01-a632-453d-9208-cb16012bcc37\nINFO     /tmp/biobb/unitests_20/bipopulations/bipopulations_log.out:file_utils.py:390 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/backbone/canal_output_zetaW.ser to /tmp/biobb/unitests_20/bipopulations/f5c68d01-a632-453d-9208-cb16012bcc37\nINFO     /tmp/biobb/unitests_20/bipopulations/bipopulations_log.out:file_utils.py:390 Creating backbone_ee0bf04e-d20e-4e04-b93c-7b83e86777e5 temporary folder\nINFO     /tmp/biobb/unitests_20/bipopulations/bipopulations_log.out:file_utils.py:390 Removed: [&amp;#x27;/tmp/biobb/unitests_20/bipopulations/f5c68d01-a632-453d-9208-cb16012bcc37&amp;#x27;, &amp;#x27;backbone_ee0bf04e-d20e-4e04-b93c-7b83e86777e5&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_20\n&#34;}], &#34;biobb_dna/test/unitests/test_backbone/test_canonical_alpha_gamma.py::TestCanonicalAlphaGamma::test_canonicalag&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_dna/test/unitests/test_backbone/test_canonical_alpha_gamma.py::TestCanonicalAlphaGamma::test_canonicalag&#34;, &#34;duration&#34;: &#34;524 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_dna/test/unitests/test_backbone/test_canonical_alpha_gamma.py::TestCanonicalAlphaGamma::test_canonicalag&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;524 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-05-07 09:06:02,400 [MainThread  ] [INFO ]  Executing biobb_dna.backbone.canonicalag Version: 4.1.0\n2024-05-07 09:06:02,401 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/backbone/canal_output_alphaC.ser to /tmp/biobb/unitests_20/canonicalag/98da34d0-6022-43d2-a5c7-0939408d436d\n2024-05-07 09:06:02,402 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/backbone/canal_output_alphaW.ser to /tmp/biobb/unitests_20/canonicalag/98da34d0-6022-43d2-a5c7-0939408d436d\n2024-05-07 09:06:02,403 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/backbone/canal_output_gammaC.ser to /tmp/biobb/unitests_20/canonicalag/98da34d0-6022-43d2-a5c7-0939408d436d\n2024-05-07 09:06:02,403 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/backbone/canal_output_gammaW.ser to /tmp/biobb/unitests_20/canonicalag/98da34d0-6022-43d2-a5c7-0939408d436d\n2024-05-07 09:06:02,404 [MainThread  ] [INFO ]  Creating backbone_f845ca61-d888-4dc3-88d7-e088a28a48e0 temporary folder\n2024-05-07 09:06:02,811 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_20/canonicalag/98da34d0-6022-43d2-a5c7-0939408d436d&amp;#x27;, &amp;#x27;backbone_f845ca61-d888-4dc3-88d7-e088a28a48e0&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_20/canonicalag/canonag.csv\nChecking if empty file: /tmp/biobb/unitests_20/canonicalag/canonag.jpg\nComparing images of both files:\n     IMAGE_A: /tmp/biobb/unitests_20/canonicalag/canonag.jpg\n     IMAGE_B: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/reference/backbone/canonag_ref.jpg\n     IMAGE_A HASH: ff8081818180f9ff SIZE: 64 bits\n     IMAGE_B HASH: ff8081818180f9ff SIZE: 64 bits\n     TOLERANCE: 1.0%, ABS TOLERANCE: 1 bits, DIFFERENCE: 0 bits\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_20/canonicalag/canonicalag_log.out:file_utils.py:390 Executing biobb_dna.backbone.canonicalag Version: 4.1.0\nINFO     /tmp/biobb/unitests_20/canonicalag/canonicalag_log.out:file_utils.py:390 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/backbone/canal_output_alphaC.ser to /tmp/biobb/unitests_20/canonicalag/98da34d0-6022-43d2-a5c7-0939408d436d\nINFO     /tmp/biobb/unitests_20/canonicalag/canonicalag_log.out:file_utils.py:390 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/backbone/canal_output_alphaW.ser to /tmp/biobb/unitests_20/canonicalag/98da34d0-6022-43d2-a5c7-0939408d436d\nINFO     /tmp/biobb/unitests_20/canonicalag/canonicalag_log.out:file_utils.py:390 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/backbone/canal_output_gammaC.ser to /tmp/biobb/unitests_20/canonicalag/98da34d0-6022-43d2-a5c7-0939408d436d\nINFO     /tmp/biobb/unitests_20/canonicalag/canonicalag_log.out:file_utils.py:390 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/backbone/canal_output_gammaW.ser to /tmp/biobb/unitests_20/canonicalag/98da34d0-6022-43d2-a5c7-0939408d436d\nINFO     /tmp/biobb/unitests_20/canonicalag/canonicalag_log.out:file_utils.py:390 Creating backbone_f845ca61-d888-4dc3-88d7-e088a28a48e0 temporary folder\nINFO     /tmp/biobb/unitests_20/canonicalag/canonicalag_log.out:file_utils.py:390 Removed: [&amp;#x27;/tmp/biobb/unitests_20/canonicalag/98da34d0-6022-43d2-a5c7-0939408d436d&amp;#x27;, &amp;#x27;backbone_f845ca61-d888-4dc3-88d7-e088a28a48e0&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_20\n&#34;}], &#34;biobb_dna/test/unitests/test_backbone/test_puckering.py::TestPuckering::test_puckering&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_dna/test/unitests/test_backbone/test_puckering.py::TestPuckering::test_puckering&#34;, &#34;duration&#34;: &#34;627 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_dna/test/unitests/test_backbone/test_puckering.py::TestPuckering::test_puckering&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;627 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-05-07 09:06:02,924 [MainThread  ] [INFO ]  Executing biobb_dna.backbone.puckering Version: 4.1.0\n2024-05-07 09:06:02,925 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/backbone/canal_output_phaseC.ser to /tmp/biobb/unitests_20/puckering/7bd5b26d-788f-4fa6-b22f-4f30d530f875\n2024-05-07 09:06:02,926 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/backbone/canal_output_phaseW.ser to /tmp/biobb/unitests_20/puckering/7bd5b26d-788f-4fa6-b22f-4f30d530f875\n2024-05-07 09:06:02,926 [MainThread  ] [INFO ]  Creating backbone_bdb061cc-6c6c-43a6-8f9e-3bcb05339241 temporary folder\n2024-05-07 09:06:03,438 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_20/puckering/7bd5b26d-788f-4fa6-b22f-4f30d530f875&amp;#x27;, &amp;#x27;backbone_bdb061cc-6c6c-43a6-8f9e-3bcb05339241&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_20/puckering/puckering.csv\nChecking if empty file: /tmp/biobb/unitests_20/puckering/puckering.jpg\nComparing images of both files:\n     IMAGE_A: /tmp/biobb/unitests_20/puckering/puckering.jpg\n     IMAGE_B: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/reference/backbone/puckering_ref.jpg\n     IMAGE_A HASH: eb8181808081ffff SIZE: 64 bits\n     IMAGE_B HASH: fb8181808081ffff SIZE: 64 bits\n     TOLERANCE: 1.0%, ABS TOLERANCE: 1 bits, DIFFERENCE: 1 bits\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_20/puckering/puckering_log.out:file_utils.py:390 Executing biobb_dna.backbone.puckering Version: 4.1.0\nINFO     /tmp/biobb/unitests_20/puckering/puckering_log.out:file_utils.py:390 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/backbone/canal_output_phaseC.ser to /tmp/biobb/unitests_20/puckering/7bd5b26d-788f-4fa6-b22f-4f30d530f875\nINFO     /tmp/biobb/unitests_20/puckering/puckering_log.out:file_utils.py:390 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/backbone/canal_output_phaseW.ser to /tmp/biobb/unitests_20/puckering/7bd5b26d-788f-4fa6-b22f-4f30d530f875\nINFO     /tmp/biobb/unitests_20/puckering/puckering_log.out:file_utils.py:390 Creating backbone_bdb061cc-6c6c-43a6-8f9e-3bcb05339241 temporary folder\nINFO     /tmp/biobb/unitests_20/puckering/puckering_log.out:file_utils.py:390 Removed: [&amp;#x27;/tmp/biobb/unitests_20/puckering/7bd5b26d-788f-4fa6-b22f-4f30d530f875&amp;#x27;, &amp;#x27;backbone_bdb061cc-6c6c-43a6-8f9e-3bcb05339241&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_20\n&#34;}], &#34;biobb_dna/test/unitests/test_correlation/test_correlation.py::TestInterHelparCorrelation::test_helparcorrelation&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_dna/test/unitests/test_correlation/test_correlation.py::TestInterHelparCorrelation::test_helparcorrelation&#34;, &#34;duration&#34;: &#34;339 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_dna/test/unitests/test_correlation/test_correlation.py::TestInterHelparCorrelation::test_helparcorrelation&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;339 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-05-07 09:06:03,553 [MainThread  ] [INFO ]  Executing biobb_dna.interbp_correlations.interhpcorr Version: 4.1.0\n2024-05-07 09:06:03,554 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_shift_AA.csv to /tmp/biobb/unitests_20/interhpcorr/b81aeb28-eed2-4ed2-89b8-62f062b0cafa\n2024-05-07 09:06:03,554 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_slide_AA.csv to /tmp/biobb/unitests_20/interhpcorr/b81aeb28-eed2-4ed2-89b8-62f062b0cafa\n2024-05-07 09:06:03,554 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_rise_AA.csv to /tmp/biobb/unitests_20/interhpcorr/b81aeb28-eed2-4ed2-89b8-62f062b0cafa\n2024-05-07 09:06:03,554 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_tilt_AA.csv to /tmp/biobb/unitests_20/interhpcorr/b81aeb28-eed2-4ed2-89b8-62f062b0cafa\n2024-05-07 09:06:03,555 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_roll_AA.csv to /tmp/biobb/unitests_20/interhpcorr/b81aeb28-eed2-4ed2-89b8-62f062b0cafa\n2024-05-07 09:06:03,555 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_twist_AA.csv to /tmp/biobb/unitests_20/interhpcorr/b81aeb28-eed2-4ed2-89b8-62f062b0cafa\n2024-05-07 09:06:03,555 [MainThread  ] [INFO ]  Creating hpcorrelation_f1380a86-41c5-4a9d-aeab-b65436d0bc7e temporary folder\n2024-05-07 09:06:03,783 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_20/interhpcorr/b81aeb28-eed2-4ed2-89b8-62f062b0cafa&amp;#x27;, &amp;#x27;hpcorrelation_f1380a86-41c5-4a9d-aeab-b65436d0bc7e&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_20/interhpcorr/inter_hpcorr.csv\nChecking if empty file: /tmp/biobb/unitests_20/interhpcorr/inter_hpcorr.jpg\nComparing images of both files:\n     IMAGE_A: /tmp/biobb/unitests_20/interhpcorr/inter_hpcorr.jpg\n     IMAGE_B: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/reference/correlation/inter_hpcorr_ref.jpg\n     IMAGE_A HASH: ff83868890a1c0ff SIZE: 64 bits\n     IMAGE_B HASH: ff83868890a1c0ff SIZE: 64 bits\n     TOLERANCE: 1.0%, ABS TOLERANCE: 1 bits, DIFFERENCE: 0 bits\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_20/interhpcorr/log.out:file_utils.py:390 Executing biobb_dna.interbp_correlations.interhpcorr Version: 4.1.0\nINFO     /tmp/biobb/unitests_20/interhpcorr/log.out:file_utils.py:390 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_shift_AA.csv to /tmp/biobb/unitests_20/interhpcorr/b81aeb28-eed2-4ed2-89b8-62f062b0cafa\nINFO     /tmp/biobb/unitests_20/interhpcorr/log.out:file_utils.py:390 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_slide_AA.csv to /tmp/biobb/unitests_20/interhpcorr/b81aeb28-eed2-4ed2-89b8-62f062b0cafa\nINFO     /tmp/biobb/unitests_20/interhpcorr/log.out:file_utils.py:390 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_rise_AA.csv to /tmp/biobb/unitests_20/interhpcorr/b81aeb28-eed2-4ed2-89b8-62f062b0cafa\nINFO     /tmp/biobb/unitests_20/interhpcorr/log.out:file_utils.py:390 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_tilt_AA.csv to /tmp/biobb/unitests_20/interhpcorr/b81aeb28-eed2-4ed2-89b8-62f062b0cafa\nINFO     /tmp/biobb/unitests_20/interhpcorr/log.out:file_utils.py:390 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_roll_AA.csv to /tmp/biobb/unitests_20/interhpcorr/b81aeb28-eed2-4ed2-89b8-62f062b0cafa\nINFO     /tmp/biobb/unitests_20/interhpcorr/log.out:file_utils.py:390 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_twist_AA.csv to /tmp/biobb/unitests_20/interhpcorr/b81aeb28-eed2-4ed2-89b8-62f062b0cafa\nINFO     /tmp/biobb/unitests_20/interhpcorr/log.out:file_utils.py:390 Creating hpcorrelation_f1380a86-41c5-4a9d-aeab-b65436d0bc7e temporary folder\nINFO     /tmp/biobb/unitests_20/interhpcorr/log.out:file_utils.py:390 Removed: [&amp;#x27;/tmp/biobb/unitests_20/interhpcorr/b81aeb28-eed2-4ed2-89b8-62f062b0cafa&amp;#x27;, &amp;#x27;hpcorrelation_f1380a86-41c5-4a9d-aeab-b65436d0bc7e&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_20\n&#34;}], &#34;biobb_dna/test/unitests/test_correlation/test_correlation.py::TestInterSequenceCorrelation::test_sequencecorrelation&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_dna/test/unitests/test_correlation/test_correlation.py::TestInterSequenceCorrelation::test_sequencecorrelation&#34;, &#34;duration&#34;: &#34;415 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_dna/test/unitests/test_correlation/test_correlation.py::TestInterSequenceCorrelation::test_sequencecorrelation&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;415 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-05-07 09:06:03,893 [MainThread  ] [INFO ]  Executing biobb_dna.interbp_correlations.interseqcorr Version: 4.1.0\n2024-05-07 09:06:03,894 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_roll.ser to /tmp/biobb/unitests_20/interseqcorr/cbe20a13-171f-47dd-83e8-0f3818d8cb12\n2024-05-07 09:06:03,895 [MainThread  ] [INFO ]  Creating bpcorrelation_ec2e7a16-0366-47ac-9b71-c2f9df2993dd temporary folder\n2024-05-07 09:06:04,197 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_20/interseqcorr/cbe20a13-171f-47dd-83e8-0f3818d8cb12&amp;#x27;, &amp;#x27;bpcorrelation_ec2e7a16-0366-47ac-9b71-c2f9df2993dd&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_20/interseqcorr/inter_seqcorr.csv\nChecking if empty file: /tmp/biobb/unitests_20/interseqcorr/inter_seqcorr.jpg\nComparing images of both files:\n     IMAGE_A: /tmp/biobb/unitests_20/interseqcorr/inter_seqcorr.jpg\n     IMAGE_B: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/reference/correlation/inter_seqcorr_roll.jpg\n     IMAGE_A HASH: ff8080889080c0ff SIZE: 64 bits\n     IMAGE_B HASH: ff8080889080c0ff SIZE: 64 bits\n     TOLERANCE: 1.0%, ABS TOLERANCE: 1 bits, DIFFERENCE: 0 bits\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_20/interseqcorr/interseqcorr_log.out:file_utils.py:390 Executing biobb_dna.interbp_correlations.interseqcorr Version: 4.1.0\nINFO     /tmp/biobb/unitests_20/interseqcorr/interseqcorr_log.out:file_utils.py:390 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_roll.ser to /tmp/biobb/unitests_20/interseqcorr/cbe20a13-171f-47dd-83e8-0f3818d8cb12\nINFO     /tmp/biobb/unitests_20/interseqcorr/interseqcorr_log.out:file_utils.py:390 Creating bpcorrelation_ec2e7a16-0366-47ac-9b71-c2f9df2993dd temporary folder\nINFO     /tmp/biobb/unitests_20/interseqcorr/interseqcorr_log.out:file_utils.py:390 Removed: [&amp;#x27;/tmp/biobb/unitests_20/interseqcorr/cbe20a13-171f-47dd-83e8-0f3818d8cb12&amp;#x27;, &amp;#x27;bpcorrelation_ec2e7a16-0366-47ac-9b71-c2f9df2993dd&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_20\n&#34;}], &#34;biobb_dna/test/unitests/test_correlation/test_correlation.py::TestInterBasepairCorrelation::test_basepaircorrelation&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_dna/test/unitests/test_correlation/test_correlation.py::TestInterBasepairCorrelation::test_basepaircorrelation&#34;, &#34;duration&#34;: &#34;932 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_dna/test/unitests/test_correlation/test_correlation.py::TestInterBasepairCorrelation::test_basepaircorrelation&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;932 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-05-07 09:06:04,310 [MainThread  ] [INFO ]  Executing biobb_dna.interbp_correlations.interbpcorr Version: 4.1.0\n2024-05-07 09:06:04,311 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_shift.ser to /tmp/biobb/unitests_20/interbpcorr/b5cfde97-87a2-4507-8e03-9ea5e3a486eb\n2024-05-07 09:06:04,311 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_slide.ser to /tmp/biobb/unitests_20/interbpcorr/b5cfde97-87a2-4507-8e03-9ea5e3a486eb\n2024-05-07 09:06:04,312 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_rise.ser to /tmp/biobb/unitests_20/interbpcorr/b5cfde97-87a2-4507-8e03-9ea5e3a486eb\n2024-05-07 09:06:04,313 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_tilt.ser to /tmp/biobb/unitests_20/interbpcorr/b5cfde97-87a2-4507-8e03-9ea5e3a486eb\n2024-05-07 09:06:04,314 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_roll.ser to /tmp/biobb/unitests_20/interbpcorr/b5cfde97-87a2-4507-8e03-9ea5e3a486eb\n2024-05-07 09:06:04,314 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_twist.ser to /tmp/biobb/unitests_20/interbpcorr/b5cfde97-87a2-4507-8e03-9ea5e3a486eb\n2024-05-07 09:06:04,315 [MainThread  ] [INFO ]  Creating bpcorrelation_e2fde7aa-25db-475b-8132-f5aafabcb8ce temporary folder\n2024-05-07 09:06:05,115 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_20/interbpcorr/b5cfde97-87a2-4507-8e03-9ea5e3a486eb&amp;#x27;, &amp;#x27;bpcorrelation_e2fde7aa-25db-475b-8132-f5aafabcb8ce&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_20/interbpcorr/inter_bpcorr.csv\nChecking if empty file: /tmp/biobb/unitests_20/interbpcorr/inter_bpcorr.jpg\nComparing images of both files:\n     IMAGE_A: /tmp/biobb/unitests_20/interbpcorr/inter_bpcorr.jpg\n     IMAGE_B: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/reference/correlation/inter_bpcorr_ref.jpg\n     IMAGE_A HASH: fd6d6dfffd6c0183 SIZE: 64 bits\n     IMAGE_B HASH: fd6d6dfffd6c0183 SIZE: 64 bits\n     TOLERANCE: 1.0%, ABS TOLERANCE: 1 bits, DIFFERENCE: 0 bits\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_20/interbpcorr/interbpcorr_log.out:file_utils.py:390 Executing biobb_dna.interbp_correlations.interbpcorr Version: 4.1.0\nINFO     /tmp/biobb/unitests_20/interbpcorr/interbpcorr_log.out:file_utils.py:390 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_shift.ser to /tmp/biobb/unitests_20/interbpcorr/b5cfde97-87a2-4507-8e03-9ea5e3a486eb\nINFO     /tmp/biobb/unitests_20/interbpcorr/interbpcorr_log.out:file_utils.py:390 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_slide.ser to /tmp/biobb/unitests_20/interbpcorr/b5cfde97-87a2-4507-8e03-9ea5e3a486eb\nINFO     /tmp/biobb/unitests_20/interbpcorr/interbpcorr_log.out:file_utils.py:390 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_rise.ser to /tmp/biobb/unitests_20/interbpcorr/b5cfde97-87a2-4507-8e03-9ea5e3a486eb\nINFO     /tmp/biobb/unitests_20/interbpcorr/interbpcorr_log.out:file_utils.py:390 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_tilt.ser to /tmp/biobb/unitests_20/interbpcorr/b5cfde97-87a2-4507-8e03-9ea5e3a486eb\nINFO     /tmp/biobb/unitests_20/interbpcorr/interbpcorr_log.out:file_utils.py:390 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_roll.ser to /tmp/biobb/unitests_20/interbpcorr/b5cfde97-87a2-4507-8e03-9ea5e3a486eb\nINFO     /tmp/biobb/unitests_20/interbpcorr/interbpcorr_log.out:file_utils.py:390 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_twist.ser to /tmp/biobb/unitests_20/interbpcorr/b5cfde97-87a2-4507-8e03-9ea5e3a486eb\nINFO     /tmp/biobb/unitests_20/interbpcorr/interbpcorr_log.out:file_utils.py:390 Creating bpcorrelation_e2fde7aa-25db-475b-8132-f5aafabcb8ce temporary folder\nINFO     /tmp/biobb/unitests_20/interbpcorr/interbpcorr_log.out:file_utils.py:390 Removed: [&amp;#x27;/tmp/biobb/unitests_20/interbpcorr/b5cfde97-87a2-4507-8e03-9ea5e3a486eb&amp;#x27;, &amp;#x27;bpcorrelation_e2fde7aa-25db-475b-8132-f5aafabcb8ce&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_20\n&#34;}], &#34;biobb_dna/test/unitests/test_correlation/test_correlation.py::TestIntraHelparCorrelation::test_helparcorrelation&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_dna/test/unitests/test_correlation/test_correlation.py::TestIntraHelparCorrelation::test_helparcorrelation&#34;, &#34;duration&#34;: &#34;871 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_dna/test/unitests/test_correlation/test_correlation.py::TestIntraHelparCorrelation::test_helparcorrelation&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;871 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-05-07 09:06:05,244 [MainThread  ] [INFO ]  Executing biobb_dna.intrabp_correlations.intrahpcorr Version: 4.1.0\n2024-05-07 09:06:05,244 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/series_shear_A.csv to /tmp/biobb/unitests_20/intrahpcorr/8ba2ea2d-ad92-480b-9a8b-5e111c9b153c\n2024-05-07 09:06:05,245 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/series_stretch_A.csv to /tmp/biobb/unitests_20/intrahpcorr/8ba2ea2d-ad92-480b-9a8b-5e111c9b153c\n2024-05-07 09:06:05,245 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/series_stagger_A.csv to /tmp/biobb/unitests_20/intrahpcorr/8ba2ea2d-ad92-480b-9a8b-5e111c9b153c\n2024-05-07 09:06:05,245 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/series_buckle_A.csv to /tmp/biobb/unitests_20/intrahpcorr/8ba2ea2d-ad92-480b-9a8b-5e111c9b153c\n2024-05-07 09:06:05,245 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/series_propel_A.csv to /tmp/biobb/unitests_20/intrahpcorr/8ba2ea2d-ad92-480b-9a8b-5e111c9b153c\n2024-05-07 09:06:05,246 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/series_opening_A.csv to /tmp/biobb/unitests_20/intrahpcorr/8ba2ea2d-ad92-480b-9a8b-5e111c9b153c\n2024-05-07 09:06:05,246 [MainThread  ] [INFO ]  Creating hpcorrelation_4cf79d6f-8a0f-4909-b002-80bbfbf54b6f temporary folder\n2024-05-07 09:06:06,002 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_20/intrahpcorr/8ba2ea2d-ad92-480b-9a8b-5e111c9b153c&amp;#x27;, &amp;#x27;hpcorrelation_4cf79d6f-8a0f-4909-b002-80bbfbf54b6f&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_20/intrahpcorr/intra_hpcorr.csv\nChecking if empty file: /tmp/biobb/unitests_20/intrahpcorr/intra_hpcorr.jpg\nComparing images of both files:\n     IMAGE_A: /tmp/biobb/unitests_20/intrahpcorr/intra_hpcorr.jpg\n     IMAGE_B: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/reference/correlation/intra_hpcorr_ref.jpg\n     IMAGE_A HASH: fb81848890a0e0ff SIZE: 64 bits\n     IMAGE_B HASH: fb81848890a0e0ff SIZE: 64 bits\n     TOLERANCE: 1.0%, ABS TOLERANCE: 1 bits, DIFFERENCE: 0 bits\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_20/intrahpcorr/log.out:file_utils.py:390 Executing biobb_dna.intrabp_correlations.intrahpcorr Version: 4.1.0\nINFO     /tmp/biobb/unitests_20/intrahpcorr/log.out:file_utils.py:390 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/series_shear_A.csv to /tmp/biobb/unitests_20/intrahpcorr/8ba2ea2d-ad92-480b-9a8b-5e111c9b153c\nINFO     /tmp/biobb/unitests_20/intrahpcorr/log.out:file_utils.py:390 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/series_stretch_A.csv to /tmp/biobb/unitests_20/intrahpcorr/8ba2ea2d-ad92-480b-9a8b-5e111c9b153c\nINFO     /tmp/biobb/unitests_20/intrahpcorr/log.out:file_utils.py:390 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/series_stagger_A.csv to /tmp/biobb/unitests_20/intrahpcorr/8ba2ea2d-ad92-480b-9a8b-5e111c9b153c\nINFO     /tmp/biobb/unitests_20/intrahpcorr/log.out:file_utils.py:390 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/series_buckle_A.csv to /tmp/biobb/unitests_20/intrahpcorr/8ba2ea2d-ad92-480b-9a8b-5e111c9b153c\nINFO     /tmp/biobb/unitests_20/intrahpcorr/log.out:file_utils.py:390 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/series_propel_A.csv to /tmp/biobb/unitests_20/intrahpcorr/8ba2ea2d-ad92-480b-9a8b-5e111c9b153c\nINFO     /tmp/biobb/unitests_20/intrahpcorr/log.out:file_utils.py:390 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/series_opening_A.csv to /tmp/biobb/unitests_20/intrahpcorr/8ba2ea2d-ad92-480b-9a8b-5e111c9b153c\nINFO     /tmp/biobb/unitests_20/intrahpcorr/log.out:file_utils.py:390 Creating hpcorrelation_4cf79d6f-8a0f-4909-b002-80bbfbf54b6f temporary folder\nINFO     /tmp/biobb/unitests_20/intrahpcorr/log.out:file_utils.py:390 Removed: [&amp;#x27;/tmp/biobb/unitests_20/intrahpcorr/8ba2ea2d-ad92-480b-9a8b-5e111c9b153c&amp;#x27;, &amp;#x27;hpcorrelation_4cf79d6f-8a0f-4909-b002-80bbfbf54b6f&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_20\n&#34;}], &#34;biobb_dna/test/unitests/test_correlation/test_correlation.py::TestIntraSequenceCorrelation::test_sequencecorrelation&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_dna/test/unitests/test_correlation/test_correlation.py::TestIntraSequenceCorrelation::test_sequencecorrelation&#34;, &#34;duration&#34;: &#34;421 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_dna/test/unitests/test_correlation/test_correlation.py::TestIntraSequenceCorrelation::test_sequencecorrelation&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;421 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-05-07 09:06:06,117 [MainThread  ] [INFO ]  Executing biobb_dna.intrabp_correlations.intraseqcorr Version: 4.1.0\n2024-05-07 09:06:06,118 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_buckle.ser to /tmp/biobb/unitests_20/intraseqcorr/e8d9c930-6be7-41db-a5d0-3c22b9042364\n2024-05-07 09:06:06,118 [MainThread  ] [INFO ]  Creating bpcorrelation_58a50fa5-e507-4ec9-8b3b-97a38942a223 temporary folder\n2024-05-07 09:06:06,424 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_20/intraseqcorr/e8d9c930-6be7-41db-a5d0-3c22b9042364&amp;#x27;, &amp;#x27;bpcorrelation_58a50fa5-e507-4ec9-8b3b-97a38942a223&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_20/intraseqcorr/intra_seqcorr.csv\nChecking if empty file: /tmp/biobb/unitests_20/intraseqcorr/intra_seqcorr.jpg\nComparing images of both files:\n     IMAGE_A: /tmp/biobb/unitests_20/intraseqcorr/intra_seqcorr.jpg\n     IMAGE_B: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/reference/correlation/intra_seqcorr_buckle.jpg\n     IMAGE_A HASH: ff83848890a0c0ff SIZE: 64 bits\n     IMAGE_B HASH: ff83848890a0c0ff SIZE: 64 bits\n     TOLERANCE: 1.0%, ABS TOLERANCE: 1 bits, DIFFERENCE: 0 bits\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_20/intraseqcorr/intraseqcorr_log.out:file_utils.py:390 Executing biobb_dna.intrabp_correlations.intraseqcorr Version: 4.1.0\nINFO     /tmp/biobb/unitests_20/intraseqcorr/intraseqcorr_log.out:file_utils.py:390 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_buckle.ser to /tmp/biobb/unitests_20/intraseqcorr/e8d9c930-6be7-41db-a5d0-3c22b9042364\nINFO     /tmp/biobb/unitests_20/intraseqcorr/intraseqcorr_log.out:file_utils.py:390 Creating bpcorrelation_58a50fa5-e507-4ec9-8b3b-97a38942a223 temporary folder\nINFO     /tmp/biobb/unitests_20/intraseqcorr/intraseqcorr_log.out:file_utils.py:390 Removed: [&amp;#x27;/tmp/biobb/unitests_20/intraseqcorr/e8d9c930-6be7-41db-a5d0-3c22b9042364&amp;#x27;, &amp;#x27;bpcorrelation_58a50fa5-e507-4ec9-8b3b-97a38942a223&amp;#x27;]\n\n&#34;}], &#34;biobb_dna/test/unitests/test_correlation/test_correlation.py::TestIntraBasepairCorrelation::test_basepaircorrelation&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_dna/test/unitests/test_correlation/test_correlation.py::TestIntraBasepairCorrelation::test_basepaircorrelation&#34;, &#34;duration&#34;: &#34;00:00:01&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_dna/test/unitests/test_correlation/test_correlation.py::TestIntraBasepairCorrelation::test_basepaircorrelation&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:00:01&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-05-07 09:06:06,539 [MainThread  ] [INFO ]  Executing biobb_dna.intrabp_correlations.intrabpcorr Version: 4.1.0\n2024-05-07 09:06:06,540 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_shear.ser to /tmp/biobb/unitests_21/intrabpcorr/a072357c-5677-4b34-a76d-f61f82f7e910\n2024-05-07 09:06:06,540 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_stretch.ser to /tmp/biobb/unitests_21/intrabpcorr/a072357c-5677-4b34-a76d-f61f82f7e910\n2024-05-07 09:06:06,541 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_stagger.ser to /tmp/biobb/unitests_21/intrabpcorr/a072357c-5677-4b34-a76d-f61f82f7e910\n2024-05-07 09:06:06,542 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_buckle.ser to /tmp/biobb/unitests_21/intrabpcorr/a072357c-5677-4b34-a76d-f61f82f7e910\n2024-05-07 09:06:06,543 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_propel.ser to /tmp/biobb/unitests_21/intrabpcorr/a072357c-5677-4b34-a76d-f61f82f7e910\n2024-05-07 09:06:06,544 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_opening.ser to /tmp/biobb/unitests_21/intrabpcorr/a072357c-5677-4b34-a76d-f61f82f7e910\n2024-05-07 09:06:06,544 [MainThread  ] [INFO ]  Creating bpcorrelation_90d3594e-0cf7-4d4d-94ef-647e3c524648 temporary folder\n2024-05-07 09:06:07,416 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_21/intrabpcorr/a072357c-5677-4b34-a76d-f61f82f7e910&amp;#x27;, &amp;#x27;bpcorrelation_90d3594e-0cf7-4d4d-94ef-647e3c524648&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_21/intrabpcorr/intra_bpcorr.csv\nChecking if empty file: /tmp/biobb/unitests_21/intrabpcorr/intra_bpcorr.jpg\nComparing images of both files:\n     IMAGE_A: /tmp/biobb/unitests_21/intrabpcorr/intra_bpcorr.jpg\n     IMAGE_B: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/reference/correlation/intra_bpcorr_ref.jpg\n     IMAGE_A HASH: 01f5f7f7fcf40183 SIZE: 64 bits\n     IMAGE_B HASH: 01f5f7f7fcf40183 SIZE: 64 bits\n     TOLERANCE: 1.0%, ABS TOLERANCE: 1 bits, DIFFERENCE: 0 bits\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_21/intrabpcorr/intrabpcorr_log.out:file_utils.py:390 Executing biobb_dna.intrabp_correlations.intrabpcorr Version: 4.1.0\nINFO     /tmp/biobb/unitests_21/intrabpcorr/intrabpcorr_log.out:file_utils.py:390 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_shear.ser to /tmp/biobb/unitests_21/intrabpcorr/a072357c-5677-4b34-a76d-f61f82f7e910\nINFO     /tmp/biobb/unitests_21/intrabpcorr/intrabpcorr_log.out:file_utils.py:390 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_stretch.ser to /tmp/biobb/unitests_21/intrabpcorr/a072357c-5677-4b34-a76d-f61f82f7e910\nINFO     /tmp/biobb/unitests_21/intrabpcorr/intrabpcorr_log.out:file_utils.py:390 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_stagger.ser to /tmp/biobb/unitests_21/intrabpcorr/a072357c-5677-4b34-a76d-f61f82f7e910\nINFO     /tmp/biobb/unitests_21/intrabpcorr/intrabpcorr_log.out:file_utils.py:390 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_buckle.ser to /tmp/biobb/unitests_21/intrabpcorr/a072357c-5677-4b34-a76d-f61f82f7e910\nINFO     /tmp/biobb/unitests_21/intrabpcorr/intrabpcorr_log.out:file_utils.py:390 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_propel.ser to /tmp/biobb/unitests_21/intrabpcorr/a072357c-5677-4b34-a76d-f61f82f7e910\nINFO     /tmp/biobb/unitests_21/intrabpcorr/intrabpcorr_log.out:file_utils.py:390 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_opening.ser to /tmp/biobb/unitests_21/intrabpcorr/a072357c-5677-4b34-a76d-f61f82f7e910\nINFO     /tmp/biobb/unitests_21/intrabpcorr/intrabpcorr_log.out:file_utils.py:390 Creating bpcorrelation_90d3594e-0cf7-4d4d-94ef-647e3c524648 temporary folder\nINFO     /tmp/biobb/unitests_21/intrabpcorr/intrabpcorr_log.out:file_utils.py:390 Removed: [&amp;#x27;/tmp/biobb/unitests_21/intrabpcorr/a072357c-5677-4b34-a76d-f61f82f7e910&amp;#x27;, &amp;#x27;bpcorrelation_90d3594e-0cf7-4d4d-94ef-647e3c524648&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_21\n&#34;}], &#34;biobb_dna/test/unitests/test_curvesplus/test_canal.py::TestCanal::test_canal&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_dna/test/unitests/test_curvesplus/test_canal.py::TestCanal::test_canal&#34;, &#34;duration&#34;: &#34;00:00:03&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_dna/test/unitests/test_curvesplus/test_canal.py::TestCanal::test_canal&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:00:03&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-05-07 09:06:07,546 [MainThread  ] [INFO ]  Executing biobb_dna.curvesplus.biobb_canal Version: 4.1.0\n2024-05-07 09:06:07,558 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/curvesplus/curves_output.cda to /tmp/biobb/unitests_21/biobb_canal/d5af399b-1081-4231-b5a6-cc2fbd925398\n2024-05-07 09:06:07,558 [MainThread  ] [INFO ]  Creating canal_58f1d732-de50-4f57-8d20-bf85a7e0270d temporary folder\n2024-05-07 09:06:07,569 [MainThread  ] [INFO ]  Creating command line with instructions and required arguments\n2024-05-07 09:06:07,569 [MainThread  ] [INFO ]  Canal &amp;lt;&amp;lt;! \n&amp;amp;inp\n  lis=canal_output,\n  cormin=0.6,\n  lev1=0,lev2=0,\n  itst=0,itnd=0,itdel=1,\n  histo=.f.,\n  series=.t.,\n  corr=.f.,\n&amp;amp;end\ncurves_output.cda CGCGAATTCGCG\n!\n\n2024-05-07 09:06:10,917 [MainThread  ] [INFO ]  Exit code 0\n\n2024-05-07 09:06:10,976 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_21/biobb_canal/d5af399b-1081-4231-b5a6-cc2fbd925398&amp;#x27;, &amp;#x27;canal_58f1d732-de50-4f57-8d20-bf85a7e0270d&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_21/biobb_canal/canal_output.zip\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_21/biobb_canal/biobb_canal_log.out:file_utils.py:390 Executing biobb_dna.curvesplus.biobb_canal Version: 4.1.0\nINFO     /tmp/biobb/unitests_21/biobb_canal/biobb_canal_log.out:file_utils.py:390 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/curvesplus/curves_output.cda to /tmp/biobb/unitests_21/biobb_canal/d5af399b-1081-4231-b5a6-cc2fbd925398\nINFO     /tmp/biobb/unitests_21/biobb_canal/biobb_canal_log.out:file_utils.py:390 Creating canal_58f1d732-de50-4f57-8d20-bf85a7e0270d temporary folder\nINFO     /tmp/biobb/unitests_21/biobb_canal/biobb_canal_log.out:file_utils.py:390 Creating command line with instructions and required arguments\nINFO     /tmp/biobb/unitests_21/biobb_canal/biobb_canal_log.out:cmd_wrapper.py:33 Canal &amp;lt;&amp;lt;! \n&amp;amp;inp\n  lis=canal_output,\n  cormin=0.6,\n  lev1=0,lev2=0,\n  itst=0,itnd=0,itdel=1,\n  histo=.f.,\n  series=.t.,\n  corr=.f.,\n&amp;amp;end\ncurves_output.cda CGCGAATTCGCG\n!\n\nINFO     /tmp/biobb/unitests_21/biobb_canal/biobb_canal_log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     /tmp/biobb/unitests_21/biobb_canal/biobb_canal_log.out:file_utils.py:390 Removed: [&amp;#x27;/tmp/biobb/unitests_21/biobb_canal/d5af399b-1081-4231-b5a6-cc2fbd925398&amp;#x27;, &amp;#x27;canal_58f1d732-de50-4f57-8d20-bf85a7e0270d&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_21\n&#34;}], &#34;biobb_dna/test/unitests/test_curvesplus/test_canion.py::TestCanal::test_canion&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_dna/test/unitests/test_curvesplus/test_canion.py::TestCanal::test_canion&#34;, &#34;duration&#34;: &#34;735 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_dna/test/unitests/test_curvesplus/test_canion.py::TestCanal::test_canion&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;735 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-05-07 09:06:11,022 [MainThread  ] [INFO ]  Executing biobb_dna.curvesplus.biobb_canion Version: 4.1.0\n2024-05-07 09:06:11,325 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/curvesplus/THGA_K.cdi to /tmp/biobb/unitests_21/biobb_canion/24ad8692-d8e7-4b59-a14a-8f70818b9fde\n2024-05-07 09:06:11,326 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/curvesplus/THGA.afr to /tmp/biobb/unitests_21/biobb_canion/24ad8692-d8e7-4b59-a14a-8f70818b9fde\n2024-05-07 09:06:11,326 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/curvesplus/THGA_avg.pdb to /tmp/biobb/unitests_21/biobb_canion/24ad8692-d8e7-4b59-a14a-8f70818b9fde\n2024-05-07 09:06:11,326 [MainThread  ] [INFO ]  Creating canion_62150d84-e5db-4035-9046-6a522701fd4d temporary folder\n2024-05-07 09:06:11,619 [MainThread  ] [INFO ]  Creating command line with instructions and required arguments\n2024-05-07 09:06:11,619 [MainThread  ] [INFO ]  Canion &amp;lt;&amp;lt;! \n&amp;amp;inp\n  lis=canion_output,\n  dat=THGA_K,\n  axfrm=THGA,\n  solute=THGA_avg,\n  type=K+,\n  dlow=5.8,\n  dhig=7.2,\n  rlow=0,\n  rhig=18,\n  alow=0,\n  ahig=360,\n&amp;amp;end\n!\n\n2024-05-07 09:06:11,632 [MainThread  ] [INFO ]  Exit code 0\n\n2024-05-07 09:06:11,717 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_21/biobb_canion/24ad8692-d8e7-4b59-a14a-8f70818b9fde&amp;#x27;, &amp;#x27;canion_62150d84-e5db-4035-9046-6a522701fd4d&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_21/biobb_canion/canion_output.zip\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_21/biobb_canion/biobb_canion_log.out:file_utils.py:390 Executing biobb_dna.curvesplus.biobb_canion Version: 4.1.0\nINFO     /tmp/biobb/unitests_21/biobb_canion/biobb_canion_log.out:file_utils.py:390 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/curvesplus/THGA_K.cdi to /tmp/biobb/unitests_21/biobb_canion/24ad8692-d8e7-4b59-a14a-8f70818b9fde\nINFO     /tmp/biobb/unitests_21/biobb_canion/biobb_canion_log.out:file_utils.py:390 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/curvesplus/THGA.afr to /tmp/biobb/unitests_21/biobb_canion/24ad8692-d8e7-4b59-a14a-8f70818b9fde\nINFO     /tmp/biobb/unitests_21/biobb_canion/biobb_canion_log.out:file_utils.py:390 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/curvesplus/THGA_avg.pdb to /tmp/biobb/unitests_21/biobb_canion/24ad8692-d8e7-4b59-a14a-8f70818b9fde\nINFO     /tmp/biobb/unitests_21/biobb_canion/biobb_canion_log.out:file_utils.py:390 Creating canion_62150d84-e5db-4035-9046-6a522701fd4d temporary folder\nINFO     /tmp/biobb/unitests_21/biobb_canion/biobb_canion_log.out:file_utils.py:390 Creating command line with instructions and required arguments\nINFO     /tmp/biobb/unitests_21/biobb_canion/biobb_canion_log.out:cmd_wrapper.py:33 Canion &amp;lt;&amp;lt;! \n&amp;amp;inp\n  lis=canion_output,\n  dat=THGA_K,\n  axfrm=THGA,\n  solute=THGA_avg,\n  type=K+,\n  dlow=5.8,\n  dhig=7.2,\n  rlow=0,\n  rhig=18,\n  alow=0,\n  ahig=360,\n&amp;amp;end\n!\n\nINFO     /tmp/biobb/unitests_21/biobb_canion/biobb_canion_log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     /tmp/biobb/unitests_21/biobb_canion/biobb_canion_log.out:file_utils.py:390 Removed: [&amp;#x27;/tmp/biobb/unitests_21/biobb_canion/24ad8692-d8e7-4b59-a14a-8f70818b9fde&amp;#x27;, &amp;#x27;canion_62150d84-e5db-4035-9046-6a522701fd4d&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_21\n&#34;}], &#34;biobb_dna/test/unitests/test_curvesplus/test_curves.py::TestCurves::test_curves&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_dna/test/unitests/test_curvesplus/test_curves.py::TestCurves::test_curves&#34;, &#34;duration&#34;: &#34;00:00:08&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_dna/test/unitests/test_curvesplus/test_curves.py::TestCurves::test_curves&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:00:08&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-05-07 09:06:11,761 [MainThread  ] [INFO ]  Executing biobb_dna.curvesplus.biobb_curves Version: 4.1.0\n2024-05-07 09:06:11,828 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/curvesplus/structure.stripped.trj to /tmp/biobb/unitests_21/biobb_curves/e3c3accd-c8b3-48dd-97e9-a8267a495481\n2024-05-07 09:06:11,829 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/curvesplus/structure.stripped.top to /tmp/biobb/unitests_21/biobb_curves/e3c3accd-c8b3-48dd-97e9-a8267a495481\n2024-05-07 09:06:11,830 [MainThread  ] [INFO ]  Creating curves_63f77f35-5ff3-4b5f-b5b9-ee043c454e0b temporary folder\n2024-05-07 09:06:11,896 [MainThread  ] [INFO ]  Appending provided topology to command\n2024-05-07 09:06:11,896 [MainThread  ] [INFO ]  Creating command line with instructions and required arguments\n2024-05-07 09:06:11,896 [MainThread  ] [INFO ]  Cur+ &amp;lt;&amp;lt;! \n&amp;amp;inp\n  file=structure.stripped.trj,\n  ftop=structure.stripped.top,\n  lis=&amp;#x27;curves_output&amp;#x27;,\n  lib=/home/user/micromamba/envs/test_environment/.curvesplus/standard,\n  ions=.f.,\n  test=.f.,\n  line=.f.,\n  fit=.t.,\n  axfrm=.f.,\n  itst=0,itnd=0,itdel=1,\n&amp;amp;end\n2 1 -1 0 0\n1:12\n24:13\n!\n\n2024-05-07 09:06:18,529 [MainThread  ] [INFO ]  Exit code 0\n\n2024-05-07 09:06:19,555 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_21/biobb_curves/e3c3accd-c8b3-48dd-97e9-a8267a495481&amp;#x27;, &amp;#x27;curves_63f77f35-5ff3-4b5f-b5b9-ee043c454e0b&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_21/biobb_curves/curves_output.cda\nChecking if empty file: /tmp/biobb/unitests_21/biobb_curves/curves_output.lis\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_21/biobb_curves/biobb_curves_log.out:file_utils.py:390 Executing biobb_dna.curvesplus.biobb_curves Version: 4.1.0\nINFO     /tmp/biobb/unitests_21/biobb_curves/biobb_curves_log.out:file_utils.py:390 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/curvesplus/structure.stripped.trj to /tmp/biobb/unitests_21/biobb_curves/e3c3accd-c8b3-48dd-97e9-a8267a495481\nINFO     /tmp/biobb/unitests_21/biobb_curves/biobb_curves_log.out:file_utils.py:390 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/curvesplus/structure.stripped.top to /tmp/biobb/unitests_21/biobb_curves/e3c3accd-c8b3-48dd-97e9-a8267a495481\nINFO     /tmp/biobb/unitests_21/biobb_curves/biobb_curves_log.out:file_utils.py:390 Creating curves_63f77f35-5ff3-4b5f-b5b9-ee043c454e0b temporary folder\nINFO     /tmp/biobb/unitests_21/biobb_curves/biobb_curves_log.out:file_utils.py:390 Appending provided topology to command\nINFO     /tmp/biobb/unitests_21/biobb_curves/biobb_curves_log.out:file_utils.py:390 Creating command line with instructions and required arguments\nINFO     /tmp/biobb/unitests_21/biobb_curves/biobb_curves_log.out:cmd_wrapper.py:33 Cur+ &amp;lt;&amp;lt;! \n&amp;amp;inp\n  file=structure.stripped.trj,\n  ftop=structure.stripped.top,\n  lis=&amp;#x27;curves_output&amp;#x27;,\n  lib=/home/user/micromamba/envs/test_environment/.curvesplus/standard,\n  ions=.f.,\n  test=.f.,\n  line=.f.,\n  fit=.t.,\n  axfrm=.f.,\n  itst=0,itnd=0,itdel=1,\n&amp;amp;end\n2 1 -1 0 0\n1:12\n24:13\n!\n\nINFO     /tmp/biobb/unitests_21/biobb_curves/biobb_curves_log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     /tmp/biobb/unitests_21/biobb_curves/biobb_curves_log.out:file_utils.py:390 Removed: [&amp;#x27;/tmp/biobb/unitests_21/biobb_curves/e3c3accd-c8b3-48dd-97e9-a8267a495481&amp;#x27;, &amp;#x27;curves_63f77f35-5ff3-4b5f-b5b9-ee043c454e0b&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_21\n&#34;}], &#34;biobb_dna/test/unitests/test_dna/test_averages.py::TestAverages::test_helparaverages&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_dna/test/unitests/test_dna/test_averages.py::TestAverages::test_helparaverages&#34;, &#34;duration&#34;: &#34;322 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_dna/test/unitests/test_dna/test_averages.py::TestAverages::test_helparaverages&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;322 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-05-07 09:06:19,601 [MainThread  ] [INFO ]  Executing biobb_dna.dna.dna_averages Version: 4.1.0\n2024-05-07 09:06:19,602 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/dna/canal_output_shift.ser to /tmp/biobb/unitests_21/dna_averages/26bc891c-778f-44a7-9f8e-45fa984d7cda\n2024-05-07 09:06:19,602 [MainThread  ] [INFO ]  Creating averages_d4367eed-e610-4fb7-b728-2fe0822b5c70 temporary folder\n2024-05-07 09:06:19,814 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_21/dna_averages/26bc891c-778f-44a7-9f8e-45fa984d7cda&amp;#x27;, &amp;#x27;averages_d4367eed-e610-4fb7-b728-2fe0822b5c70&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_21/dna_averages/avg_out.csv\nChecking if empty file: /tmp/biobb/unitests_21/dna_averages/avg_out.jpg\nComparing images of both files:\n     IMAGE_A: /tmp/biobb/unitests_21/dna_averages/avg_out.jpg\n     IMAGE_B: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/reference/dna/shift_avg.jpg\n     IMAGE_A HASH: c07e3e32163f3ee3 SIZE: 64 bits\n     IMAGE_B HASH: c07e3e32163f3ee3 SIZE: 64 bits\n     TOLERANCE: 1.0%, ABS TOLERANCE: 1 bits, DIFFERENCE: 0 bits\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_21/dna_averages/dna_averages_log.out:file_utils.py:390 Executing biobb_dna.dna.dna_averages Version: 4.1.0\nINFO     /tmp/biobb/unitests_21/dna_averages/dna_averages_log.out:file_utils.py:390 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/dna/canal_output_shift.ser to /tmp/biobb/unitests_21/dna_averages/26bc891c-778f-44a7-9f8e-45fa984d7cda\nINFO     /tmp/biobb/unitests_21/dna_averages/dna_averages_log.out:file_utils.py:390 Creating averages_d4367eed-e610-4fb7-b728-2fe0822b5c70 temporary folder\nINFO     /tmp/biobb/unitests_21/dna_averages/dna_averages_log.out:file_utils.py:390 Removed: [&amp;#x27;/tmp/biobb/unitests_21/dna_averages/26bc891c-778f-44a7-9f8e-45fa984d7cda&amp;#x27;, &amp;#x27;averages_d4367eed-e610-4fb7-b728-2fe0822b5c70&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_21\n&#34;}], &#34;biobb_dna/test/unitests/test_dna/test_bimodality.py::TestBimodality::test_helparbimodality&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_dna/test/unitests/test_dna/test_bimodality.py::TestBimodality::test_helparbimodality&#34;, &#34;duration&#34;: &#34;711 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_dna/test/unitests/test_dna/test_bimodality.py::TestBimodality::test_helparbimodality&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;711 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-05-07 09:06:19,925 [MainThread  ] [INFO ]  Executing biobb_dna.dna.dna_bimodality Version: 4.1.0\n2024-05-07 09:06:19,925 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/dna/series_shift_AT.csv to /tmp/biobb/unitests_21/dna_bimodality/13ca29f7-8185-48c3-8f80-31481bf3114c\n2024-05-07 09:06:19,925 [MainThread  ] [INFO ]  Creating bimodality_5b827ac3-fa77-457a-9317-fe5cbba59fab temporary folder\n2024-05-07 09:06:20,595 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_21/dna_bimodality/13ca29f7-8185-48c3-8f80-31481bf3114c&amp;#x27;, &amp;#x27;bimodality_5b827ac3-fa77-457a-9317-fe5cbba59fab&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_21/dna_bimodality/bimod_out.csv\nChecking if empty file: /tmp/biobb/unitests_21/dna_bimodality/bimod_out.jpg\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_21/dna_bimodality/dna_bimodality_log.out:file_utils.py:390 Executing biobb_dna.dna.dna_bimodality Version: 4.1.0\nINFO     /tmp/biobb/unitests_21/dna_bimodality/dna_bimodality_log.out:file_utils.py:390 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/dna/series_shift_AT.csv to /tmp/biobb/unitests_21/dna_bimodality/13ca29f7-8185-48c3-8f80-31481bf3114c\nINFO     /tmp/biobb/unitests_21/dna_bimodality/dna_bimodality_log.out:file_utils.py:390 Creating bimodality_5b827ac3-fa77-457a-9317-fe5cbba59fab temporary folder\nINFO     /tmp/biobb/unitests_21/dna_bimodality/dna_bimodality_log.out:file_utils.py:390 Removed: [&amp;#x27;/tmp/biobb/unitests_21/dna_bimodality/13ca29f7-8185-48c3-8f80-31481bf3114c&amp;#x27;, &amp;#x27;bimodality_5b827ac3-fa77-457a-9317-fe5cbba59fab&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_21\n&#34;}], &#34;biobb_dna/test/unitests/test_dna/test_timeseries.py::TestTimeSeries::test_helpartimeseries&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_dna/test/unitests/test_dna/test_timeseries.py::TestTimeSeries::test_helpartimeseries&#34;, &#34;duration&#34;: &#34;00:00:04&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_dna/test/unitests/test_dna/test_timeseries.py::TestTimeSeries::test_helpartimeseries&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:00:04&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-05-07 09:06:20,639 [MainThread  ] [INFO ]  Executing biobb_dna.dna.dna_timeseries Version: 4.1.0\n2024-05-07 09:06:20,640 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/dna/canal_output_shift.ser to /tmp/biobb/unitests_21/dna_timeseries/4265b8a7-51eb-4cfe-b9b0-c418aa69a05c\n2024-05-07 09:06:20,640 [MainThread  ] [INFO ]  Creating timeseries_c7b4b900-9215-4b32-89e6-1d9fbc1979bf temporary folder\n2024-05-07 09:06:25,066 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_21/dna_timeseries/4265b8a7-51eb-4cfe-b9b0-c418aa69a05c&amp;#x27;, &amp;#x27;timeseries_c7b4b900-9215-4b32-89e6-1d9fbc1979bf&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_21/dna_timeseries/timeseries_output.zip\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_21/dna_timeseries/dna_timeseries_log.out:file_utils.py:390 Executing biobb_dna.dna.dna_timeseries Version: 4.1.0\nINFO     /tmp/biobb/unitests_21/dna_timeseries/dna_timeseries_log.out:file_utils.py:390 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/dna/canal_output_shift.ser to /tmp/biobb/unitests_21/dna_timeseries/4265b8a7-51eb-4cfe-b9b0-c418aa69a05c\nINFO     /tmp/biobb/unitests_21/dna_timeseries/dna_timeseries_log.out:file_utils.py:390 Creating timeseries_c7b4b900-9215-4b32-89e6-1d9fbc1979bf temporary folder\nINFO     /tmp/biobb/unitests_21/dna_timeseries/dna_timeseries_log.out:file_utils.py:390 Removed: [&amp;#x27;/tmp/biobb/unitests_21/dna_timeseries/4265b8a7-51eb-4cfe-b9b0-c418aa69a05c&amp;#x27;, &amp;#x27;timeseries_c7b4b900-9215-4b32-89e6-1d9fbc1979bf&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_21\n&#34;}], &#34;biobb_dna/test/unitests/test_stiffness/test_stiffness.py::TestAvgStiffness::test_averagestiffness&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_dna/test/unitests/test_stiffness/test_stiffness.py::TestAvgStiffness::test_averagestiffness&#34;, &#34;duration&#34;: &#34;313 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_dna/test/unitests/test_stiffness/test_stiffness.py::TestAvgStiffness::test_averagestiffness&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;313 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-05-07 09:06:25,107 [MainThread  ] [INFO ]  Executing biobb_dna.stiffness.average_stiffness Version: 4.1.0\n2024-05-07 09:06:25,108 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/canal_output_roll.ser to /tmp/biobb/unitests_21/average_stiffness/aafe6e34-1e91-46fb-8fca-58936ecfaca2\n2024-05-07 09:06:25,109 [MainThread  ] [INFO ]  Creating avgstiffness_b3d7e91a-00e2-446d-8a26-e10415361ee9 temporary folder\n2024-05-07 09:06:25,314 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_21/average_stiffness/aafe6e34-1e91-46fb-8fca-58936ecfaca2&amp;#x27;, &amp;#x27;avgstiffness_b3d7e91a-00e2-446d-8a26-e10415361ee9&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_21/average_stiffness/avgstiff.csv\nChecking if empty file: /tmp/biobb/unitests_21/average_stiffness/avgstiff.jpg\nComparing images of both files:\n     IMAGE_A: /tmp/biobb/unitests_21/average_stiffness/avgstiff.jpg\n     IMAGE_B: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/reference/stiffness/stiffavg_roll.jpg\n     IMAGE_A HASH: 017f7f7f1d7f7e80 SIZE: 64 bits\n     IMAGE_B HASH: 017f7f7f1d7f7e80 SIZE: 64 bits\n     TOLERANCE: 1.0%, ABS TOLERANCE: 1 bits, DIFFERENCE: 0 bits\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_21/average_stiffness/average_stiffness_log.out:file_utils.py:390 Executing biobb_dna.stiffness.average_stiffness Version: 4.1.0\nINFO     /tmp/biobb/unitests_21/average_stiffness/average_stiffness_log.out:file_utils.py:390 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/canal_output_roll.ser to /tmp/biobb/unitests_21/average_stiffness/aafe6e34-1e91-46fb-8fca-58936ecfaca2\nINFO     /tmp/biobb/unitests_21/average_stiffness/average_stiffness_log.out:file_utils.py:390 Creating avgstiffness_b3d7e91a-00e2-446d-8a26-e10415361ee9 temporary folder\nINFO     /tmp/biobb/unitests_21/average_stiffness/average_stiffness_log.out:file_utils.py:390 Removed: [&amp;#x27;/tmp/biobb/unitests_21/average_stiffness/aafe6e34-1e91-46fb-8fca-58936ecfaca2&amp;#x27;, &amp;#x27;avgstiffness_b3d7e91a-00e2-446d-8a26-e10415361ee9&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_21\n&#34;}], &#34;biobb_dna/test/unitests/test_stiffness/test_stiffness.py::TestBasePairStiffness::test_basepairstiffness&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_dna/test/unitests/test_stiffness/test_stiffness.py::TestBasePairStiffness::test_basepairstiffness&#34;, &#34;duration&#34;: &#34;363 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_dna/test/unitests/test_stiffness/test_stiffness.py::TestBasePairStiffness::test_basepairstiffness&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;363 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-05-07 09:06:25,422 [MainThread  ] [INFO ]  Executing biobb_dna.stiffness.basepair_stiffness Version: 4.1.0\n2024-05-07 09:06:25,422 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_shift_AA.csv to /tmp/biobb/unitests_21/basepair_stiffness/e99266c8-b536-4189-b219-57b10d0835d1\n2024-05-07 09:06:25,423 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_slide_AA.csv to /tmp/biobb/unitests_21/basepair_stiffness/e99266c8-b536-4189-b219-57b10d0835d1\n2024-05-07 09:06:25,423 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_rise_AA.csv to /tmp/biobb/unitests_21/basepair_stiffness/e99266c8-b536-4189-b219-57b10d0835d1\n2024-05-07 09:06:25,423 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_tilt_AA.csv to /tmp/biobb/unitests_21/basepair_stiffness/e99266c8-b536-4189-b219-57b10d0835d1\n2024-05-07 09:06:25,423 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_roll_AA.csv to /tmp/biobb/unitests_21/basepair_stiffness/e99266c8-b536-4189-b219-57b10d0835d1\n2024-05-07 09:06:25,424 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_twist_AA.csv to /tmp/biobb/unitests_21/basepair_stiffness/e99266c8-b536-4189-b219-57b10d0835d1\n2024-05-07 09:06:25,424 [MainThread  ] [INFO ]  Creating bp_stiffness_1001b597-2e15-4ceb-82b0-309dafaf1131 temporary folder\nChecking if empty file: /tmp/biobb/unitests_21/basepair_stiffness/bpstiff.csv\nChecking if empty file: /tmp/biobb/unitests_21/basepair_stiffness/bpstiff.jpg\nComparing images of both files:\n     IMAGE_A: /tmp/biobb/unitests_21/basepair_stiffness/bpstiff.jpg\n     IMAGE_B: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/reference/stiffness/stiffbp_ref.jpg\n     IMAGE_A HASH: ff8080909080ffff SIZE: 64 bits\n     IMAGE_B HASH: ff8080909080ffff SIZE: 64 bits\n     TOLERANCE: 1.0%, ABS TOLERANCE: 1 bits, DIFFERENCE: 0 bits\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_21/basepair_stiffness/basepair_stiffness_log.out:file_utils.py:390 Executing biobb_dna.stiffness.basepair_stiffness Version: 4.1.0\nINFO     /tmp/biobb/unitests_21/basepair_stiffness/basepair_stiffness_log.out:file_utils.py:390 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_shift_AA.csv to /tmp/biobb/unitests_21/basepair_stiffness/e99266c8-b536-4189-b219-57b10d0835d1\nINFO     /tmp/biobb/unitests_21/basepair_stiffness/basepair_stiffness_log.out:file_utils.py:390 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_slide_AA.csv to /tmp/biobb/unitests_21/basepair_stiffness/e99266c8-b536-4189-b219-57b10d0835d1\nINFO     /tmp/biobb/unitests_21/basepair_stiffness/basepair_stiffness_log.out:file_utils.py:390 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_rise_AA.csv to /tmp/biobb/unitests_21/basepair_stiffness/e99266c8-b536-4189-b219-57b10d0835d1\nINFO     /tmp/biobb/unitests_21/basepair_stiffness/basepair_stiffness_log.out:file_utils.py:390 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_tilt_AA.csv to /tmp/biobb/unitests_21/basepair_stiffness/e99266c8-b536-4189-b219-57b10d0835d1\nINFO     /tmp/biobb/unitests_21/basepair_stiffness/basepair_stiffness_log.out:file_utils.py:390 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_roll_AA.csv to /tmp/biobb/unitests_21/basepair_stiffness/e99266c8-b536-4189-b219-57b10d0835d1\nINFO     /tmp/biobb/unitests_21/basepair_stiffness/basepair_stiffness_log.out:file_utils.py:390 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_twist_AA.csv to /tmp/biobb/unitests_21/basepair_stiffness/e99266c8-b536-4189-b219-57b10d0835d1\nINFO     /tmp/biobb/unitests_21/basepair_stiffness/basepair_stiffness_log.out:file_utils.py:390 Creating bp_stiffness_1001b597-2e15-4ceb-82b0-309dafaf1131 temporary folder\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_21\n&#34;}]}, &#34;renderCollapsed&#34;: [&#34;passed&#34;], &#34;initialSort&#34;: &#34;result&#34;, &#34;title&#34;: &#34;report.html&#34;}"></div>
+    <div id="data-container" data-jsonblob="{&#34;environment&#34;: {&#34;Python&#34;: &#34;3.8.19&#34;, &#34;Platform&#34;: &#34;Linux-5.4.0-159-generic-x86_64-with-glibc2.10&#34;, &#34;Packages&#34;: {&#34;pytest&#34;: &#34;8.2.1&#34;, &#34;pluggy&#34;: &#34;1.5.0&#34;}, &#34;Plugins&#34;: {&#34;metadata&#34;: &#34;3.1.1&#34;, &#34;html&#34;: &#34;4.1.1&#34;, &#34;cov&#34;: &#34;5.0.0&#34;}, &#34;CI&#34;: &#34;true&#34;}, &#34;tests&#34;: {&#34;biobb_dna/test/unitests/test_backbone/test_bipopulations.py::TestBIPopulations::test_bipopulations&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_dna/test/unitests/test_backbone/test_bipopulations.py::TestBIPopulations::test_bipopulations&#34;, &#34;duration&#34;: &#34;578 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_dna/test/unitests/test_backbone/test_bipopulations.py::TestBIPopulations::test_bipopulations&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;578 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-05-24 09:29:33,039 [MainThread  ] [INFO ]  Executing biobb_dna.backbone.bipopulations Version: 4.1.0\n2024-05-24 09:29:33,040 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/backbone/canal_output_epsilC.ser to /tmp/biobb/unitests_34/bipopulations/5683acd2-3345-45cc-9f4b-b6c0ee222f99\n2024-05-24 09:29:33,040 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/backbone/canal_output_epsilW.ser to /tmp/biobb/unitests_34/bipopulations/5683acd2-3345-45cc-9f4b-b6c0ee222f99\n2024-05-24 09:29:33,041 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/backbone/canal_output_zetaC.ser to /tmp/biobb/unitests_34/bipopulations/5683acd2-3345-45cc-9f4b-b6c0ee222f99\n2024-05-24 09:29:33,042 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/backbone/canal_output_zetaW.ser to /tmp/biobb/unitests_34/bipopulations/5683acd2-3345-45cc-9f4b-b6c0ee222f99\n2024-05-24 09:29:33,042 [MainThread  ] [INFO ]  Creating backbone_4e9521d5-ae42-4b87-859c-6380d642605b temporary folder\n2024-05-24 09:29:33,493 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_34/bipopulations/5683acd2-3345-45cc-9f4b-b6c0ee222f99&amp;#x27;, &amp;#x27;backbone_4e9521d5-ae42-4b87-859c-6380d642605b&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_34/bipopulations/bipop.csv\nChecking if empty file: /tmp/biobb/unitests_34/bipopulations/bipop.jpg\nComparing images of both files:\n     IMAGE_A: /tmp/biobb/unitests_34/bipopulations/bipop.jpg\n     IMAGE_B: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/reference/backbone/bipop_ref.jpg\n     IMAGE_A HASH: ff8981818181c9ff SIZE: 64 bits\n     IMAGE_B HASH: ff8981818181c9ff SIZE: 64 bits\n     TOLERANCE: 1.0%, ABS TOLERANCE: 1 bits, DIFFERENCE: 0 bits\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_34/bipopulations/bipopulations_log.out:file_utils.py:391 Executing biobb_dna.backbone.bipopulations Version: 4.1.0\nINFO     /tmp/biobb/unitests_34/bipopulations/bipopulations_log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/backbone/canal_output_epsilC.ser to /tmp/biobb/unitests_34/bipopulations/5683acd2-3345-45cc-9f4b-b6c0ee222f99\nINFO     /tmp/biobb/unitests_34/bipopulations/bipopulations_log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/backbone/canal_output_epsilW.ser to /tmp/biobb/unitests_34/bipopulations/5683acd2-3345-45cc-9f4b-b6c0ee222f99\nINFO     /tmp/biobb/unitests_34/bipopulations/bipopulations_log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/backbone/canal_output_zetaC.ser to /tmp/biobb/unitests_34/bipopulations/5683acd2-3345-45cc-9f4b-b6c0ee222f99\nINFO     /tmp/biobb/unitests_34/bipopulations/bipopulations_log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/backbone/canal_output_zetaW.ser to /tmp/biobb/unitests_34/bipopulations/5683acd2-3345-45cc-9f4b-b6c0ee222f99\nINFO     /tmp/biobb/unitests_34/bipopulations/bipopulations_log.out:file_utils.py:391 Creating backbone_4e9521d5-ae42-4b87-859c-6380d642605b temporary folder\nINFO     /tmp/biobb/unitests_34/bipopulations/bipopulations_log.out:file_utils.py:391 Removed: [&amp;#x27;/tmp/biobb/unitests_34/bipopulations/5683acd2-3345-45cc-9f4b-b6c0ee222f99&amp;#x27;, &amp;#x27;backbone_4e9521d5-ae42-4b87-859c-6380d642605b&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_34\n&#34;}], &#34;biobb_dna/test/unitests/test_backbone/test_canonical_alpha_gamma.py::TestCanonicalAlphaGamma::test_canonicalag&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_dna/test/unitests/test_backbone/test_canonical_alpha_gamma.py::TestCanonicalAlphaGamma::test_canonicalag&#34;, &#34;duration&#34;: &#34;529 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_dna/test/unitests/test_backbone/test_canonical_alpha_gamma.py::TestCanonicalAlphaGamma::test_canonicalag&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;529 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-05-24 09:29:33,635 [MainThread  ] [INFO ]  Executing biobb_dna.backbone.canonicalag Version: 4.1.0\n2024-05-24 09:29:33,635 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/backbone/canal_output_alphaC.ser to /tmp/biobb/unitests_34/canonicalag/7fc28bf9-79b4-4e41-ad93-c37ac41ffbf7\n2024-05-24 09:29:33,636 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/backbone/canal_output_alphaW.ser to /tmp/biobb/unitests_34/canonicalag/7fc28bf9-79b4-4e41-ad93-c37ac41ffbf7\n2024-05-24 09:29:33,637 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/backbone/canal_output_gammaC.ser to /tmp/biobb/unitests_34/canonicalag/7fc28bf9-79b4-4e41-ad93-c37ac41ffbf7\n2024-05-24 09:29:33,638 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/backbone/canal_output_gammaW.ser to /tmp/biobb/unitests_34/canonicalag/7fc28bf9-79b4-4e41-ad93-c37ac41ffbf7\n2024-05-24 09:29:33,638 [MainThread  ] [INFO ]  Creating backbone_ddcdc2e2-8207-4a0b-8622-6d1e159cbe80 temporary folder\n2024-05-24 09:29:34,059 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_34/canonicalag/7fc28bf9-79b4-4e41-ad93-c37ac41ffbf7&amp;#x27;, &amp;#x27;backbone_ddcdc2e2-8207-4a0b-8622-6d1e159cbe80&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_34/canonicalag/canonag.csv\nChecking if empty file: /tmp/biobb/unitests_34/canonicalag/canonag.jpg\nComparing images of both files:\n     IMAGE_A: /tmp/biobb/unitests_34/canonicalag/canonag.jpg\n     IMAGE_B: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/reference/backbone/canonag_ref.jpg\n     IMAGE_A HASH: ff8081818180f9ff SIZE: 64 bits\n     IMAGE_B HASH: ff8081818180f9ff SIZE: 64 bits\n     TOLERANCE: 1.0%, ABS TOLERANCE: 1 bits, DIFFERENCE: 0 bits\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_34/canonicalag/canonicalag_log.out:file_utils.py:391 Executing biobb_dna.backbone.canonicalag Version: 4.1.0\nINFO     /tmp/biobb/unitests_34/canonicalag/canonicalag_log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/backbone/canal_output_alphaC.ser to /tmp/biobb/unitests_34/canonicalag/7fc28bf9-79b4-4e41-ad93-c37ac41ffbf7\nINFO     /tmp/biobb/unitests_34/canonicalag/canonicalag_log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/backbone/canal_output_alphaW.ser to /tmp/biobb/unitests_34/canonicalag/7fc28bf9-79b4-4e41-ad93-c37ac41ffbf7\nINFO     /tmp/biobb/unitests_34/canonicalag/canonicalag_log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/backbone/canal_output_gammaC.ser to /tmp/biobb/unitests_34/canonicalag/7fc28bf9-79b4-4e41-ad93-c37ac41ffbf7\nINFO     /tmp/biobb/unitests_34/canonicalag/canonicalag_log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/backbone/canal_output_gammaW.ser to /tmp/biobb/unitests_34/canonicalag/7fc28bf9-79b4-4e41-ad93-c37ac41ffbf7\nINFO     /tmp/biobb/unitests_34/canonicalag/canonicalag_log.out:file_utils.py:391 Creating backbone_ddcdc2e2-8207-4a0b-8622-6d1e159cbe80 temporary folder\nINFO     /tmp/biobb/unitests_34/canonicalag/canonicalag_log.out:file_utils.py:391 Removed: [&amp;#x27;/tmp/biobb/unitests_34/canonicalag/7fc28bf9-79b4-4e41-ad93-c37ac41ffbf7&amp;#x27;, &amp;#x27;backbone_ddcdc2e2-8207-4a0b-8622-6d1e159cbe80&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_34\n&#34;}], &#34;biobb_dna/test/unitests/test_backbone/test_puckering.py::TestPuckering::test_puckering&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_dna/test/unitests/test_backbone/test_puckering.py::TestPuckering::test_puckering&#34;, &#34;duration&#34;: &#34;693 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_dna/test/unitests/test_backbone/test_puckering.py::TestPuckering::test_puckering&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;693 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-05-24 09:29:34,225 [MainThread  ] [INFO ]  Executing biobb_dna.backbone.puckering Version: 4.1.0\n2024-05-24 09:29:34,226 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/backbone/canal_output_phaseC.ser to /tmp/biobb/unitests_34/puckering/64d6a3ab-7065-4c7c-ae0c-b742fe30a3b0\n2024-05-24 09:29:34,227 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/backbone/canal_output_phaseW.ser to /tmp/biobb/unitests_34/puckering/64d6a3ab-7065-4c7c-ae0c-b742fe30a3b0\n2024-05-24 09:29:34,227 [MainThread  ] [INFO ]  Creating backbone_95ba5aaf-be3e-4ee5-bec8-e58ff220bac1 temporary folder\n2024-05-24 09:29:34,753 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_34/puckering/64d6a3ab-7065-4c7c-ae0c-b742fe30a3b0&amp;#x27;, &amp;#x27;backbone_95ba5aaf-be3e-4ee5-bec8-e58ff220bac1&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_34/puckering/puckering.csv\nChecking if empty file: /tmp/biobb/unitests_34/puckering/puckering.jpg\nComparing images of both files:\n     IMAGE_A: /tmp/biobb/unitests_34/puckering/puckering.jpg\n     IMAGE_B: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/reference/backbone/puckering_ref.jpg\n     IMAGE_A HASH: eb8181808081ffff SIZE: 64 bits\n     IMAGE_B HASH: fb8181808081ffff SIZE: 64 bits\n     TOLERANCE: 1.0%, ABS TOLERANCE: 1 bits, DIFFERENCE: 1 bits\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_34/puckering/puckering_log.out:file_utils.py:391 Executing biobb_dna.backbone.puckering Version: 4.1.0\nINFO     /tmp/biobb/unitests_34/puckering/puckering_log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/backbone/canal_output_phaseC.ser to /tmp/biobb/unitests_34/puckering/64d6a3ab-7065-4c7c-ae0c-b742fe30a3b0\nINFO     /tmp/biobb/unitests_34/puckering/puckering_log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/backbone/canal_output_phaseW.ser to /tmp/biobb/unitests_34/puckering/64d6a3ab-7065-4c7c-ae0c-b742fe30a3b0\nINFO     /tmp/biobb/unitests_34/puckering/puckering_log.out:file_utils.py:391 Creating backbone_95ba5aaf-be3e-4ee5-bec8-e58ff220bac1 temporary folder\nINFO     /tmp/biobb/unitests_34/puckering/puckering_log.out:file_utils.py:391 Removed: [&amp;#x27;/tmp/biobb/unitests_34/puckering/64d6a3ab-7065-4c7c-ae0c-b742fe30a3b0&amp;#x27;, &amp;#x27;backbone_95ba5aaf-be3e-4ee5-bec8-e58ff220bac1&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_34\n&#34;}], &#34;biobb_dna/test/unitests/test_correlation/test_correlation.py::TestInterHelparCorrelation::test_helparcorrelation&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_dna/test/unitests/test_correlation/test_correlation.py::TestInterHelparCorrelation::test_helparcorrelation&#34;, &#34;duration&#34;: &#34;356 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_dna/test/unitests/test_correlation/test_correlation.py::TestInterHelparCorrelation::test_helparcorrelation&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;356 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-05-24 09:29:34,861 [MainThread  ] [INFO ]  Executing biobb_dna.interbp_correlations.interhpcorr Version: 4.1.0\n2024-05-24 09:29:34,862 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_shift_AA.csv to /tmp/biobb/unitests_34/interhpcorr/d4386fa8-b803-4657-b3ad-8abb285cbc54\n2024-05-24 09:29:34,862 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_slide_AA.csv to /tmp/biobb/unitests_34/interhpcorr/d4386fa8-b803-4657-b3ad-8abb285cbc54\n2024-05-24 09:29:34,862 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_rise_AA.csv to /tmp/biobb/unitests_34/interhpcorr/d4386fa8-b803-4657-b3ad-8abb285cbc54\n2024-05-24 09:29:34,862 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_tilt_AA.csv to /tmp/biobb/unitests_34/interhpcorr/d4386fa8-b803-4657-b3ad-8abb285cbc54\n2024-05-24 09:29:34,863 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_roll_AA.csv to /tmp/biobb/unitests_34/interhpcorr/d4386fa8-b803-4657-b3ad-8abb285cbc54\n2024-05-24 09:29:34,863 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_twist_AA.csv to /tmp/biobb/unitests_34/interhpcorr/d4386fa8-b803-4657-b3ad-8abb285cbc54\n2024-05-24 09:29:34,863 [MainThread  ] [INFO ]  Creating hpcorrelation_069eb5d9-736f-4f94-8b98-832f58498dcc temporary folder\n2024-05-24 09:29:35,114 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_34/interhpcorr/d4386fa8-b803-4657-b3ad-8abb285cbc54&amp;#x27;, &amp;#x27;hpcorrelation_069eb5d9-736f-4f94-8b98-832f58498dcc&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_34/interhpcorr/inter_hpcorr.csv\nChecking if empty file: /tmp/biobb/unitests_34/interhpcorr/inter_hpcorr.jpg\nComparing images of both files:\n     IMAGE_A: /tmp/biobb/unitests_34/interhpcorr/inter_hpcorr.jpg\n     IMAGE_B: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/reference/correlation/inter_hpcorr_ref.jpg\n     IMAGE_A HASH: ff83868890a1c0ff SIZE: 64 bits\n     IMAGE_B HASH: ff83868890a1c0ff SIZE: 64 bits\n     TOLERANCE: 1.0%, ABS TOLERANCE: 1 bits, DIFFERENCE: 0 bits\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_34/interhpcorr/log.out:file_utils.py:391 Executing biobb_dna.interbp_correlations.interhpcorr Version: 4.1.0\nINFO     /tmp/biobb/unitests_34/interhpcorr/log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_shift_AA.csv to /tmp/biobb/unitests_34/interhpcorr/d4386fa8-b803-4657-b3ad-8abb285cbc54\nINFO     /tmp/biobb/unitests_34/interhpcorr/log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_slide_AA.csv to /tmp/biobb/unitests_34/interhpcorr/d4386fa8-b803-4657-b3ad-8abb285cbc54\nINFO     /tmp/biobb/unitests_34/interhpcorr/log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_rise_AA.csv to /tmp/biobb/unitests_34/interhpcorr/d4386fa8-b803-4657-b3ad-8abb285cbc54\nINFO     /tmp/biobb/unitests_34/interhpcorr/log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_tilt_AA.csv to /tmp/biobb/unitests_34/interhpcorr/d4386fa8-b803-4657-b3ad-8abb285cbc54\nINFO     /tmp/biobb/unitests_34/interhpcorr/log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_roll_AA.csv to /tmp/biobb/unitests_34/interhpcorr/d4386fa8-b803-4657-b3ad-8abb285cbc54\nINFO     /tmp/biobb/unitests_34/interhpcorr/log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_twist_AA.csv to /tmp/biobb/unitests_34/interhpcorr/d4386fa8-b803-4657-b3ad-8abb285cbc54\nINFO     /tmp/biobb/unitests_34/interhpcorr/log.out:file_utils.py:391 Creating hpcorrelation_069eb5d9-736f-4f94-8b98-832f58498dcc temporary folder\nINFO     /tmp/biobb/unitests_34/interhpcorr/log.out:file_utils.py:391 Removed: [&amp;#x27;/tmp/biobb/unitests_34/interhpcorr/d4386fa8-b803-4657-b3ad-8abb285cbc54&amp;#x27;, &amp;#x27;hpcorrelation_069eb5d9-736f-4f94-8b98-832f58498dcc&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_34\n&#34;}], &#34;biobb_dna/test/unitests/test_correlation/test_correlation.py::TestInterSequenceCorrelation::test_sequencecorrelation&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_dna/test/unitests/test_correlation/test_correlation.py::TestInterSequenceCorrelation::test_sequencecorrelation&#34;, &#34;duration&#34;: &#34;514 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_dna/test/unitests/test_correlation/test_correlation.py::TestInterSequenceCorrelation::test_sequencecorrelation&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;514 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-05-24 09:29:35,221 [MainThread  ] [INFO ]  Executing biobb_dna.interbp_correlations.interseqcorr Version: 4.1.0\n2024-05-24 09:29:35,221 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_roll.ser to /tmp/biobb/unitests_34/interseqcorr/26653852-439c-43c7-b267-8ab1dd9a7807\n2024-05-24 09:29:35,222 [MainThread  ] [INFO ]  Creating bpcorrelation_2c9a69ab-c3df-4395-957f-be180e3a2740 temporary folder\n2024-05-24 09:29:35,537 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_34/interseqcorr/26653852-439c-43c7-b267-8ab1dd9a7807&amp;#x27;, &amp;#x27;bpcorrelation_2c9a69ab-c3df-4395-957f-be180e3a2740&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_34/interseqcorr/inter_seqcorr.csv\nChecking if empty file: /tmp/biobb/unitests_34/interseqcorr/inter_seqcorr.jpg\nComparing images of both files:\n     IMAGE_A: /tmp/biobb/unitests_34/interseqcorr/inter_seqcorr.jpg\n     IMAGE_B: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/reference/correlation/inter_seqcorr_roll.jpg\n     IMAGE_A HASH: ff8080889080c0ff SIZE: 64 bits\n     IMAGE_B HASH: ff8080889080c0ff SIZE: 64 bits\n     TOLERANCE: 1.0%, ABS TOLERANCE: 1 bits, DIFFERENCE: 0 bits\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_34/interseqcorr/interseqcorr_log.out:file_utils.py:391 Executing biobb_dna.interbp_correlations.interseqcorr Version: 4.1.0\nINFO     /tmp/biobb/unitests_34/interseqcorr/interseqcorr_log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_roll.ser to /tmp/biobb/unitests_34/interseqcorr/26653852-439c-43c7-b267-8ab1dd9a7807\nINFO     /tmp/biobb/unitests_34/interseqcorr/interseqcorr_log.out:file_utils.py:391 Creating bpcorrelation_2c9a69ab-c3df-4395-957f-be180e3a2740 temporary folder\nINFO     /tmp/biobb/unitests_34/interseqcorr/interseqcorr_log.out:file_utils.py:391 Removed: [&amp;#x27;/tmp/biobb/unitests_34/interseqcorr/26653852-439c-43c7-b267-8ab1dd9a7807&amp;#x27;, &amp;#x27;bpcorrelation_2c9a69ab-c3df-4395-957f-be180e3a2740&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_34\n&#34;}], &#34;biobb_dna/test/unitests/test_correlation/test_correlation.py::TestInterBasepairCorrelation::test_basepaircorrelation&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_dna/test/unitests/test_correlation/test_correlation.py::TestInterBasepairCorrelation::test_basepaircorrelation&#34;, &#34;duration&#34;: &#34;00:00:01&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_dna/test/unitests/test_correlation/test_correlation.py::TestInterBasepairCorrelation::test_basepaircorrelation&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:00:01&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-05-24 09:29:35,736 [MainThread  ] [INFO ]  Executing biobb_dna.interbp_correlations.interbpcorr Version: 4.1.0\n2024-05-24 09:29:35,737 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_shift.ser to /tmp/biobb/unitests_34/interbpcorr/e8a7085a-d674-41b8-befc-4775b7dd4b91\n2024-05-24 09:29:35,737 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_slide.ser to /tmp/biobb/unitests_34/interbpcorr/e8a7085a-d674-41b8-befc-4775b7dd4b91\n2024-05-24 09:29:35,738 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_rise.ser to /tmp/biobb/unitests_34/interbpcorr/e8a7085a-d674-41b8-befc-4775b7dd4b91\n2024-05-24 09:29:35,739 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_tilt.ser to /tmp/biobb/unitests_34/interbpcorr/e8a7085a-d674-41b8-befc-4775b7dd4b91\n2024-05-24 09:29:35,740 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_roll.ser to /tmp/biobb/unitests_34/interbpcorr/e8a7085a-d674-41b8-befc-4775b7dd4b91\n2024-05-24 09:29:35,741 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_twist.ser to /tmp/biobb/unitests_34/interbpcorr/e8a7085a-d674-41b8-befc-4775b7dd4b91\n2024-05-24 09:29:35,741 [MainThread  ] [INFO ]  Creating bpcorrelation_70fe47bd-b481-4dd0-9acd-9f36b432ffa7 temporary folder\n2024-05-24 09:29:36,625 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_34/interbpcorr/e8a7085a-d674-41b8-befc-4775b7dd4b91&amp;#x27;, &amp;#x27;bpcorrelation_70fe47bd-b481-4dd0-9acd-9f36b432ffa7&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_34/interbpcorr/inter_bpcorr.csv\nChecking if empty file: /tmp/biobb/unitests_34/interbpcorr/inter_bpcorr.jpg\nComparing images of both files:\n     IMAGE_A: /tmp/biobb/unitests_34/interbpcorr/inter_bpcorr.jpg\n     IMAGE_B: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/reference/correlation/inter_bpcorr_ref.jpg\n     IMAGE_A HASH: fd6d6dfffd6c0183 SIZE: 64 bits\n     IMAGE_B HASH: fd6d6dfffd6c0183 SIZE: 64 bits\n     TOLERANCE: 1.0%, ABS TOLERANCE: 1 bits, DIFFERENCE: 0 bits\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_34/interbpcorr/interbpcorr_log.out:file_utils.py:391 Executing biobb_dna.interbp_correlations.interbpcorr Version: 4.1.0\nINFO     /tmp/biobb/unitests_34/interbpcorr/interbpcorr_log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_shift.ser to /tmp/biobb/unitests_34/interbpcorr/e8a7085a-d674-41b8-befc-4775b7dd4b91\nINFO     /tmp/biobb/unitests_34/interbpcorr/interbpcorr_log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_slide.ser to /tmp/biobb/unitests_34/interbpcorr/e8a7085a-d674-41b8-befc-4775b7dd4b91\nINFO     /tmp/biobb/unitests_34/interbpcorr/interbpcorr_log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_rise.ser to /tmp/biobb/unitests_34/interbpcorr/e8a7085a-d674-41b8-befc-4775b7dd4b91\nINFO     /tmp/biobb/unitests_34/interbpcorr/interbpcorr_log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_tilt.ser to /tmp/biobb/unitests_34/interbpcorr/e8a7085a-d674-41b8-befc-4775b7dd4b91\nINFO     /tmp/biobb/unitests_34/interbpcorr/interbpcorr_log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_roll.ser to /tmp/biobb/unitests_34/interbpcorr/e8a7085a-d674-41b8-befc-4775b7dd4b91\nINFO     /tmp/biobb/unitests_34/interbpcorr/interbpcorr_log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_twist.ser to /tmp/biobb/unitests_34/interbpcorr/e8a7085a-d674-41b8-befc-4775b7dd4b91\nINFO     /tmp/biobb/unitests_34/interbpcorr/interbpcorr_log.out:file_utils.py:391 Creating bpcorrelation_70fe47bd-b481-4dd0-9acd-9f36b432ffa7 temporary folder\nINFO     /tmp/biobb/unitests_34/interbpcorr/interbpcorr_log.out:file_utils.py:391 Removed: [&amp;#x27;/tmp/biobb/unitests_34/interbpcorr/e8a7085a-d674-41b8-befc-4775b7dd4b91&amp;#x27;, &amp;#x27;bpcorrelation_70fe47bd-b481-4dd0-9acd-9f36b432ffa7&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_34\n&#34;}], &#34;biobb_dna/test/unitests/test_correlation/test_correlation.py::TestIntraHelparCorrelation::test_helparcorrelation&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_dna/test/unitests/test_correlation/test_correlation.py::TestIntraHelparCorrelation::test_helparcorrelation&#34;, &#34;duration&#34;: &#34;352 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_dna/test/unitests/test_correlation/test_correlation.py::TestIntraHelparCorrelation::test_helparcorrelation&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;352 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-05-24 09:29:36,747 [MainThread  ] [INFO ]  Executing biobb_dna.intrabp_correlations.intrahpcorr Version: 4.1.0\n2024-05-24 09:29:36,747 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/series_shear_A.csv to /tmp/biobb/unitests_34/intrahpcorr/7ee9547a-036f-49cb-b57f-9af38cec7b0b\n2024-05-24 09:29:36,748 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/series_stretch_A.csv to /tmp/biobb/unitests_34/intrahpcorr/7ee9547a-036f-49cb-b57f-9af38cec7b0b\n2024-05-24 09:29:36,748 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/series_stagger_A.csv to /tmp/biobb/unitests_34/intrahpcorr/7ee9547a-036f-49cb-b57f-9af38cec7b0b\n2024-05-24 09:29:36,748 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/series_buckle_A.csv to /tmp/biobb/unitests_34/intrahpcorr/7ee9547a-036f-49cb-b57f-9af38cec7b0b\n2024-05-24 09:29:36,749 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/series_propel_A.csv to /tmp/biobb/unitests_34/intrahpcorr/7ee9547a-036f-49cb-b57f-9af38cec7b0b\n2024-05-24 09:29:36,749 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/series_opening_A.csv to /tmp/biobb/unitests_34/intrahpcorr/7ee9547a-036f-49cb-b57f-9af38cec7b0b\n2024-05-24 09:29:36,749 [MainThread  ] [INFO ]  Creating hpcorrelation_62dc7388-e2e5-4833-aa19-e8db3d95f9f0 temporary folder\n2024-05-24 09:29:36,997 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_34/intrahpcorr/7ee9547a-036f-49cb-b57f-9af38cec7b0b&amp;#x27;, &amp;#x27;hpcorrelation_62dc7388-e2e5-4833-aa19-e8db3d95f9f0&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_34/intrahpcorr/intra_hpcorr.csv\nChecking if empty file: /tmp/biobb/unitests_34/intrahpcorr/intra_hpcorr.jpg\nComparing images of both files:\n     IMAGE_A: /tmp/biobb/unitests_34/intrahpcorr/intra_hpcorr.jpg\n     IMAGE_B: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/reference/correlation/intra_hpcorr_ref.jpg\n     IMAGE_A HASH: fb81848890a0e0ff SIZE: 64 bits\n     IMAGE_B HASH: fb81848890a0e0ff SIZE: 64 bits\n     TOLERANCE: 1.0%, ABS TOLERANCE: 1 bits, DIFFERENCE: 0 bits\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_34/intrahpcorr/log.out:file_utils.py:391 Executing biobb_dna.intrabp_correlations.intrahpcorr Version: 4.1.0\nINFO     /tmp/biobb/unitests_34/intrahpcorr/log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/series_shear_A.csv to /tmp/biobb/unitests_34/intrahpcorr/7ee9547a-036f-49cb-b57f-9af38cec7b0b\nINFO     /tmp/biobb/unitests_34/intrahpcorr/log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/series_stretch_A.csv to /tmp/biobb/unitests_34/intrahpcorr/7ee9547a-036f-49cb-b57f-9af38cec7b0b\nINFO     /tmp/biobb/unitests_34/intrahpcorr/log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/series_stagger_A.csv to /tmp/biobb/unitests_34/intrahpcorr/7ee9547a-036f-49cb-b57f-9af38cec7b0b\nINFO     /tmp/biobb/unitests_34/intrahpcorr/log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/series_buckle_A.csv to /tmp/biobb/unitests_34/intrahpcorr/7ee9547a-036f-49cb-b57f-9af38cec7b0b\nINFO     /tmp/biobb/unitests_34/intrahpcorr/log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/series_propel_A.csv to /tmp/biobb/unitests_34/intrahpcorr/7ee9547a-036f-49cb-b57f-9af38cec7b0b\nINFO     /tmp/biobb/unitests_34/intrahpcorr/log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/series_opening_A.csv to /tmp/biobb/unitests_34/intrahpcorr/7ee9547a-036f-49cb-b57f-9af38cec7b0b\nINFO     /tmp/biobb/unitests_34/intrahpcorr/log.out:file_utils.py:391 Creating hpcorrelation_62dc7388-e2e5-4833-aa19-e8db3d95f9f0 temporary folder\nINFO     /tmp/biobb/unitests_34/intrahpcorr/log.out:file_utils.py:391 Removed: [&amp;#x27;/tmp/biobb/unitests_34/intrahpcorr/7ee9547a-036f-49cb-b57f-9af38cec7b0b&amp;#x27;, &amp;#x27;hpcorrelation_62dc7388-e2e5-4833-aa19-e8db3d95f9f0&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_34\n&#34;}], &#34;biobb_dna/test/unitests/test_correlation/test_correlation.py::TestIntraSequenceCorrelation::test_sequencecorrelation&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_dna/test/unitests/test_correlation/test_correlation.py::TestIntraSequenceCorrelation::test_sequencecorrelation&#34;, &#34;duration&#34;: &#34;413 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_dna/test/unitests/test_correlation/test_correlation.py::TestIntraSequenceCorrelation::test_sequencecorrelation&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;413 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-05-24 09:29:37,101 [MainThread  ] [INFO ]  Executing biobb_dna.intrabp_correlations.intraseqcorr Version: 4.1.0\n2024-05-24 09:29:37,102 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_buckle.ser to /tmp/biobb/unitests_34/intraseqcorr/12b8bd94-aaa3-411b-b4ef-40bb280351d1\n2024-05-24 09:29:37,102 [MainThread  ] [INFO ]  Creating bpcorrelation_913bddfc-de61-46b2-aca0-113de71d2b4d temporary folder\n2024-05-24 09:29:37,409 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_34/intraseqcorr/12b8bd94-aaa3-411b-b4ef-40bb280351d1&amp;#x27;, &amp;#x27;bpcorrelation_913bddfc-de61-46b2-aca0-113de71d2b4d&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_34/intraseqcorr/intra_seqcorr.csv\nChecking if empty file: /tmp/biobb/unitests_34/intraseqcorr/intra_seqcorr.jpg\nComparing images of both files:\n     IMAGE_A: /tmp/biobb/unitests_34/intraseqcorr/intra_seqcorr.jpg\n     IMAGE_B: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/reference/correlation/intra_seqcorr_buckle.jpg\n     IMAGE_A HASH: ff83848890a0c0ff SIZE: 64 bits\n     IMAGE_B HASH: ff83848890a0c0ff SIZE: 64 bits\n     TOLERANCE: 1.0%, ABS TOLERANCE: 1 bits, DIFFERENCE: 0 bits\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_34/intraseqcorr/intraseqcorr_log.out:file_utils.py:391 Executing biobb_dna.intrabp_correlations.intraseqcorr Version: 4.1.0\nINFO     /tmp/biobb/unitests_34/intraseqcorr/intraseqcorr_log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_buckle.ser to /tmp/biobb/unitests_34/intraseqcorr/12b8bd94-aaa3-411b-b4ef-40bb280351d1\nINFO     /tmp/biobb/unitests_34/intraseqcorr/intraseqcorr_log.out:file_utils.py:391 Creating bpcorrelation_913bddfc-de61-46b2-aca0-113de71d2b4d temporary folder\nINFO     /tmp/biobb/unitests_34/intraseqcorr/intraseqcorr_log.out:file_utils.py:391 Removed: [&amp;#x27;/tmp/biobb/unitests_34/intraseqcorr/12b8bd94-aaa3-411b-b4ef-40bb280351d1&amp;#x27;, &amp;#x27;bpcorrelation_913bddfc-de61-46b2-aca0-113de71d2b4d&amp;#x27;]\n\n&#34;}], &#34;biobb_dna/test/unitests/test_correlation/test_correlation.py::TestIntraBasepairCorrelation::test_basepaircorrelation&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_dna/test/unitests/test_correlation/test_correlation.py::TestIntraBasepairCorrelation::test_basepaircorrelation&#34;, &#34;duration&#34;: &#34;00:00:01&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_dna/test/unitests/test_correlation/test_correlation.py::TestIntraBasepairCorrelation::test_basepaircorrelation&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:00:01&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-05-24 09:29:37,515 [MainThread  ] [INFO ]  Executing biobb_dna.intrabp_correlations.intrabpcorr Version: 4.1.0\n2024-05-24 09:29:37,516 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_shear.ser to /tmp/biobb/unitests_35/intrabpcorr/b1820535-5822-4a1b-8131-e582c7d04cde\n2024-05-24 09:29:37,516 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_stretch.ser to /tmp/biobb/unitests_35/intrabpcorr/b1820535-5822-4a1b-8131-e582c7d04cde\n2024-05-24 09:29:37,517 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_stagger.ser to /tmp/biobb/unitests_35/intrabpcorr/b1820535-5822-4a1b-8131-e582c7d04cde\n2024-05-24 09:29:37,518 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_buckle.ser to /tmp/biobb/unitests_35/intrabpcorr/b1820535-5822-4a1b-8131-e582c7d04cde\n2024-05-24 09:29:37,519 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_propel.ser to /tmp/biobb/unitests_35/intrabpcorr/b1820535-5822-4a1b-8131-e582c7d04cde\n2024-05-24 09:29:37,519 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_opening.ser to /tmp/biobb/unitests_35/intrabpcorr/b1820535-5822-4a1b-8131-e582c7d04cde\n2024-05-24 09:29:37,520 [MainThread  ] [INFO ]  Creating bpcorrelation_56eeb8b8-c739-47db-9756-28d574c06e13 temporary folder\n2024-05-24 09:29:38,458 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_35/intrabpcorr/b1820535-5822-4a1b-8131-e582c7d04cde&amp;#x27;, &amp;#x27;bpcorrelation_56eeb8b8-c739-47db-9756-28d574c06e13&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_35/intrabpcorr/intra_bpcorr.csv\nChecking if empty file: /tmp/biobb/unitests_35/intrabpcorr/intra_bpcorr.jpg\nComparing images of both files:\n     IMAGE_A: /tmp/biobb/unitests_35/intrabpcorr/intra_bpcorr.jpg\n     IMAGE_B: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/reference/correlation/intra_bpcorr_ref.jpg\n     IMAGE_A HASH: 01f5f7f7fcf40183 SIZE: 64 bits\n     IMAGE_B HASH: 01f5f7f7fcf40183 SIZE: 64 bits\n     TOLERANCE: 1.0%, ABS TOLERANCE: 1 bits, DIFFERENCE: 0 bits\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_35/intrabpcorr/intrabpcorr_log.out:file_utils.py:391 Executing biobb_dna.intrabp_correlations.intrabpcorr Version: 4.1.0\nINFO     /tmp/biobb/unitests_35/intrabpcorr/intrabpcorr_log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_shear.ser to /tmp/biobb/unitests_35/intrabpcorr/b1820535-5822-4a1b-8131-e582c7d04cde\nINFO     /tmp/biobb/unitests_35/intrabpcorr/intrabpcorr_log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_stretch.ser to /tmp/biobb/unitests_35/intrabpcorr/b1820535-5822-4a1b-8131-e582c7d04cde\nINFO     /tmp/biobb/unitests_35/intrabpcorr/intrabpcorr_log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_stagger.ser to /tmp/biobb/unitests_35/intrabpcorr/b1820535-5822-4a1b-8131-e582c7d04cde\nINFO     /tmp/biobb/unitests_35/intrabpcorr/intrabpcorr_log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_buckle.ser to /tmp/biobb/unitests_35/intrabpcorr/b1820535-5822-4a1b-8131-e582c7d04cde\nINFO     /tmp/biobb/unitests_35/intrabpcorr/intrabpcorr_log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_propel.ser to /tmp/biobb/unitests_35/intrabpcorr/b1820535-5822-4a1b-8131-e582c7d04cde\nINFO     /tmp/biobb/unitests_35/intrabpcorr/intrabpcorr_log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_opening.ser to /tmp/biobb/unitests_35/intrabpcorr/b1820535-5822-4a1b-8131-e582c7d04cde\nINFO     /tmp/biobb/unitests_35/intrabpcorr/intrabpcorr_log.out:file_utils.py:391 Creating bpcorrelation_56eeb8b8-c739-47db-9756-28d574c06e13 temporary folder\nINFO     /tmp/biobb/unitests_35/intrabpcorr/intrabpcorr_log.out:file_utils.py:391 Removed: [&amp;#x27;/tmp/biobb/unitests_35/intrabpcorr/b1820535-5822-4a1b-8131-e582c7d04cde&amp;#x27;, &amp;#x27;bpcorrelation_56eeb8b8-c739-47db-9756-28d574c06e13&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_35\n&#34;}], &#34;biobb_dna/test/unitests/test_curvesplus/test_canal.py::TestCanal::test_canal&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_dna/test/unitests/test_curvesplus/test_canal.py::TestCanal::test_canal&#34;, &#34;duration&#34;: &#34;00:00:04&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_dna/test/unitests/test_curvesplus/test_canal.py::TestCanal::test_canal&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:00:04&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-05-24 09:29:38,582 [MainThread  ] [INFO ]  Executing biobb_dna.curvesplus.biobb_canal Version: 4.1.0\n2024-05-24 09:29:38,593 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/curvesplus/curves_output.cda to /tmp/biobb/unitests_35/biobb_canal/1584ef5e-7ec9-4d43-9511-f309f03e8828\n2024-05-24 09:29:38,593 [MainThread  ] [INFO ]  Creating canal_7af87d0b-1323-4ad1-8275-cd5bd1ff0732 temporary folder\n2024-05-24 09:29:38,605 [MainThread  ] [INFO ]  Creating command line with instructions and required arguments\n2024-05-24 09:29:38,605 [MainThread  ] [INFO ]  Canal &amp;lt;&amp;lt;! \n&amp;amp;inp\n  lis=canal_output,\n  cormin=0.6,\n  lev1=0,lev2=0,\n  itst=0,itnd=0,itdel=1,\n  histo=.f.,\n  series=.t.,\n  corr=.f.,\n&amp;amp;end\ncurves_output.cda CGCGAATTCGCG\n!\n\n2024-05-24 09:29:42,186 [MainThread  ] [INFO ]  Exit code 0\n\n2024-05-24 09:29:42,244 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_35/biobb_canal/1584ef5e-7ec9-4d43-9511-f309f03e8828&amp;#x27;, &amp;#x27;canal_7af87d0b-1323-4ad1-8275-cd5bd1ff0732&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_35/biobb_canal/canal_output.zip\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_35/biobb_canal/biobb_canal_log.out:file_utils.py:391 Executing biobb_dna.curvesplus.biobb_canal Version: 4.1.0\nINFO     /tmp/biobb/unitests_35/biobb_canal/biobb_canal_log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/curvesplus/curves_output.cda to /tmp/biobb/unitests_35/biobb_canal/1584ef5e-7ec9-4d43-9511-f309f03e8828\nINFO     /tmp/biobb/unitests_35/biobb_canal/biobb_canal_log.out:file_utils.py:391 Creating canal_7af87d0b-1323-4ad1-8275-cd5bd1ff0732 temporary folder\nINFO     /tmp/biobb/unitests_35/biobb_canal/biobb_canal_log.out:file_utils.py:391 Creating command line with instructions and required arguments\nINFO     /tmp/biobb/unitests_35/biobb_canal/biobb_canal_log.out:cmd_wrapper.py:33 Canal &amp;lt;&amp;lt;! \n&amp;amp;inp\n  lis=canal_output,\n  cormin=0.6,\n  lev1=0,lev2=0,\n  itst=0,itnd=0,itdel=1,\n  histo=.f.,\n  series=.t.,\n  corr=.f.,\n&amp;amp;end\ncurves_output.cda CGCGAATTCGCG\n!\n\nINFO     /tmp/biobb/unitests_35/biobb_canal/biobb_canal_log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     /tmp/biobb/unitests_35/biobb_canal/biobb_canal_log.out:file_utils.py:391 Removed: [&amp;#x27;/tmp/biobb/unitests_35/biobb_canal/1584ef5e-7ec9-4d43-9511-f309f03e8828&amp;#x27;, &amp;#x27;canal_7af87d0b-1323-4ad1-8275-cd5bd1ff0732&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_35\n&#34;}], &#34;biobb_dna/test/unitests/test_curvesplus/test_canion.py::TestCanal::test_canion&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_dna/test/unitests/test_curvesplus/test_canion.py::TestCanal::test_canion&#34;, &#34;duration&#34;: &#34;723 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_dna/test/unitests/test_curvesplus/test_canion.py::TestCanal::test_canion&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;723 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-05-24 09:29:42,291 [MainThread  ] [INFO ]  Executing biobb_dna.curvesplus.biobb_canion Version: 4.1.0\n2024-05-24 09:29:42,575 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/curvesplus/THGA_K.cdi to /tmp/biobb/unitests_35/biobb_canion/6a034018-c54c-45b0-9fa5-2831680905db\n2024-05-24 09:29:42,576 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/curvesplus/THGA.afr to /tmp/biobb/unitests_35/biobb_canion/6a034018-c54c-45b0-9fa5-2831680905db\n2024-05-24 09:29:42,576 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/curvesplus/THGA_avg.pdb to /tmp/biobb/unitests_35/biobb_canion/6a034018-c54c-45b0-9fa5-2831680905db\n2024-05-24 09:29:42,577 [MainThread  ] [INFO ]  Creating canion_1969a448-0a71-44f4-8422-300473478eaa temporary folder\n2024-05-24 09:29:42,874 [MainThread  ] [INFO ]  Creating command line with instructions and required arguments\n2024-05-24 09:29:42,875 [MainThread  ] [INFO ]  Canion &amp;lt;&amp;lt;! \n&amp;amp;inp\n  lis=canion_output,\n  dat=THGA_K,\n  axfrm=THGA,\n  solute=THGA_avg,\n  type=K+,\n  dlow=5.8,\n  dhig=7.2,\n  rlow=0,\n  rhig=18,\n  alow=0,\n  ahig=360,\n&amp;amp;end\n!\n\n2024-05-24 09:29:42,891 [MainThread  ] [INFO ]  Exit code 0\n\n2024-05-24 09:29:42,975 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_35/biobb_canion/6a034018-c54c-45b0-9fa5-2831680905db&amp;#x27;, &amp;#x27;canion_1969a448-0a71-44f4-8422-300473478eaa&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_35/biobb_canion/canion_output.zip\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_35/biobb_canion/biobb_canion_log.out:file_utils.py:391 Executing biobb_dna.curvesplus.biobb_canion Version: 4.1.0\nINFO     /tmp/biobb/unitests_35/biobb_canion/biobb_canion_log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/curvesplus/THGA_K.cdi to /tmp/biobb/unitests_35/biobb_canion/6a034018-c54c-45b0-9fa5-2831680905db\nINFO     /tmp/biobb/unitests_35/biobb_canion/biobb_canion_log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/curvesplus/THGA.afr to /tmp/biobb/unitests_35/biobb_canion/6a034018-c54c-45b0-9fa5-2831680905db\nINFO     /tmp/biobb/unitests_35/biobb_canion/biobb_canion_log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/curvesplus/THGA_avg.pdb to /tmp/biobb/unitests_35/biobb_canion/6a034018-c54c-45b0-9fa5-2831680905db\nINFO     /tmp/biobb/unitests_35/biobb_canion/biobb_canion_log.out:file_utils.py:391 Creating canion_1969a448-0a71-44f4-8422-300473478eaa temporary folder\nINFO     /tmp/biobb/unitests_35/biobb_canion/biobb_canion_log.out:file_utils.py:391 Creating command line with instructions and required arguments\nINFO     /tmp/biobb/unitests_35/biobb_canion/biobb_canion_log.out:cmd_wrapper.py:33 Canion &amp;lt;&amp;lt;! \n&amp;amp;inp\n  lis=canion_output,\n  dat=THGA_K,\n  axfrm=THGA,\n  solute=THGA_avg,\n  type=K+,\n  dlow=5.8,\n  dhig=7.2,\n  rlow=0,\n  rhig=18,\n  alow=0,\n  ahig=360,\n&amp;amp;end\n!\n\nINFO     /tmp/biobb/unitests_35/biobb_canion/biobb_canion_log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     /tmp/biobb/unitests_35/biobb_canion/biobb_canion_log.out:file_utils.py:391 Removed: [&amp;#x27;/tmp/biobb/unitests_35/biobb_canion/6a034018-c54c-45b0-9fa5-2831680905db&amp;#x27;, &amp;#x27;canion_1969a448-0a71-44f4-8422-300473478eaa&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_35\n&#34;}], &#34;biobb_dna/test/unitests/test_curvesplus/test_curves.py::TestCurves::test_curves&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_dna/test/unitests/test_curvesplus/test_curves.py::TestCurves::test_curves&#34;, &#34;duration&#34;: &#34;00:00:07&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_dna/test/unitests/test_curvesplus/test_curves.py::TestCurves::test_curves&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:00:07&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-05-24 09:29:43,016 [MainThread  ] [INFO ]  Executing biobb_dna.curvesplus.biobb_curves Version: 4.1.0\n2024-05-24 09:29:43,082 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/curvesplus/structure.stripped.trj to /tmp/biobb/unitests_35/biobb_curves/b8596be5-530e-4b9d-bf23-6c79ba3637fb\n2024-05-24 09:29:43,083 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/curvesplus/structure.stripped.top to /tmp/biobb/unitests_35/biobb_curves/b8596be5-530e-4b9d-bf23-6c79ba3637fb\n2024-05-24 09:29:43,084 [MainThread  ] [INFO ]  Creating curves_343479bd-6692-42c7-9128-05d7303ed3cc temporary folder\n2024-05-24 09:29:43,150 [MainThread  ] [INFO ]  Appending provided topology to command\n2024-05-24 09:29:43,150 [MainThread  ] [INFO ]  Creating command line with instructions and required arguments\n2024-05-24 09:29:43,150 [MainThread  ] [INFO ]  Cur+ &amp;lt;&amp;lt;! \n&amp;amp;inp\n  file=structure.stripped.trj,\n  ftop=structure.stripped.top,\n  lis=&amp;#x27;curves_output&amp;#x27;,\n  lib=/home/user/micromamba/envs/test_environment/.curvesplus/standard,\n  ions=.f.,\n  test=.f.,\n  line=.f.,\n  fit=.t.,\n  axfrm=.f.,\n  itst=0,itnd=0,itdel=1,\n&amp;amp;end\n2 1 -1 0 0\n1:12\n24:13\n!\n\n2024-05-24 09:29:49,642 [MainThread  ] [INFO ]  Exit code 0\n\n2024-05-24 09:29:49,663 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_35/biobb_curves/b8596be5-530e-4b9d-bf23-6c79ba3637fb&amp;#x27;, &amp;#x27;curves_343479bd-6692-42c7-9128-05d7303ed3cc&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_35/biobb_curves/curves_output.cda\nChecking if empty file: /tmp/biobb/unitests_35/biobb_curves/curves_output.lis\nComparing ignoring lines containing this words: [2]\n     FILE_A: /tmp/biobb/unitests_35/biobb_curves/curves_output.lis\n     FILE_B: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/reference/curvesplus/curves_trj_output.lis\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_35/biobb_curves/biobb_curves_log.out:file_utils.py:391 Executing biobb_dna.curvesplus.biobb_curves Version: 4.1.0\nINFO     /tmp/biobb/unitests_35/biobb_curves/biobb_curves_log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/curvesplus/structure.stripped.trj to /tmp/biobb/unitests_35/biobb_curves/b8596be5-530e-4b9d-bf23-6c79ba3637fb\nINFO     /tmp/biobb/unitests_35/biobb_curves/biobb_curves_log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/curvesplus/structure.stripped.top to /tmp/biobb/unitests_35/biobb_curves/b8596be5-530e-4b9d-bf23-6c79ba3637fb\nINFO     /tmp/biobb/unitests_35/biobb_curves/biobb_curves_log.out:file_utils.py:391 Creating curves_343479bd-6692-42c7-9128-05d7303ed3cc temporary folder\nINFO     /tmp/biobb/unitests_35/biobb_curves/biobb_curves_log.out:file_utils.py:391 Appending provided topology to command\nINFO     /tmp/biobb/unitests_35/biobb_curves/biobb_curves_log.out:file_utils.py:391 Creating command line with instructions and required arguments\nINFO     /tmp/biobb/unitests_35/biobb_curves/biobb_curves_log.out:cmd_wrapper.py:33 Cur+ &amp;lt;&amp;lt;! \n&amp;amp;inp\n  file=structure.stripped.trj,\n  ftop=structure.stripped.top,\n  lis=&amp;#x27;curves_output&amp;#x27;,\n  lib=/home/user/micromamba/envs/test_environment/.curvesplus/standard,\n  ions=.f.,\n  test=.f.,\n  line=.f.,\n  fit=.t.,\n  axfrm=.f.,\n  itst=0,itnd=0,itdel=1,\n&amp;amp;end\n2 1 -1 0 0\n1:12\n24:13\n!\n\nINFO     /tmp/biobb/unitests_35/biobb_curves/biobb_curves_log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     /tmp/biobb/unitests_35/biobb_curves/biobb_curves_log.out:file_utils.py:391 Removed: [&amp;#x27;/tmp/biobb/unitests_35/biobb_curves/b8596be5-530e-4b9d-bf23-6c79ba3637fb&amp;#x27;, &amp;#x27;curves_343479bd-6692-42c7-9128-05d7303ed3cc&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_35\n&#34;}], &#34;biobb_dna/test/unitests/test_dna/test_averages.py::TestAverages::test_helparaverages&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_dna/test/unitests/test_dna/test_averages.py::TestAverages::test_helparaverages&#34;, &#34;duration&#34;: &#34;378 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_dna/test/unitests/test_dna/test_averages.py::TestAverages::test_helparaverages&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;378 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-05-24 09:29:49,707 [MainThread  ] [INFO ]  Executing biobb_dna.dna.dna_averages Version: 4.1.0\n2024-05-24 09:29:49,709 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/dna/canal_output_shift.ser to /tmp/biobb/unitests_35/dna_averages/ec23415c-6089-4ace-b2a4-2833f3d240d3\n2024-05-24 09:29:49,709 [MainThread  ] [INFO ]  Creating averages_b9a1f35c-96c7-435a-ba0f-66c7353ba478 temporary folder\n2024-05-24 09:29:49,984 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_35/dna_averages/ec23415c-6089-4ace-b2a4-2833f3d240d3&amp;#x27;, &amp;#x27;averages_b9a1f35c-96c7-435a-ba0f-66c7353ba478&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_35/dna_averages/avg_out.csv\nChecking if empty file: /tmp/biobb/unitests_35/dna_averages/avg_out.jpg\nComparing images of both files:\n     IMAGE_A: /tmp/biobb/unitests_35/dna_averages/avg_out.jpg\n     IMAGE_B: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/reference/dna/shift_avg.jpg\n     IMAGE_A HASH: c07e3e32163f3ee3 SIZE: 64 bits\n     IMAGE_B HASH: c07e3e32163f3ee3 SIZE: 64 bits\n     TOLERANCE: 1.0%, ABS TOLERANCE: 1 bits, DIFFERENCE: 0 bits\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_35/dna_averages/dna_averages_log.out:file_utils.py:391 Executing biobb_dna.dna.dna_averages Version: 4.1.0\nINFO     /tmp/biobb/unitests_35/dna_averages/dna_averages_log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/dna/canal_output_shift.ser to /tmp/biobb/unitests_35/dna_averages/ec23415c-6089-4ace-b2a4-2833f3d240d3\nINFO     /tmp/biobb/unitests_35/dna_averages/dna_averages_log.out:file_utils.py:391 Creating averages_b9a1f35c-96c7-435a-ba0f-66c7353ba478 temporary folder\nINFO     /tmp/biobb/unitests_35/dna_averages/dna_averages_log.out:file_utils.py:391 Removed: [&amp;#x27;/tmp/biobb/unitests_35/dna_averages/ec23415c-6089-4ace-b2a4-2833f3d240d3&amp;#x27;, &amp;#x27;averages_b9a1f35c-96c7-435a-ba0f-66c7353ba478&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_35\n&#34;}], &#34;biobb_dna/test/unitests/test_dna/test_bimodality.py::TestBimodality::test_helparbimodality&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_dna/test/unitests/test_dna/test_bimodality.py::TestBimodality::test_helparbimodality&#34;, &#34;duration&#34;: &#34;551 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_dna/test/unitests/test_dna/test_bimodality.py::TestBimodality::test_helparbimodality&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;551 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-05-24 09:29:50,086 [MainThread  ] [INFO ]  Executing biobb_dna.dna.dna_bimodality Version: 4.1.0\n2024-05-24 09:29:50,087 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/dna/series_shift_AT.csv to /tmp/biobb/unitests_35/dna_bimodality/a49d6983-e224-4d81-8fc3-e8372552623b\n2024-05-24 09:29:50,087 [MainThread  ] [INFO ]  Creating bimodality_ed3d3ac4-3b50-43fc-a723-0ee50478e6d6 temporary folder\n2024-05-24 09:29:50,599 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_35/dna_bimodality/a49d6983-e224-4d81-8fc3-e8372552623b&amp;#x27;, &amp;#x27;bimodality_ed3d3ac4-3b50-43fc-a723-0ee50478e6d6&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_35/dna_bimodality/bimod_out.csv\nChecking if empty file: /tmp/biobb/unitests_35/dna_bimodality/bimod_out.jpg\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_35/dna_bimodality/dna_bimodality_log.out:file_utils.py:391 Executing biobb_dna.dna.dna_bimodality Version: 4.1.0\nINFO     /tmp/biobb/unitests_35/dna_bimodality/dna_bimodality_log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/dna/series_shift_AT.csv to /tmp/biobb/unitests_35/dna_bimodality/a49d6983-e224-4d81-8fc3-e8372552623b\nINFO     /tmp/biobb/unitests_35/dna_bimodality/dna_bimodality_log.out:file_utils.py:391 Creating bimodality_ed3d3ac4-3b50-43fc-a723-0ee50478e6d6 temporary folder\nINFO     /tmp/biobb/unitests_35/dna_bimodality/dna_bimodality_log.out:file_utils.py:391 Removed: [&amp;#x27;/tmp/biobb/unitests_35/dna_bimodality/a49d6983-e224-4d81-8fc3-e8372552623b&amp;#x27;, &amp;#x27;bimodality_ed3d3ac4-3b50-43fc-a723-0ee50478e6d6&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_35\n&#34;}], &#34;biobb_dna/test/unitests/test_dna/test_timeseries.py::TestTimeSeries::test_helpartimeseries&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_dna/test/unitests/test_dna/test_timeseries.py::TestTimeSeries::test_helpartimeseries&#34;, &#34;duration&#34;: &#34;00:00:01&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_dna/test/unitests/test_dna/test_timeseries.py::TestTimeSeries::test_helpartimeseries&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:00:01&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-05-24 09:29:50,664 [MainThread  ] [INFO ]  Executing biobb_dna.dna.dna_timeseries Version: 4.1.0\n2024-05-24 09:29:50,665 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/dna/canal_output_shift.ser to /tmp/biobb/unitests_35/dna_timeseries/458d7662-b6bc-4c2b-8ebc-d1f47304dcd6\n2024-05-24 09:29:50,665 [MainThread  ] [INFO ]  Creating timeseries_ed6f0002-b9cc-4dd0-833d-7d7fe7ee089c temporary folder\n2024-05-24 09:29:51,678 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_35/dna_timeseries/458d7662-b6bc-4c2b-8ebc-d1f47304dcd6&amp;#x27;, &amp;#x27;timeseries_ed6f0002-b9cc-4dd0-833d-7d7fe7ee089c&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_35/dna_timeseries/timeseries_output.zip\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_35/dna_timeseries/dna_timeseries_log.out:file_utils.py:391 Executing biobb_dna.dna.dna_timeseries Version: 4.1.0\nINFO     /tmp/biobb/unitests_35/dna_timeseries/dna_timeseries_log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/dna/canal_output_shift.ser to /tmp/biobb/unitests_35/dna_timeseries/458d7662-b6bc-4c2b-8ebc-d1f47304dcd6\nINFO     /tmp/biobb/unitests_35/dna_timeseries/dna_timeseries_log.out:file_utils.py:391 Creating timeseries_ed6f0002-b9cc-4dd0-833d-7d7fe7ee089c temporary folder\nINFO     /tmp/biobb/unitests_35/dna_timeseries/dna_timeseries_log.out:file_utils.py:391 Removed: [&amp;#x27;/tmp/biobb/unitests_35/dna_timeseries/458d7662-b6bc-4c2b-8ebc-d1f47304dcd6&amp;#x27;, &amp;#x27;timeseries_ed6f0002-b9cc-4dd0-833d-7d7fe7ee089c&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_35\n&#34;}], &#34;biobb_dna/test/unitests/test_stiffness/test_stiffness.py::TestAvgStiffness::test_averagestiffness&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_dna/test/unitests/test_stiffness/test_stiffness.py::TestAvgStiffness::test_averagestiffness&#34;, &#34;duration&#34;: &#34;317 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_dna/test/unitests/test_stiffness/test_stiffness.py::TestAvgStiffness::test_averagestiffness&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;317 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-05-24 09:29:51,718 [MainThread  ] [INFO ]  Executing biobb_dna.stiffness.average_stiffness Version: 4.1.0\n2024-05-24 09:29:51,719 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/canal_output_roll.ser to /tmp/biobb/unitests_35/average_stiffness/d98a45a1-6e71-4589-81c7-7ccdbe22dd56\n2024-05-24 09:29:51,719 [MainThread  ] [INFO ]  Creating avgstiffness_0974a0b7-2e52-4a71-9966-bdf5cd2497b2 temporary folder\n2024-05-24 09:29:51,935 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_35/average_stiffness/d98a45a1-6e71-4589-81c7-7ccdbe22dd56&amp;#x27;, &amp;#x27;avgstiffness_0974a0b7-2e52-4a71-9966-bdf5cd2497b2&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_35/average_stiffness/avgstiff.csv\nChecking if empty file: /tmp/biobb/unitests_35/average_stiffness/avgstiff.jpg\nComparing images of both files:\n     IMAGE_A: /tmp/biobb/unitests_35/average_stiffness/avgstiff.jpg\n     IMAGE_B: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/reference/stiffness/stiffavg_roll.jpg\n     IMAGE_A HASH: 017f7f7f1d7f7e80 SIZE: 64 bits\n     IMAGE_B HASH: 017f7f7f1d7f7e80 SIZE: 64 bits\n     TOLERANCE: 1.0%, ABS TOLERANCE: 1 bits, DIFFERENCE: 0 bits\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_35/average_stiffness/average_stiffness_log.out:file_utils.py:391 Executing biobb_dna.stiffness.average_stiffness Version: 4.1.0\nINFO     /tmp/biobb/unitests_35/average_stiffness/average_stiffness_log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/canal_output_roll.ser to /tmp/biobb/unitests_35/average_stiffness/d98a45a1-6e71-4589-81c7-7ccdbe22dd56\nINFO     /tmp/biobb/unitests_35/average_stiffness/average_stiffness_log.out:file_utils.py:391 Creating avgstiffness_0974a0b7-2e52-4a71-9966-bdf5cd2497b2 temporary folder\nINFO     /tmp/biobb/unitests_35/average_stiffness/average_stiffness_log.out:file_utils.py:391 Removed: [&amp;#x27;/tmp/biobb/unitests_35/average_stiffness/d98a45a1-6e71-4589-81c7-7ccdbe22dd56&amp;#x27;, &amp;#x27;avgstiffness_0974a0b7-2e52-4a71-9966-bdf5cd2497b2&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_35\n&#34;}], &#34;biobb_dna/test/unitests/test_stiffness/test_stiffness.py::TestBasePairStiffness::test_basepairstiffness&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_dna/test/unitests/test_stiffness/test_stiffness.py::TestBasePairStiffness::test_basepairstiffness&#34;, &#34;duration&#34;: &#34;328 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_dna/test/unitests/test_stiffness/test_stiffness.py::TestBasePairStiffness::test_basepairstiffness&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;328 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-05-24 09:29:52,037 [MainThread  ] [INFO ]  Executing biobb_dna.stiffness.basepair_stiffness Version: 4.1.0\n2024-05-24 09:29:52,037 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_shift_AA.csv to /tmp/biobb/unitests_35/basepair_stiffness/9d52f38f-b4a7-4aed-8bf3-ea1a71172142\n2024-05-24 09:29:52,037 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_slide_AA.csv to /tmp/biobb/unitests_35/basepair_stiffness/9d52f38f-b4a7-4aed-8bf3-ea1a71172142\n2024-05-24 09:29:52,038 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_rise_AA.csv to /tmp/biobb/unitests_35/basepair_stiffness/9d52f38f-b4a7-4aed-8bf3-ea1a71172142\n2024-05-24 09:29:52,038 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_tilt_AA.csv to /tmp/biobb/unitests_35/basepair_stiffness/9d52f38f-b4a7-4aed-8bf3-ea1a71172142\n2024-05-24 09:29:52,038 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_roll_AA.csv to /tmp/biobb/unitests_35/basepair_stiffness/9d52f38f-b4a7-4aed-8bf3-ea1a71172142\n2024-05-24 09:29:52,039 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_twist_AA.csv to /tmp/biobb/unitests_35/basepair_stiffness/9d52f38f-b4a7-4aed-8bf3-ea1a71172142\n2024-05-24 09:29:52,039 [MainThread  ] [INFO ]  Creating bp_stiffness_4f51882c-c35c-4d7a-a6e5-001e04635865 temporary folder\nChecking if empty file: /tmp/biobb/unitests_35/basepair_stiffness/bpstiff.csv\nChecking if empty file: /tmp/biobb/unitests_35/basepair_stiffness/bpstiff.jpg\nComparing images of both files:\n     IMAGE_A: /tmp/biobb/unitests_35/basepair_stiffness/bpstiff.jpg\n     IMAGE_B: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/reference/stiffness/stiffbp_ref.jpg\n     IMAGE_A HASH: ff8080909080ffff SIZE: 64 bits\n     IMAGE_B HASH: ff8080909080ffff SIZE: 64 bits\n     TOLERANCE: 1.0%, ABS TOLERANCE: 1 bits, DIFFERENCE: 0 bits\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_35/basepair_stiffness/basepair_stiffness_log.out:file_utils.py:391 Executing biobb_dna.stiffness.basepair_stiffness Version: 4.1.0\nINFO     /tmp/biobb/unitests_35/basepair_stiffness/basepair_stiffness_log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_shift_AA.csv to /tmp/biobb/unitests_35/basepair_stiffness/9d52f38f-b4a7-4aed-8bf3-ea1a71172142\nINFO     /tmp/biobb/unitests_35/basepair_stiffness/basepair_stiffness_log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_slide_AA.csv to /tmp/biobb/unitests_35/basepair_stiffness/9d52f38f-b4a7-4aed-8bf3-ea1a71172142\nINFO     /tmp/biobb/unitests_35/basepair_stiffness/basepair_stiffness_log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_rise_AA.csv to /tmp/biobb/unitests_35/basepair_stiffness/9d52f38f-b4a7-4aed-8bf3-ea1a71172142\nINFO     /tmp/biobb/unitests_35/basepair_stiffness/basepair_stiffness_log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_tilt_AA.csv to /tmp/biobb/unitests_35/basepair_stiffness/9d52f38f-b4a7-4aed-8bf3-ea1a71172142\nINFO     /tmp/biobb/unitests_35/basepair_stiffness/basepair_stiffness_log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_roll_AA.csv to /tmp/biobb/unitests_35/basepair_stiffness/9d52f38f-b4a7-4aed-8bf3-ea1a71172142\nINFO     /tmp/biobb/unitests_35/basepair_stiffness/basepair_stiffness_log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_twist_AA.csv to /tmp/biobb/unitests_35/basepair_stiffness/9d52f38f-b4a7-4aed-8bf3-ea1a71172142\nINFO     /tmp/biobb/unitests_35/basepair_stiffness/basepair_stiffness_log.out:file_utils.py:391 Creating bp_stiffness_4f51882c-c35c-4d7a-a6e5-001e04635865 temporary folder\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_35\n&#34;}]}, &#34;renderCollapsed&#34;: [&#34;passed&#34;], &#34;initialSort&#34;: &#34;result&#34;, &#34;title&#34;: &#34;report.html&#34;}"></div>
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