diff --git a/coverage/class_index.html b/coverage/class_index.html
index 225b90b..570820d 100644
--- a/coverage/class_index.html
+++ b/coverage/class_index.html
@@ -54,8 +54,8 @@ <h2>
                 <a class="button current">Classes</a>
         </h2>
         <p class="text">
-            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.4">coverage.py v7.6.4</a>,
-            created at 2024-11-04 11:05 +0000
+            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
+            created at 2024-11-15 12:07 +0000
         </p>
     </div>
 </header>
@@ -89,52 +89,52 @@ <h2>
                 <td class="right" data-ratio="5 5">100%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_159731231e5c9c9d_bipopulations_py.html#t17">biobb_dna/backbone/bipopulations.py</a></td>
-                <td class="name left"><a href="z_159731231e5c9c9d_bipopulations_py.html#t17"><data value='BIPopulations'>BIPopulations</data></a></td>
-                <td>64</td>
+                <td class="name left"><a href="z_159731231e5c9c9d_bipopulations_py.html#t19">biobb_dna/backbone/bipopulations.py</a></td>
+                <td class="name left"><a href="z_159731231e5c9c9d_bipopulations_py.html#t19"><data value='BIPopulations'>BIPopulations</data></a></td>
+                <td>67</td>
                 <td>8</td>
                 <td>0</td>
-                <td class="right" data-ratio="56 64">88%</td>
+                <td class="right" data-ratio="59 67">88%</td>
             </tr>
             <tr class="region">
                 <td class="name left"><a href="z_159731231e5c9c9d_bipopulations_py.html">biobb_dna/backbone/bipopulations.py</a></td>
                 <td class="name left"><a href="z_159731231e5c9c9d_bipopulations_py.html"><data value=''><span class='no-noun'>(no class)</span></data></a></td>
-                <td>34</td>
+                <td>35</td>
                 <td>14</td>
                 <td>0</td>
-                <td class="right" data-ratio="20 34">59%</td>
+                <td class="right" data-ratio="21 35">60%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_159731231e5c9c9d_canonicalag_py.html#t17">biobb_dna/backbone/canonicalag.py</a></td>
-                <td class="name left"><a href="z_159731231e5c9c9d_canonicalag_py.html#t17"><data value='CanonicalAG'>CanonicalAG</data></a></td>
-                <td>73</td>
+                <td class="name left"><a href="z_159731231e5c9c9d_canonicalag_py.html#t19">biobb_dna/backbone/canonicalag.py</a></td>
+                <td class="name left"><a href="z_159731231e5c9c9d_canonicalag_py.html#t19"><data value='CanonicalAG'>CanonicalAG</data></a></td>
+                <td>74</td>
                 <td>8</td>
                 <td>0</td>
-                <td class="right" data-ratio="65 73">89%</td>
+                <td class="right" data-ratio="66 74">89%</td>
             </tr>
             <tr class="region">
                 <td class="name left"><a href="z_159731231e5c9c9d_canonicalag_py.html">biobb_dna/backbone/canonicalag.py</a></td>
                 <td class="name left"><a href="z_159731231e5c9c9d_canonicalag_py.html"><data value=''><span class='no-noun'>(no class)</span></data></a></td>
-                <td>35</td>
+                <td>36</td>
                 <td>14</td>
                 <td>0</td>
-                <td class="right" data-ratio="21 35">60%</td>
+                <td class="right" data-ratio="22 36">61%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_159731231e5c9c9d_puckering_py.html#t17">biobb_dna/backbone/puckering.py</a></td>
-                <td class="name left"><a href="z_159731231e5c9c9d_puckering_py.html#t17"><data value='Puckering'>Puckering</data></a></td>
-                <td>70</td>
+                <td class="name left"><a href="z_159731231e5c9c9d_puckering_py.html#t19">biobb_dna/backbone/puckering.py</a></td>
+                <td class="name left"><a href="z_159731231e5c9c9d_puckering_py.html#t19"><data value='Puckering'>Puckering</data></a></td>
+                <td>71</td>
                 <td>8</td>
                 <td>0</td>
-                <td class="right" data-ratio="62 70">89%</td>
+                <td class="right" data-ratio="63 71">89%</td>
             </tr>
             <tr class="region">
                 <td class="name left"><a href="z_159731231e5c9c9d_puckering_py.html">biobb_dna/backbone/puckering.py</a></td>
                 <td class="name left"><a href="z_159731231e5c9c9d_puckering_py.html"><data value=''><span class='no-noun'>(no class)</span></data></a></td>
-                <td>33</td>
+                <td>34</td>
                 <td>12</td>
                 <td>0</td>
-                <td class="right" data-ratio="21 33">64%</td>
+                <td class="right" data-ratio="22 34">65%</td>
             </tr>
             <tr class="region">
                 <td class="name left"><a href="z_74fa14c6d0e940a4___init___py.html">biobb_dna/curvesplus/__init__.py</a></td>
@@ -217,20 +217,20 @@ <h2>
                 <td class="right" data-ratio="6 6">100%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_3afbcd666ed82c91_dna_averages_py.html#t17">biobb_dna/dna/dna_averages.py</a></td>
-                <td class="name left"><a href="z_3afbcd666ed82c91_dna_averages_py.html#t17"><data value='HelParAverages'>HelParAverages</data></a></td>
-                <td>64</td>
-                <td>14</td>
+                <td class="name left"><a href="z_3afbcd666ed82c91_dna_averages_py.html#t20">biobb_dna/dna/dna_averages.py</a></td>
+                <td class="name left"><a href="z_3afbcd666ed82c91_dna_averages_py.html#t20"><data value='HelParAverages'>HelParAverages</data></a></td>
+                <td>65</td>
+                <td>15</td>
                 <td>0</td>
-                <td class="right" data-ratio="50 64">78%</td>
+                <td class="right" data-ratio="50 65">77%</td>
             </tr>
             <tr class="region">
                 <td class="name left"><a href="z_3afbcd666ed82c91_dna_averages_py.html">biobb_dna/dna/dna_averages.py</a></td>
                 <td class="name left"><a href="z_3afbcd666ed82c91_dna_averages_py.html"><data value=''><span class='no-noun'>(no class)</span></data></a></td>
-                <td>29</td>
+                <td>30</td>
                 <td>11</td>
                 <td>0</td>
-                <td class="right" data-ratio="18 29">62%</td>
+                <td class="right" data-ratio="19 30">63%</td>
             </tr>
             <tr class="region">
                 <td class="name left"><a href="z_3afbcd666ed82c91_dna_bimodality_py.html#t21">biobb_dna/dna/dna_bimodality.py</a></td>
@@ -249,8 +249,8 @@ <h2>
                 <td class="right" data-ratio="25 37">68%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_3afbcd666ed82c91_dna_timeseries_py.html#t20">biobb_dna/dna/dna_timeseries.py</a></td>
-                <td class="name left"><a href="z_3afbcd666ed82c91_dna_timeseries_py.html#t20"><data value='HelParTimeSeries'>HelParTimeSeries</data></a></td>
+                <td class="name left"><a href="z_3afbcd666ed82c91_dna_timeseries_py.html#t23">biobb_dna/dna/dna_timeseries.py</a></td>
+                <td class="name left"><a href="z_3afbcd666ed82c91_dna_timeseries_py.html#t23"><data value='HelParTimeSeries'>HelParTimeSeries</data></a></td>
                 <td>99</td>
                 <td>21</td>
                 <td>0</td>
@@ -259,10 +259,10 @@ <h2>
             <tr class="region">
                 <td class="name left"><a href="z_3afbcd666ed82c91_dna_timeseries_py.html">biobb_dna/dna/dna_timeseries.py</a></td>
                 <td class="name left"><a href="z_3afbcd666ed82c91_dna_timeseries_py.html"><data value=''><span class='no-noun'>(no class)</span></data></a></td>
-                <td>31</td>
+                <td>32</td>
                 <td>10</td>
                 <td>0</td>
-                <td class="right" data-ratio="21 31">68%</td>
+                <td class="right" data-ratio="22 32">69%</td>
             </tr>
             <tr class="region">
                 <td class="name left"><a href="z_3afbcd666ed82c91_dna_timeseries_unzip_py.html#t17">biobb_dna/dna/dna_timeseries_unzip.py</a></td>
@@ -289,20 +289,20 @@ <h2>
                 <td class="right" data-ratio="5 5">100%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_8a2a7f872cf1434f_interbpcorr_py.html#t20">biobb_dna/interbp_correlations/interbpcorr.py</a></td>
-                <td class="name left"><a href="z_8a2a7f872cf1434f_interbpcorr_py.html#t20"><data value='InterBasePairCorrelation'>InterBasePairCorrelation</data></a></td>
-                <td>102</td>
+                <td class="name left"><a href="z_8a2a7f872cf1434f_interbpcorr_py.html#t22">biobb_dna/interbp_correlations/interbpcorr.py</a></td>
+                <td class="name left"><a href="z_8a2a7f872cf1434f_interbpcorr_py.html#t22"><data value='InterBasePairCorrelation'>InterBasePairCorrelation</data></a></td>
+                <td>103</td>
                 <td>6</td>
                 <td>0</td>
-                <td class="right" data-ratio="96 102">94%</td>
+                <td class="right" data-ratio="97 103">94%</td>
             </tr>
             <tr class="region">
                 <td class="name left"><a href="z_8a2a7f872cf1434f_interbpcorr_py.html">biobb_dna/interbp_correlations/interbpcorr.py</a></td>
                 <td class="name left"><a href="z_8a2a7f872cf1434f_interbpcorr_py.html"><data value=''><span class='no-noun'>(no class)</span></data></a></td>
-                <td>40</td>
+                <td>41</td>
                 <td>16</td>
                 <td>0</td>
-                <td class="right" data-ratio="24 40">60%</td>
+                <td class="right" data-ratio="25 41">61%</td>
             </tr>
             <tr class="region">
                 <td class="name left"><a href="z_8a2a7f872cf1434f_interhpcorr_py.html#t17">biobb_dna/interbp_correlations/interhpcorr.py</a></td>
@@ -321,20 +321,20 @@ <h2>
                 <td class="right" data-ratio="22 38">58%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_8a2a7f872cf1434f_interseqcorr_py.html#t18">biobb_dna/interbp_correlations/interseqcorr.py</a></td>
-                <td class="name left"><a href="z_8a2a7f872cf1434f_interseqcorr_py.html#t18"><data value='InterSequenceCorrelation'>InterSequenceCorrelation</data></a></td>
-                <td>63</td>
+                <td class="name left"><a href="z_8a2a7f872cf1434f_interseqcorr_py.html#t20">biobb_dna/interbp_correlations/interseqcorr.py</a></td>
+                <td class="name left"><a href="z_8a2a7f872cf1434f_interseqcorr_py.html#t20"><data value='InterSequenceCorrelation'>InterSequenceCorrelation</data></a></td>
+                <td>64</td>
                 <td>16</td>
                 <td>0</td>
-                <td class="right" data-ratio="47 63">75%</td>
+                <td class="right" data-ratio="48 64">75%</td>
             </tr>
             <tr class="region">
                 <td class="name left"><a href="z_8a2a7f872cf1434f_interseqcorr_py.html">biobb_dna/interbp_correlations/interseqcorr.py</a></td>
                 <td class="name left"><a href="z_8a2a7f872cf1434f_interseqcorr_py.html"><data value=''><span class='no-noun'>(no class)</span></data></a></td>
-                <td>31</td>
+                <td>32</td>
                 <td>11</td>
                 <td>0</td>
-                <td class="right" data-ratio="20 31">65%</td>
+                <td class="right" data-ratio="21 32">66%</td>
             </tr>
             <tr class="region">
                 <td class="name left"><a href="z_64e03be4370b7ecc___init___py.html">biobb_dna/intrabp_correlations/__init__.py</a></td>
@@ -345,20 +345,20 @@ <h2>
                 <td class="right" data-ratio="5 5">100%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_64e03be4370b7ecc_intrabpcorr_py.html#t20">biobb_dna/intrabp_correlations/intrabpcorr.py</a></td>
-                <td class="name left"><a href="z_64e03be4370b7ecc_intrabpcorr_py.html#t20"><data value='IntraBasePairCorrelation'>IntraBasePairCorrelation</data></a></td>
-                <td>102</td>
+                <td class="name left"><a href="z_64e03be4370b7ecc_intrabpcorr_py.html#t22">biobb_dna/intrabp_correlations/intrabpcorr.py</a></td>
+                <td class="name left"><a href="z_64e03be4370b7ecc_intrabpcorr_py.html#t22"><data value='IntraBasePairCorrelation'>IntraBasePairCorrelation</data></a></td>
+                <td>103</td>
                 <td>6</td>
                 <td>0</td>
-                <td class="right" data-ratio="96 102">94%</td>
+                <td class="right" data-ratio="97 103">94%</td>
             </tr>
             <tr class="region">
                 <td class="name left"><a href="z_64e03be4370b7ecc_intrabpcorr_py.html">biobb_dna/intrabp_correlations/intrabpcorr.py</a></td>
                 <td class="name left"><a href="z_64e03be4370b7ecc_intrabpcorr_py.html"><data value=''><span class='no-noun'>(no class)</span></data></a></td>
-                <td>40</td>
+                <td>41</td>
                 <td>16</td>
                 <td>0</td>
-                <td class="right" data-ratio="24 40">60%</td>
+                <td class="right" data-ratio="25 41">61%</td>
             </tr>
             <tr class="region">
                 <td class="name left"><a href="z_64e03be4370b7ecc_intrahpcorr_py.html#t17">biobb_dna/intrabp_correlations/intrahpcorr.py</a></td>
@@ -377,20 +377,20 @@ <h2>
                 <td class="right" data-ratio="22 38">58%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_64e03be4370b7ecc_intraseqcorr_py.html#t18">biobb_dna/intrabp_correlations/intraseqcorr.py</a></td>
-                <td class="name left"><a href="z_64e03be4370b7ecc_intraseqcorr_py.html#t18"><data value='IntraSequenceCorrelation'>IntraSequenceCorrelation</data></a></td>
-                <td>63</td>
+                <td class="name left"><a href="z_64e03be4370b7ecc_intraseqcorr_py.html#t20">biobb_dna/intrabp_correlations/intraseqcorr.py</a></td>
+                <td class="name left"><a href="z_64e03be4370b7ecc_intraseqcorr_py.html#t20"><data value='IntraSequenceCorrelation'>IntraSequenceCorrelation</data></a></td>
+                <td>64</td>
                 <td>16</td>
                 <td>0</td>
-                <td class="right" data-ratio="47 63">75%</td>
+                <td class="right" data-ratio="48 64">75%</td>
             </tr>
             <tr class="region">
                 <td class="name left"><a href="z_64e03be4370b7ecc_intraseqcorr_py.html">biobb_dna/intrabp_correlations/intraseqcorr.py</a></td>
                 <td class="name left"><a href="z_64e03be4370b7ecc_intraseqcorr_py.html"><data value=''><span class='no-noun'>(no class)</span></data></a></td>
-                <td>31</td>
+                <td>32</td>
                 <td>11</td>
                 <td>0</td>
-                <td class="right" data-ratio="20 31">65%</td>
+                <td class="right" data-ratio="21 32">66%</td>
             </tr>
             <tr class="region">
                 <td class="name left"><a href="z_9de9475b0a6fab52___init___py.html">biobb_dna/stiffness/__init__.py</a></td>
@@ -401,24 +401,24 @@ <h2>
                 <td class="right" data-ratio="4 4">100%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_9de9475b0a6fab52_average_stiffness_py.html#t18">biobb_dna/stiffness/average_stiffness.py</a></td>
-                <td class="name left"><a href="z_9de9475b0a6fab52_average_stiffness_py.html#t18"><data value='AverageStiffness'>AverageStiffness</data></a></td>
-                <td>60</td>
+                <td class="name left"><a href="z_9de9475b0a6fab52_average_stiffness_py.html#t20">biobb_dna/stiffness/average_stiffness.py</a></td>
+                <td class="name left"><a href="z_9de9475b0a6fab52_average_stiffness_py.html#t20"><data value='AverageStiffness'>AverageStiffness</data></a></td>
+                <td>61</td>
                 <td>13</td>
                 <td>0</td>
-                <td class="right" data-ratio="47 60">78%</td>
+                <td class="right" data-ratio="48 61">79%</td>
             </tr>
             <tr class="region">
                 <td class="name left"><a href="z_9de9475b0a6fab52_average_stiffness_py.html">biobb_dna/stiffness/average_stiffness.py</a></td>
                 <td class="name left"><a href="z_9de9475b0a6fab52_average_stiffness_py.html"><data value=''><span class='no-noun'>(no class)</span></data></a></td>
-                <td>30</td>
+                <td>31</td>
                 <td>11</td>
                 <td>0</td>
-                <td class="right" data-ratio="19 30">63%</td>
+                <td class="right" data-ratio="20 31">65%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_9de9475b0a6fab52_basepair_stiffness_py.html#t18">biobb_dna/stiffness/basepair_stiffness.py</a></td>
-                <td class="name left"><a href="z_9de9475b0a6fab52_basepair_stiffness_py.html#t18"><data value='BPStiffness'>BPStiffness</data></a></td>
+                <td class="name left"><a href="z_9de9475b0a6fab52_basepair_stiffness_py.html#t20">biobb_dna/stiffness/basepair_stiffness.py</a></td>
+                <td class="name left"><a href="z_9de9475b0a6fab52_basepair_stiffness_py.html#t20"><data value='BPStiffness'>BPStiffness</data></a></td>
                 <td>47</td>
                 <td>1</td>
                 <td>0</td>
@@ -427,10 +427,10 @@ <h2>
             <tr class="region">
                 <td class="name left"><a href="z_9de9475b0a6fab52_basepair_stiffness_py.html">biobb_dna/stiffness/basepair_stiffness.py</a></td>
                 <td class="name left"><a href="z_9de9475b0a6fab52_basepair_stiffness_py.html"><data value=''><span class='no-noun'>(no class)</span></data></a></td>
-                <td>34</td>
+                <td>35</td>
                 <td>16</td>
                 <td>0</td>
-                <td class="right" data-ratio="18 34">53%</td>
+                <td class="right" data-ratio="19 35">54%</td>
             </tr>
             <tr class="region">
                 <td class="name left"><a href="z_957b841f7413f0a1___init___py.html">biobb_dna/test/__init__.py</a></td>
@@ -441,8 +441,8 @@ <h2>
                 <td class="right" data-ratio="0 0">100%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_020f76a90aa51c7b_test_bipopulations_py.html#t7">biobb_dna/test/unitests/test_backbone/test_bipopulations.py</a></td>
-                <td class="name left"><a href="z_020f76a90aa51c7b_test_bipopulations_py.html#t7"><data value='TestBIPopulations'>TestBIPopulations</data></a></td>
+                <td class="name left"><a href="z_020f76a90aa51c7b_test_bipopulations_py.html#t9">biobb_dna/test/unitests/test_backbone/test_bipopulations.py</a></td>
+                <td class="name left"><a href="z_020f76a90aa51c7b_test_bipopulations_py.html#t9"><data value='TestBIPopulations'>TestBIPopulations</data></a></td>
                 <td>9</td>
                 <td>1</td>
                 <td>0</td>
@@ -704,6 +704,14 @@ <h2>
                 <td>0</td>
                 <td class="right" data-ratio="0 0">100%</td>
             </tr>
+            <tr class="region">
+                <td class="name left"><a href="z_833b0317e3c43dca_common_py.html">biobb_dna/utils/common.py</a></td>
+                <td class="name left"><a href="z_833b0317e3c43dca_common_py.html"><data value=''><span class='no-noun'>(no class)</span></data></a></td>
+                <td>10</td>
+                <td>4</td>
+                <td>0</td>
+                <td class="right" data-ratio="6 10">60%</td>
+            </tr>
             <tr class="region">
                 <td class="name left"><a href="z_833b0317e3c43dca_constants_py.html">biobb_dna/utils/constants.py</a></td>
                 <td class="name left"><a href="z_833b0317e3c43dca_constants_py.html"><data value=''><span class='no-noun'>(no class)</span></data></a></td>
@@ -733,10 +741,10 @@ <h2>
             <tr class="total">
                 <td class="name left">Total</td>
                 <td class="name left">&nbsp;</td>
-                <td>2404</td>
-                <td>508</td>
+                <td>2436</td>
+                <td>513</td>
                 <td>0</td>
-                <td class="right" data-ratio="1896 2404">79%</td>
+                <td class="right" data-ratio="1923 2436">79%</td>
             </tr>
         </tfoot>
     </table>
@@ -747,8 +755,8 @@ <h2>
 <footer>
     <div class="content">
         <p>
-            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.4">coverage.py v7.6.4</a>,
-            created at 2024-11-04 11:05 +0000
+            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
+            created at 2024-11-15 12:07 +0000
         </p>
     </div>
     <aside class="hidden">
diff --git a/coverage/coverage.xml b/coverage/coverage.xml
index dd86617..2a46ba3 100644
--- a/coverage/coverage.xml
+++ b/coverage/coverage.xml
@@ -1,6 +1,6 @@
 <?xml version="1.0" ?>
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-	<!-- Generated by coverage.py: https://coverage.readthedocs.io/en/7.6.4 -->
+<coverage version="7.6.5" timestamp="1731672452387" lines-valid="2436" lines-covered="1923" line-rate="0.7894" branches-covered="0" branches-valid="0" branch-rate="0" complexity="0">
+	<!-- Generated by coverage.py: https://coverage.readthedocs.io/en/7.6.5 -->
 	<!-- Based on https://raw.githubusercontent.com/cobertura/web/master/htdocs/xml/coverage-04.dtd -->
 	<sources>
 		<source>/home/user/actions-runner/_work/biobb_dna/biobb_dna</source>
@@ -24,7 +24,7 @@
 				</class>
 			</classes>
 		</package>
-		<package name="biobb_dna.backbone" line-rate="0.7962" branch-rate="0" complexity="0">
+		<package name="biobb_dna.backbone" line-rate="0.8012" branch-rate="0" complexity="0">
 			<classes>
 				<class name="__init__.py" filename="biobb_dna/backbone/__init__.py" complexity="0" line-rate="1" branch-rate="0">
 					<methods/>
@@ -36,7 +36,7 @@
 						<line number="5" hits="1"/>
 					</lines>
 				</class>
-				<class name="bipopulations.py" filename="biobb_dna/backbone/bipopulations.py" complexity="0" line-rate="0.7755" branch-rate="0">
+				<class name="bipopulations.py" filename="biobb_dna/backbone/bipopulations.py" complexity="0" line-rate="0.7843" branch-rate="0">
 					<methods/>
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@@ -47,99 +47,103 @@
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+				<class name="canonicalag.py" filename="biobb_dna/backbone/canonicalag.py" complexity="0" line-rate="0.8" branch-rate="0">
 					<methods/>
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@@ -150,109 +154,111 @@
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+		<package name="biobb_dna.dna" line-rate="0.7213" branch-rate="0" complexity="0">
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@@ -1022,139 +1032,140 @@
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@@ -1250,7 +1261,7 @@
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@@ -1262,122 +1273,112 @@
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@@ -1547,108 +1560,110 @@
 						<line number="341" hits="0"/>
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 				</class>
-				<class name="interseqcorr.py" filename="biobb_dna/interbp_correlations/interseqcorr.py" complexity="0" line-rate="0.7128" branch-rate="0">
+				<class name="interseqcorr.py" filename="biobb_dna/interbp_correlations/interseqcorr.py" complexity="0" line-rate="0.7188" branch-rate="0">
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+		<package name="biobb_dna.intrabp_correlations" line-rate="0.8042" branch-rate="0" complexity="0">
 			<classes>
 				<class name="__init__.py" filename="biobb_dna/intrabp_correlations/__init__.py" complexity="0" line-rate="1" branch-rate="0">
 					<methods/>
@@ -1660,119 +1675,113 @@
 						<line number="6" hits="1"/>
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-				<class name="intrabpcorr.py" filename="biobb_dna/intrabp_correlations/intrabpcorr.py" complexity="0" line-rate="0.8451" branch-rate="0">
+				<class name="intrabpcorr.py" filename="biobb_dna/intrabp_correlations/intrabpcorr.py" complexity="0" line-rate="0.8472" branch-rate="0">
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+				<class name="intraseqcorr.py" filename="biobb_dna/intrabp_correlations/intraseqcorr.py" complexity="0" line-rate="0.7188" branch-rate="0">
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+		<package name="biobb_dna.stiffness" line-rate="0.7697" branch-rate="0" complexity="0">
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@@ -2057,7 +2076,7 @@
 						<line number="4" hits="1"/>
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-				<class name="average_stiffness.py" filename="biobb_dna/stiffness/average_stiffness.py" complexity="0" line-rate="0.7333" branch-rate="0">
+				<class name="average_stiffness.py" filename="biobb_dna/stiffness/average_stiffness.py" complexity="0" line-rate="0.7391" branch-rate="0">
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+				<class name="basepair_stiffness.py" filename="biobb_dna/stiffness/basepair_stiffness.py" complexity="0" line-rate="0.7927" branch-rate="0">
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 						<line number="21" hits="1"/>
+						<line number="22" hits="1"/>
+						<line number="23" hits="1"/>
+						<line number="24" hits="0"/>
+						<line number="25" hits="1"/>
 					</lines>
 				</class>
 				<class name="test_canonical_alpha_gamma.py" filename="biobb_dna/test/unitests/test_backbone/test_canonical_alpha_gamma.py" complexity="0" line-rate="0.9375" branch-rate="0">
@@ -2623,12 +2645,27 @@
 				</class>
 			</classes>
 		</package>
-		<package name="biobb_dna.utils" line-rate="0.7105" branch-rate="0" complexity="0">
+		<package name="biobb_dna.utils" line-rate="0.6875" branch-rate="0" complexity="0">
 			<classes>
 				<class name="__init__.py" filename="biobb_dna/utils/__init__.py" complexity="0" line-rate="1" branch-rate="0">
 					<methods/>
 					<lines/>
 				</class>
+				<class name="common.py" filename="biobb_dna/utils/common.py" complexity="0" line-rate="0.6" branch-rate="0">
+					<methods/>
+					<lines>
+						<line number="1" hits="1"/>
+						<line number="5" hits="1"/>
+						<line number="16" hits="1"/>
+						<line number="17" hits="1"/>
+						<line number="19" hits="1"/>
+						<line number="21" hits="1"/>
+						<line number="24" hits="0"/>
+						<line number="25" hits="0"/>
+						<line number="28" hits="0"/>
+						<line number="30" hits="0"/>
+					</lines>
+				</class>
 				<class name="constants.py" filename="biobb_dna/utils/constants.py" complexity="0" line-rate="1" branch-rate="0">
 					<methods/>
 					<lines>
diff --git a/coverage/coveragebadge.svg b/coverage/coveragebadge.svg
index f43e5de..a3f20e5 100644
--- a/coverage/coveragebadge.svg
+++ b/coverage/coveragebadge.svg
@@ -1 +1 @@
-<svg xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" width="116" height="20" role="img" aria-label="Coverage: 78.87%"><title>Coverage: 78.87%</title><linearGradient id="s" x2="0" y2="100%"><stop offset="0" stop-color="#bbb" stop-opacity=".1"/><stop offset="1" stop-opacity=".1"/></linearGradient><clipPath id="r"><rect width="116" height="20" rx="3" fill="#fff"/></clipPath><g clip-path="url(#r)"><rect width="63" height="20" fill="#555"/><rect x="63" width="53" height="20" fill="#97ca00"/><rect width="116" height="20" fill="url(#s)"/></g><g fill="#fff" text-anchor="middle" font-family="Verdana,Geneva,DejaVu Sans,sans-serif" text-rendering="geometricPrecision" font-size="110"><text aria-hidden="true" x="325" y="150" fill="#010101" fill-opacity=".3" transform="scale(.1)" textLength="530">Coverage</text><text x="325" y="140" transform="scale(.1)" fill="#fff" textLength="530">Coverage</text><text aria-hidden="true" x="885" y="150" fill="#010101" fill-opacity=".3" transform="scale(.1)" textLength="430">78.87%</text><text x="885" y="140" transform="scale(.1)" fill="#fff" textLength="430">78.87%</text></g></svg>
\ No newline at end of file
+<svg xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" width="116" height="20" role="img" aria-label="Coverage: 78.94%"><title>Coverage: 78.94%</title><linearGradient id="s" x2="0" y2="100%"><stop offset="0" stop-color="#bbb" stop-opacity=".1"/><stop offset="1" stop-opacity=".1"/></linearGradient><clipPath id="r"><rect width="116" height="20" rx="3" fill="#fff"/></clipPath><g clip-path="url(#r)"><rect width="63" height="20" fill="#555"/><rect x="63" width="53" height="20" fill="#97ca00"/><rect width="116" height="20" fill="url(#s)"/></g><g fill="#fff" text-anchor="middle" font-family="Verdana,Geneva,DejaVu Sans,sans-serif" text-rendering="geometricPrecision" font-size="110"><text aria-hidden="true" x="325" y="150" fill="#010101" fill-opacity=".3" transform="scale(.1)" textLength="530">Coverage</text><text x="325" y="140" transform="scale(.1)" fill="#fff" textLength="530">Coverage</text><text aria-hidden="true" x="885" y="150" fill="#010101" fill-opacity=".3" transform="scale(.1)" textLength="430">78.94%</text><text x="885" y="140" transform="scale(.1)" fill="#fff" textLength="430">78.94%</text></g></svg>
\ No newline at end of file
diff --git a/coverage/function_index.html b/coverage/function_index.html
index 219919c..01d45bd 100644
--- a/coverage/function_index.html
+++ b/coverage/function_index.html
@@ -54,8 +54,8 @@ <h2>
                 <a class="button" href="class_index.html">Classes</a>
         </h2>
         <p class="text">
-            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.4">coverage.py v7.6.4</a>,
-            created at 2024-11-04 11:05 +0000
+            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
+            created at 2024-11-15 12:07 +0000
         </p>
     </div>
 </header>
@@ -89,48 +89,48 @@ <h2>
                 <td class="right" data-ratio="5 5">100%</td>
             </tr>
             <tr class="region">
-                <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 class="name left"><a href="z_159731231e5c9c9d_bipopulations_py.html#t65">biobb_dna/backbone/bipopulations.py</a></td>
+                <td class="name left"><a href="z_159731231e5c9c9d_bipopulations_py.html#t65"><data value='init__'>BIPopulations.__init__</data></a></td>
+                <td>11</td>
                 <td>0</td>
                 <td>0</td>
-                <td class="right" data-ratio="9 9">100%</td>
+                <td class="right" data-ratio="11 11">100%</td>
             </tr>
             <tr class="region">
-                <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>37</td>
+                <td class="name left"><a href="z_159731231e5c9c9d_bipopulations_py.html#t109">biobb_dna/backbone/bipopulations.py</a></td>
+                <td class="name left"><a href="z_159731231e5c9c9d_bipopulations_py.html#t109"><data value='launch'>BIPopulations.launch</data></a></td>
+                <td>38</td>
                 <td>6</td>
                 <td>0</td>
-                <td class="right" data-ratio="31 37">84%</td>
+                <td class="right" data-ratio="32 38">84%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_159731231e5c9c9d_bipopulations_py.html#t195">biobb_dna/backbone/bipopulations.py</a></td>
-                <td class="name left"><a href="z_159731231e5c9c9d_bipopulations_py.html#t195"><data value='get_xlabels'>BIPopulations.get_xlabels</data></a></td>
+                <td class="name left"><a href="z_159731231e5c9c9d_bipopulations_py.html#t188">biobb_dna/backbone/bipopulations.py</a></td>
+                <td class="name left"><a href="z_159731231e5c9c9d_bipopulations_py.html#t188"><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#t214">biobb_dna/backbone/bipopulations.py</a></td>
-                <td class="name left"><a href="z_159731231e5c9c9d_bipopulations_py.html#t214"><data value='get_angles_difference'>BIPopulations.get_angles_difference</data></a></td>
+                <td class="name left"><a href="z_159731231e5c9c9d_bipopulations_py.html#t205">biobb_dna/backbone/bipopulations.py</a></td>
+                <td class="name left"><a href="z_159731231e5c9c9d_bipopulations_py.html#t205"><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#t233">biobb_dna/backbone/bipopulations.py</a></td>
-                <td class="name left"><a href="z_159731231e5c9c9d_bipopulations_py.html#t233"><data value='bipopulations'>bipopulations</data></a></td>
+                <td class="name left"><a href="z_159731231e5c9c9d_bipopulations_py.html#t216">biobb_dna/backbone/bipopulations.py</a></td>
+                <td class="name left"><a href="z_159731231e5c9c9d_bipopulations_py.html#t216"><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#t251">biobb_dna/backbone/bipopulations.py</a></td>
-                <td class="name left"><a href="z_159731231e5c9c9d_bipopulations_py.html#t251"><data value='main'>main</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='main'>main</data></a></td>
                 <td>13</td>
                 <td>13</td>
                 <td>0</td>
@@ -139,62 +139,62 @@ <h2>
             <tr class="region">
                 <td class="name left"><a href="z_159731231e5c9c9d_bipopulations_py.html">biobb_dna/backbone/bipopulations.py</a></td>
                 <td class="name left"><a href="z_159731231e5c9c9d_bipopulations_py.html"><data value=''><span class='no-noun'>(no function)</span></data></a></td>
-                <td>20</td>
+                <td>21</td>
                 <td>1</td>
                 <td>0</td>
-                <td class="right" data-ratio="19 20">95%</td>
+                <td class="right" data-ratio="20 21">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#t66">biobb_dna/backbone/canonicalag.py</a></td>
+                <td class="name left"><a href="z_159731231e5c9c9d_canonicalag_py.html#t66"><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>39</td>
+                <td class="name left"><a href="z_159731231e5c9c9d_canonicalag_py.html#t109">biobb_dna/backbone/canonicalag.py</a></td>
+                <td class="name left"><a href="z_159731231e5c9c9d_canonicalag_py.html#t109"><data value='launch'>CanonicalAG.launch</data></a></td>
+                <td>40</td>
                 <td>6</td>
                 <td>0</td>
-                <td class="right" data-ratio="33 39">85%</td>
+                <td class="right" data-ratio="34 40">85%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_159731231e5c9c9d_canonicalag_py.html#t195">biobb_dna/backbone/canonicalag.py</a></td>
-                <td class="name left"><a href="z_159731231e5c9c9d_canonicalag_py.html#t195"><data value='get_xlabels'>CanonicalAG.get_xlabels</data></a></td>
+                <td class="name left"><a href="z_159731231e5c9c9d_canonicalag_py.html#t196">biobb_dna/backbone/canonicalag.py</a></td>
+                <td class="name left"><a href="z_159731231e5c9c9d_canonicalag_py.html#t196"><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#t214">biobb_dna/backbone/canonicalag.py</a></td>
-                <td class="name left"><a href="z_159731231e5c9c9d_canonicalag_py.html#t214"><data value='check_alpha_gamma'>CanonicalAG.check_alpha_gamma</data></a></td>
+                <td class="name left"><a href="z_159731231e5c9c9d_canonicalag_py.html#t213">biobb_dna/backbone/canonicalag.py</a></td>
+                <td class="name left"><a href="z_159731231e5c9c9d_canonicalag_py.html#t213"><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#t234">biobb_dna/backbone/canonicalag.py</a></td>
-                <td class="name left"><a href="z_159731231e5c9c9d_canonicalag_py.html#t234"><data value='fix_angles'>CanonicalAG.fix_angles</data></a></td>
+                <td class="name left"><a href="z_159731231e5c9c9d_canonicalag_py.html#t224">biobb_dna/backbone/canonicalag.py</a></td>
+                <td class="name left"><a href="z_159731231e5c9c9d_canonicalag_py.html#t224"><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#t241">biobb_dna/backbone/canonicalag.py</a></td>
-                <td class="name left"><a href="z_159731231e5c9c9d_canonicalag_py.html#t241"><data value='canonicalag'>canonicalag</data></a></td>
+                <td class="name left"><a href="z_159731231e5c9c9d_canonicalag_py.html#t231">biobb_dna/backbone/canonicalag.py</a></td>
+                <td class="name left"><a href="z_159731231e5c9c9d_canonicalag_py.html#t231"><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#t259">biobb_dna/backbone/canonicalag.py</a></td>
-                <td class="name left"><a href="z_159731231e5c9c9d_canonicalag_py.html#t259"><data value='main'>main</data></a></td>
+                <td class="name left"><a href="z_159731231e5c9c9d_canonicalag_py.html#t256">biobb_dna/backbone/canonicalag.py</a></td>
+                <td class="name left"><a href="z_159731231e5c9c9d_canonicalag_py.html#t256"><data value='main'>main</data></a></td>
                 <td>13</td>
                 <td>13</td>
                 <td>0</td>
@@ -203,62 +203,62 @@ <h2>
             <tr class="region">
                 <td class="name left"><a href="z_159731231e5c9c9d_canonicalag_py.html">biobb_dna/backbone/canonicalag.py</a></td>
                 <td class="name left"><a href="z_159731231e5c9c9d_canonicalag_py.html"><data value=''><span class='no-noun'>(no function)</span></data></a></td>
-                <td>21</td>
+                <td>22</td>
                 <td>1</td>
                 <td>0</td>
-                <td class="right" data-ratio="20 21">95%</td>
+                <td class="right" data-ratio="21 22">95%</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#t62">biobb_dna/backbone/puckering.py</a></td>
+                <td class="name left"><a href="z_159731231e5c9c9d_puckering_py.html#t62"><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>37</td>
+                <td class="name left"><a href="z_159731231e5c9c9d_puckering_py.html#t101">biobb_dna/backbone/puckering.py</a></td>
+                <td class="name left"><a href="z_159731231e5c9c9d_puckering_py.html#t101"><data value='launch'>Puckering.launch</data></a></td>
+                <td>38</td>
                 <td>6</td>
                 <td>0</td>
-                <td class="right" data-ratio="31 37">84%</td>
+                <td class="right" data-ratio="32 38">84%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_159731231e5c9c9d_puckering_py.html#t195">biobb_dna/backbone/puckering.py</a></td>
-                <td class="name left"><a href="z_159731231e5c9c9d_puckering_py.html#t195"><data value='get_xlabels'>Puckering.get_xlabels</data></a></td>
+                <td class="name left"><a href="z_159731231e5c9c9d_puckering_py.html#t181">biobb_dna/backbone/puckering.py</a></td>
+                <td class="name left"><a href="z_159731231e5c9c9d_puckering_py.html#t181"><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#t214">biobb_dna/backbone/puckering.py</a></td>
-                <td class="name left"><a href="z_159731231e5c9c9d_puckering_py.html#t214"><data value='check_puckering'>Puckering.check_puckering</data></a></td>
+                <td class="name left"><a href="z_159731231e5c9c9d_puckering_py.html#t198">biobb_dna/backbone/puckering.py</a></td>
+                <td class="name left"><a href="z_159731231e5c9c9d_puckering_py.html#t198"><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#t229">biobb_dna/backbone/puckering.py</a></td>
-                <td class="name left"><a href="z_159731231e5c9c9d_puckering_py.html#t229"><data value='fix_angles'>Puckering.fix_angles</data></a></td>
+                <td class="name left"><a href="z_159731231e5c9c9d_puckering_py.html#t209">biobb_dna/backbone/puckering.py</a></td>
+                <td class="name left"><a href="z_159731231e5c9c9d_puckering_py.html#t209"><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#t236">biobb_dna/backbone/puckering.py</a></td>
-                <td class="name left"><a href="z_159731231e5c9c9d_puckering_py.html#t236"><data value='puckering'>puckering</data></a></td>
+                <td class="name left"><a href="z_159731231e5c9c9d_puckering_py.html#t216">biobb_dna/backbone/puckering.py</a></td>
+                <td class="name left"><a href="z_159731231e5c9c9d_puckering_py.html#t216"><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#t251">biobb_dna/backbone/puckering.py</a></td>
-                <td class="name left"><a href="z_159731231e5c9c9d_puckering_py.html#t251"><data value='main'>main</data></a></td>
+                <td class="name left"><a href="z_159731231e5c9c9d_puckering_py.html#t237">biobb_dna/backbone/puckering.py</a></td>
+                <td class="name left"><a href="z_159731231e5c9c9d_puckering_py.html#t237"><data value='main'>main</data></a></td>
                 <td>11</td>
                 <td>11</td>
                 <td>0</td>
@@ -267,10 +267,10 @@ <h2>
             <tr class="region">
                 <td class="name left"><a href="z_159731231e5c9c9d_puckering_py.html">biobb_dna/backbone/puckering.py</a></td>
                 <td class="name left"><a href="z_159731231e5c9c9d_puckering_py.html"><data value=''><span class='no-noun'>(no function)</span></data></a></td>
-                <td>21</td>
+                <td>22</td>
                 <td>1</td>
                 <td>0</td>
-                <td class="right" data-ratio="20 21">95%</td>
+                <td class="right" data-ratio="21 22">95%</td>
             </tr>
             <tr class="region">
                 <td class="name left"><a href="z_74fa14c6d0e940a4___init___py.html">biobb_dna/curvesplus/__init__.py</a></td>
@@ -457,32 +457,32 @@ <h2>
                 <td class="right" data-ratio="6 6">100%</td>
             </tr>
             <tr class="region">
-                <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 class="name left"><a href="z_3afbcd666ed82c91_dna_averages_py.html#t64">biobb_dna/dna/dna_averages.py</a></td>
+                <td class="name left"><a href="z_3afbcd666ed82c91_dna_averages_py.html#t64"><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#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>53</td>
-                <td>14</td>
+                <td class="name left"><a href="z_3afbcd666ed82c91_dna_averages_py.html#t103">biobb_dna/dna/dna_averages.py</a></td>
+                <td class="name left"><a href="z_3afbcd666ed82c91_dna_averages_py.html#t103"><data value='launch'>HelParAverages.launch</data></a></td>
+                <td>54</td>
+                <td>15</td>
                 <td>0</td>
-                <td class="right" data-ratio="39 53">74%</td>
+                <td class="right" data-ratio="39 54">72%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_3afbcd666ed82c91_dna_averages_py.html#t218">biobb_dna/dna/dna_averages.py</a></td>
-                <td class="name left"><a href="z_3afbcd666ed82c91_dna_averages_py.html#t218"><data value='dna_averages'>dna_averages</data></a></td>
+                <td class="name left"><a href="z_3afbcd666ed82c91_dna_averages_py.html#t223">biobb_dna/dna/dna_averages.py</a></td>
+                <td class="name left"><a href="z_3afbcd666ed82c91_dna_averages_py.html#t223"><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#t230">biobb_dna/dna/dna_averages.py</a></td>
-                <td class="name left"><a href="z_3afbcd666ed82c91_dna_averages_py.html#t230"><data value='main'>main</data></a></td>
+                <td class="name left"><a href="z_3afbcd666ed82c91_dna_averages_py.html#t242">biobb_dna/dna/dna_averages.py</a></td>
+                <td class="name left"><a href="z_3afbcd666ed82c91_dna_averages_py.html#t242"><data value='main'>main</data></a></td>
                 <td>10</td>
                 <td>10</td>
                 <td>0</td>
@@ -491,10 +491,10 @@ <h2>
             <tr class="region">
                 <td class="name left"><a href="z_3afbcd666ed82c91_dna_averages_py.html">biobb_dna/dna/dna_averages.py</a></td>
                 <td class="name left"><a href="z_3afbcd666ed82c91_dna_averages_py.html"><data value=''><span class='no-noun'>(no function)</span></data></a></td>
-                <td>18</td>
+                <td>19</td>
                 <td>1</td>
                 <td>0</td>
-                <td class="right" data-ratio="17 18">94%</td>
+                <td class="right" data-ratio="18 19">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>
@@ -561,32 +561,32 @@ <h2>
                 <td class="right" data-ratio="24 25">96%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_3afbcd666ed82c91_dna_timeseries_py.html#t63">biobb_dna/dna/dna_timeseries.py</a></td>
-                <td class="name left"><a href="z_3afbcd666ed82c91_dna_timeseries_py.html#t63"><data value='init__'>HelParTimeSeries.__init__</data></a></td>
+                <td class="name left"><a href="z_3afbcd666ed82c91_dna_timeseries_py.html#t66">biobb_dna/dna/dna_timeseries.py</a></td>
+                <td class="name left"><a href="z_3afbcd666ed82c91_dna_timeseries_py.html#t66"><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#t122">biobb_dna/dna/dna_timeseries.py</a></td>
-                <td class="name left"><a href="z_3afbcd666ed82c91_dna_timeseries_py.html#t122"><data value='launch'>HelParTimeSeries.launch</data></a></td>
+                <td class="name left"><a href="z_3afbcd666ed82c91_dna_timeseries_py.html#t125">biobb_dna/dna/dna_timeseries.py</a></td>
+                <td class="name left"><a href="z_3afbcd666ed82c91_dna_timeseries_py.html#t125"><data value='launch'>HelParTimeSeries.launch</data></a></td>
                 <td>73</td>
                 <td>16</td>
                 <td>0</td>
                 <td class="right" data-ratio="57 73">78%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_3afbcd666ed82c91_dna_timeseries_py.html#t276">biobb_dna/dna/dna_timeseries.py</a></td>
-                <td class="name left"><a href="z_3afbcd666ed82c91_dna_timeseries_py.html#t276"><data value='dna_timeseries'>dna_timeseries</data></a></td>
+                <td class="name left"><a href="z_3afbcd666ed82c91_dna_timeseries_py.html#t288">biobb_dna/dna/dna_timeseries.py</a></td>
+                <td class="name left"><a href="z_3afbcd666ed82c91_dna_timeseries_py.html#t288"><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#t288">biobb_dna/dna/dna_timeseries.py</a></td>
-                <td class="name left"><a href="z_3afbcd666ed82c91_dna_timeseries_py.html#t288"><data value='main'>main</data></a></td>
+                <td class="name left"><a href="z_3afbcd666ed82c91_dna_timeseries_py.html#t305">biobb_dna/dna/dna_timeseries.py</a></td>
+                <td class="name left"><a href="z_3afbcd666ed82c91_dna_timeseries_py.html#t305"><data value='main'>main</data></a></td>
                 <td>9</td>
                 <td>9</td>
                 <td>0</td>
@@ -595,10 +595,10 @@ <h2>
             <tr class="region">
                 <td class="name left"><a href="z_3afbcd666ed82c91_dna_timeseries_py.html">biobb_dna/dna/dna_timeseries.py</a></td>
                 <td class="name left"><a href="z_3afbcd666ed82c91_dna_timeseries_py.html"><data value=''><span class='no-noun'>(no function)</span></data></a></td>
-                <td>21</td>
+                <td>22</td>
                 <td>1</td>
                 <td>0</td>
-                <td class="right" data-ratio="20 21">95%</td>
+                <td class="right" data-ratio="21 22">95%</td>
             </tr>
             <tr class="region">
                 <td class="name left"><a href="z_3afbcd666ed82c91_dna_timeseries_unzip_py.html#t60">biobb_dna/dna/dna_timeseries_unzip.py</a></td>
@@ -649,48 +649,48 @@ <h2>
                 <td class="right" data-ratio="5 5">100%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_8a2a7f872cf1434f_interbpcorr_py.html#t67">biobb_dna/interbp_correlations/interbpcorr.py</a></td>
-                <td class="name left"><a href="z_8a2a7f872cf1434f_interbpcorr_py.html#t67"><data value='init__'>InterBasePairCorrelation.__init__</data></a></td>
+                <td class="name left"><a href="z_8a2a7f872cf1434f_interbpcorr_py.html#t69">biobb_dna/interbp_correlations/interbpcorr.py</a></td>
+                <td class="name left"><a href="z_8a2a7f872cf1434f_interbpcorr_py.html#t69"><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#t104">biobb_dna/interbp_correlations/interbpcorr.py</a></td>
-                <td class="name left"><a href="z_8a2a7f872cf1434f_interbpcorr_py.html#t104"><data value='launch'>InterBasePairCorrelation.launch</data></a></td>
-                <td>76</td>
+                <td class="name left"><a href="z_8a2a7f872cf1434f_interbpcorr_py.html#t115">biobb_dna/interbp_correlations/interbpcorr.py</a></td>
+                <td class="name left"><a href="z_8a2a7f872cf1434f_interbpcorr_py.html#t115"><data value='launch'>InterBasePairCorrelation.launch</data></a></td>
+                <td>77</td>
                 <td>6</td>
                 <td>0</td>
-                <td class="right" data-ratio="70 76">92%</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#t259">biobb_dna/interbp_correlations/interbpcorr.py</a></td>
+                <td class="name left"><a href="z_8a2a7f872cf1434f_interbpcorr_py.html#t259"><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#t269">biobb_dna/interbp_correlations/interbpcorr.py</a></td>
+                <td class="name left"><a href="z_8a2a7f872cf1434f_interbpcorr_py.html#t269"><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#t282">biobb_dna/interbp_correlations/interbpcorr.py</a></td>
+                <td class="name left"><a href="z_8a2a7f872cf1434f_interbpcorr_py.html#t282"><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#t311">biobb_dna/interbp_correlations/interbpcorr.py</a></td>
+                <td class="name left"><a href="z_8a2a7f872cf1434f_interbpcorr_py.html#t311"><data value='main'>main</data></a></td>
                 <td>15</td>
                 <td>15</td>
                 <td>0</td>
@@ -699,10 +699,10 @@ <h2>
             <tr class="region">
                 <td class="name left"><a href="z_8a2a7f872cf1434f_interbpcorr_py.html">biobb_dna/interbp_correlations/interbpcorr.py</a></td>
                 <td class="name left"><a href="z_8a2a7f872cf1434f_interbpcorr_py.html"><data value=''><span class='no-noun'>(no function)</span></data></a></td>
-                <td>24</td>
+                <td>25</td>
                 <td>1</td>
                 <td>0</td>
-                <td class="right" data-ratio="23 24">96%</td>
+                <td class="right" data-ratio="24 25">96%</td>
             </tr>
             <tr class="region">
                 <td class="name left"><a href="z_8a2a7f872cf1434f_interhpcorr_py.html#t66">biobb_dna/interbp_correlations/interhpcorr.py</a></td>
@@ -769,40 +769,40 @@ <h2>
                 <td class="right" data-ratio="21 22">95%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_8a2a7f872cf1434f_interseqcorr_py.html#t60">biobb_dna/interbp_correlations/interseqcorr.py</a></td>
-                <td class="name left"><a href="z_8a2a7f872cf1434f_interseqcorr_py.html#t60"><data value='init__'>InterSequenceCorrelation.__init__</data></a></td>
+                <td class="name left"><a href="z_8a2a7f872cf1434f_interseqcorr_py.html#t62">biobb_dna/interbp_correlations/interseqcorr.py</a></td>
+                <td class="name left"><a href="z_8a2a7f872cf1434f_interseqcorr_py.html#t62"><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#t90">biobb_dna/interbp_correlations/interseqcorr.py</a></td>
-                <td class="name left"><a href="z_8a2a7f872cf1434f_interseqcorr_py.html#t90"><data value='launch'>InterSequenceCorrelation.launch</data></a></td>
-                <td>46</td>
+                <td class="name left"><a href="z_8a2a7f872cf1434f_interseqcorr_py.html#t97">biobb_dna/interbp_correlations/interseqcorr.py</a></td>
+                <td class="name left"><a href="z_8a2a7f872cf1434f_interseqcorr_py.html#t97"><data value='launch'>InterSequenceCorrelation.launch</data></a></td>
+                <td>47</td>
                 <td>9</td>
                 <td>0</td>
-                <td class="right" data-ratio="37 46">80%</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#t198">biobb_dna/interbp_correlations/interseqcorr.py</a></td>
+                <td class="name left"><a href="z_8a2a7f872cf1434f_interseqcorr_py.html#t198"><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#t208">biobb_dna/interbp_correlations/interseqcorr.py</a></td>
+                <td class="name left"><a href="z_8a2a7f872cf1434f_interseqcorr_py.html#t208"><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#t227">biobb_dna/interbp_correlations/interseqcorr.py</a></td>
+                <td class="name left"><a href="z_8a2a7f872cf1434f_interseqcorr_py.html#t227"><data value='main'>main</data></a></td>
                 <td>10</td>
                 <td>10</td>
                 <td>0</td>
@@ -811,10 +811,10 @@ <h2>
             <tr class="region">
                 <td class="name left"><a href="z_8a2a7f872cf1434f_interseqcorr_py.html">biobb_dna/interbp_correlations/interseqcorr.py</a></td>
                 <td class="name left"><a href="z_8a2a7f872cf1434f_interseqcorr_py.html"><data value=''><span class='no-noun'>(no function)</span></data></a></td>
-                <td>20</td>
+                <td>21</td>
                 <td>1</td>
                 <td>0</td>
-                <td class="right" data-ratio="19 20">95%</td>
+                <td class="right" data-ratio="20 21">95%</td>
             </tr>
             <tr class="region">
                 <td class="name left"><a href="z_64e03be4370b7ecc___init___py.html">biobb_dna/intrabp_correlations/__init__.py</a></td>
@@ -825,48 +825,48 @@ <h2>
                 <td class="right" data-ratio="5 5">100%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_64e03be4370b7ecc_intrabpcorr_py.html#t67">biobb_dna/intrabp_correlations/intrabpcorr.py</a></td>
-                <td class="name left"><a href="z_64e03be4370b7ecc_intrabpcorr_py.html#t67"><data value='init__'>IntraBasePairCorrelation.__init__</data></a></td>
+                <td class="name left"><a href="z_64e03be4370b7ecc_intrabpcorr_py.html#t69">biobb_dna/intrabp_correlations/intrabpcorr.py</a></td>
+                <td class="name left"><a href="z_64e03be4370b7ecc_intrabpcorr_py.html#t69"><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#t104">biobb_dna/intrabp_correlations/intrabpcorr.py</a></td>
-                <td class="name left"><a href="z_64e03be4370b7ecc_intrabpcorr_py.html#t104"><data value='launch'>IntraBasePairCorrelation.launch</data></a></td>
-                <td>76</td>
+                <td class="name left"><a href="z_64e03be4370b7ecc_intrabpcorr_py.html#t115">biobb_dna/intrabp_correlations/intrabpcorr.py</a></td>
+                <td class="name left"><a href="z_64e03be4370b7ecc_intrabpcorr_py.html#t115"><data value='launch'>IntraBasePairCorrelation.launch</data></a></td>
+                <td>77</td>
                 <td>6</td>
                 <td>0</td>
-                <td class="right" data-ratio="70 76">92%</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#t255">biobb_dna/intrabp_correlations/intrabpcorr.py</a></td>
+                <td class="name left"><a href="z_64e03be4370b7ecc_intrabpcorr_py.html#t255"><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#t265">biobb_dna/intrabp_correlations/intrabpcorr.py</a></td>
+                <td class="name left"><a href="z_64e03be4370b7ecc_intrabpcorr_py.html#t265"><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#t278">biobb_dna/intrabp_correlations/intrabpcorr.py</a></td>
+                <td class="name left"><a href="z_64e03be4370b7ecc_intrabpcorr_py.html#t278"><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#t307">biobb_dna/intrabp_correlations/intrabpcorr.py</a></td>
+                <td class="name left"><a href="z_64e03be4370b7ecc_intrabpcorr_py.html#t307"><data value='main'>main</data></a></td>
                 <td>15</td>
                 <td>15</td>
                 <td>0</td>
@@ -875,10 +875,10 @@ <h2>
             <tr class="region">
                 <td class="name left"><a href="z_64e03be4370b7ecc_intrabpcorr_py.html">biobb_dna/intrabp_correlations/intrabpcorr.py</a></td>
                 <td class="name left"><a href="z_64e03be4370b7ecc_intrabpcorr_py.html"><data value=''><span class='no-noun'>(no function)</span></data></a></td>
-                <td>24</td>
+                <td>25</td>
                 <td>1</td>
                 <td>0</td>
-                <td class="right" data-ratio="23 24">96%</td>
+                <td class="right" data-ratio="24 25">96%</td>
             </tr>
             <tr class="region">
                 <td class="name left"><a href="z_64e03be4370b7ecc_intrahpcorr_py.html#t66">biobb_dna/intrabp_correlations/intrahpcorr.py</a></td>
@@ -945,40 +945,40 @@ <h2>
                 <td class="right" data-ratio="21 22">95%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_64e03be4370b7ecc_intraseqcorr_py.html#t56">biobb_dna/intrabp_correlations/intraseqcorr.py</a></td>
-                <td class="name left"><a href="z_64e03be4370b7ecc_intraseqcorr_py.html#t56"><data value='init__'>IntraSequenceCorrelation.__init__</data></a></td>
+                <td class="name left"><a href="z_64e03be4370b7ecc_intraseqcorr_py.html#t58">biobb_dna/intrabp_correlations/intraseqcorr.py</a></td>
+                <td class="name left"><a href="z_64e03be4370b7ecc_intraseqcorr_py.html#t58"><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#t86">biobb_dna/intrabp_correlations/intraseqcorr.py</a></td>
-                <td class="name left"><a href="z_64e03be4370b7ecc_intraseqcorr_py.html#t86"><data value='launch'>IntraSequenceCorrelation.launch</data></a></td>
-                <td>46</td>
+                <td class="name left"><a href="z_64e03be4370b7ecc_intraseqcorr_py.html#t93">biobb_dna/intrabp_correlations/intraseqcorr.py</a></td>
+                <td class="name left"><a href="z_64e03be4370b7ecc_intraseqcorr_py.html#t93"><data value='launch'>IntraSequenceCorrelation.launch</data></a></td>
+                <td>47</td>
                 <td>9</td>
                 <td>0</td>
-                <td class="right" data-ratio="37 46">80%</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#t194">biobb_dna/intrabp_correlations/intraseqcorr.py</a></td>
+                <td class="name left"><a href="z_64e03be4370b7ecc_intraseqcorr_py.html#t194"><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#t204">biobb_dna/intrabp_correlations/intraseqcorr.py</a></td>
+                <td class="name left"><a href="z_64e03be4370b7ecc_intraseqcorr_py.html#t204"><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#t223">biobb_dna/intrabp_correlations/intraseqcorr.py</a></td>
+                <td class="name left"><a href="z_64e03be4370b7ecc_intraseqcorr_py.html#t223"><data value='main'>main</data></a></td>
                 <td>10</td>
                 <td>10</td>
                 <td>0</td>
@@ -987,10 +987,10 @@ <h2>
             <tr class="region">
                 <td class="name left"><a href="z_64e03be4370b7ecc_intraseqcorr_py.html">biobb_dna/intrabp_correlations/intraseqcorr.py</a></td>
                 <td class="name left"><a href="z_64e03be4370b7ecc_intraseqcorr_py.html"><data value=''><span class='no-noun'>(no function)</span></data></a></td>
-                <td>20</td>
+                <td>21</td>
                 <td>1</td>
                 <td>0</td>
-                <td class="right" data-ratio="19 20">95%</td>
+                <td class="right" data-ratio="20 21">95%</td>
             </tr>
             <tr class="region">
                 <td class="name left"><a href="z_9de9475b0a6fab52___init___py.html">biobb_dna/stiffness/__init__.py</a></td>
@@ -1001,32 +1001,32 @@ <h2>
                 <td class="right" data-ratio="4 4">100%</td>
             </tr>
             <tr class="region">
-                <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 class="name left"><a href="z_9de9475b0a6fab52_average_stiffness_py.html#t63">biobb_dna/stiffness/average_stiffness.py</a></td>
+                <td class="name left"><a href="z_9de9475b0a6fab52_average_stiffness_py.html#t63"><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#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>49</td>
+                <td class="name left"><a href="z_9de9475b0a6fab52_average_stiffness_py.html#t101">biobb_dna/stiffness/average_stiffness.py</a></td>
+                <td class="name left"><a href="z_9de9475b0a6fab52_average_stiffness_py.html#t101"><data value='launch'>AverageStiffness.launch</data></a></td>
+                <td>50</td>
                 <td>13</td>
                 <td>0</td>
-                <td class="right" data-ratio="36 49">73%</td>
+                <td class="right" data-ratio="37 50">74%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_9de9475b0a6fab52_average_stiffness_py.html#t199">biobb_dna/stiffness/average_stiffness.py</a></td>
-                <td class="name left"><a href="z_9de9475b0a6fab52_average_stiffness_py.html#t199"><data value='average_stiffness'>average_stiffness</data></a></td>
+                <td class="name left"><a href="z_9de9475b0a6fab52_average_stiffness_py.html#t202">biobb_dna/stiffness/average_stiffness.py</a></td>
+                <td class="name left"><a href="z_9de9475b0a6fab52_average_stiffness_py.html#t202"><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#t212">biobb_dna/stiffness/average_stiffness.py</a></td>
-                <td class="name left"><a href="z_9de9475b0a6fab52_average_stiffness_py.html#t212"><data value='main'>main</data></a></td>
+                <td class="name left"><a href="z_9de9475b0a6fab52_average_stiffness_py.html#t221">biobb_dna/stiffness/average_stiffness.py</a></td>
+                <td class="name left"><a href="z_9de9475b0a6fab52_average_stiffness_py.html#t221"><data value='main'>main</data></a></td>
                 <td>10</td>
                 <td>10</td>
                 <td>0</td>
@@ -1035,38 +1035,38 @@ <h2>
             <tr class="region">
                 <td class="name left"><a href="z_9de9475b0a6fab52_average_stiffness_py.html">biobb_dna/stiffness/average_stiffness.py</a></td>
                 <td class="name left"><a href="z_9de9475b0a6fab52_average_stiffness_py.html"><data value=''><span class='no-noun'>(no function)</span></data></a></td>
-                <td>19</td>
+                <td>20</td>
                 <td>1</td>
                 <td>0</td>
-                <td class="right" data-ratio="18 19">95%</td>
+                <td class="right" data-ratio="19 20">95%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_9de9475b0a6fab52_basepair_stiffness_py.html#t69">biobb_dna/stiffness/basepair_stiffness.py</a></td>
-                <td class="name left"><a href="z_9de9475b0a6fab52_basepair_stiffness_py.html#t69"><data value='init__'>BPStiffness.__init__</data></a></td>
+                <td class="name left"><a href="z_9de9475b0a6fab52_basepair_stiffness_py.html#t71">biobb_dna/stiffness/basepair_stiffness.py</a></td>
+                <td class="name left"><a href="z_9de9475b0a6fab52_basepair_stiffness_py.html#t71"><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#t106">biobb_dna/stiffness/basepair_stiffness.py</a></td>
-                <td class="name left"><a href="z_9de9475b0a6fab52_basepair_stiffness_py.html#t106"><data value='launch'>BPStiffness.launch</data></a></td>
+                <td class="name left"><a href="z_9de9475b0a6fab52_basepair_stiffness_py.html#t120">biobb_dna/stiffness/basepair_stiffness.py</a></td>
+                <td class="name left"><a href="z_9de9475b0a6fab52_basepair_stiffness_py.html#t120"><data value='launch'>BPStiffness.launch</data></a></td>
                 <td>38</td>
                 <td>1</td>
                 <td>0</td>
                 <td class="right" data-ratio="37 38">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#t195">biobb_dna/stiffness/basepair_stiffness.py</a></td>
+                <td class="name left"><a href="z_9de9475b0a6fab52_basepair_stiffness_py.html#t195"><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>
             </tr>
             <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#t224">biobb_dna/stiffness/basepair_stiffness.py</a></td>
+                <td class="name left"><a href="z_9de9475b0a6fab52_basepair_stiffness_py.html#t224"><data value='main'>main</data></a></td>
                 <td>15</td>
                 <td>15</td>
                 <td>0</td>
@@ -1075,10 +1075,10 @@ <h2>
             <tr class="region">
                 <td class="name left"><a href="z_9de9475b0a6fab52_basepair_stiffness_py.html">biobb_dna/stiffness/basepair_stiffness.py</a></td>
                 <td class="name left"><a href="z_9de9475b0a6fab52_basepair_stiffness_py.html"><data value=''><span class='no-noun'>(no function)</span></data></a></td>
-                <td>18</td>
+                <td>19</td>
                 <td>1</td>
                 <td>0</td>
-                <td class="right" data-ratio="17 18">94%</td>
+                <td class="right" data-ratio="18 19">95%</td>
             </tr>
             <tr class="region">
                 <td class="name left"><a href="z_957b841f7413f0a1___init___py.html">biobb_dna/test/__init__.py</a></td>
@@ -1089,24 +1089,24 @@ <h2>
                 <td class="right" data-ratio="0 0">100%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_020f76a90aa51c7b_test_bipopulations_py.html#t8">biobb_dna/test/unitests/test_backbone/test_bipopulations.py</a></td>
-                <td class="name left"><a href="z_020f76a90aa51c7b_test_bipopulations_py.html#t8"><data value='setup_class'>TestBIPopulations.setup_class</data></a></td>
+                <td class="name left"><a href="z_020f76a90aa51c7b_test_bipopulations_py.html#t10">biobb_dna/test/unitests/test_backbone/test_bipopulations.py</a></td>
+                <td class="name left"><a href="z_020f76a90aa51c7b_test_bipopulations_py.html#t10"><data value='setup_class'>TestBIPopulations.setup_class</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_020f76a90aa51c7b_test_bipopulations_py.html#t11">biobb_dna/test/unitests/test_backbone/test_bipopulations.py</a></td>
-                <td class="name left"><a href="z_020f76a90aa51c7b_test_bipopulations_py.html#t11"><data value='teardown_class'>TestBIPopulations.teardown_class</data></a></td>
+                <td class="name left"><a href="z_020f76a90aa51c7b_test_bipopulations_py.html#t13">biobb_dna/test/unitests/test_backbone/test_bipopulations.py</a></td>
+                <td class="name left"><a href="z_020f76a90aa51c7b_test_bipopulations_py.html#t13"><data value='teardown_class'>TestBIPopulations.teardown_class</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_020f76a90aa51c7b_test_bipopulations_py.html#t14">biobb_dna/test/unitests/test_backbone/test_bipopulations.py</a></td>
-                <td class="name left"><a href="z_020f76a90aa51c7b_test_bipopulations_py.html#t14"><data value='test_bipopulations'>TestBIPopulations.test_bipopulations</data></a></td>
+                <td class="name left"><a href="z_020f76a90aa51c7b_test_bipopulations_py.html#t18">biobb_dna/test/unitests/test_backbone/test_bipopulations.py</a></td>
+                <td class="name left"><a href="z_020f76a90aa51c7b_test_bipopulations_py.html#t18"><data value='test_bipopulations'>TestBIPopulations.test_bipopulations</data></a></td>
                 <td>7</td>
                 <td>1</td>
                 <td>0</td>
@@ -1648,6 +1648,22 @@ <h2>
                 <td>0</td>
                 <td class="right" data-ratio="0 0">100%</td>
             </tr>
+            <tr class="region">
+                <td class="name left"><a href="z_833b0317e3c43dca_common_py.html#t5">biobb_dna/utils/common.py</a></td>
+                <td class="name left"><a href="z_833b0317e3c43dca_common_py.html#t5"><data value='from_string_to_list'>_from_string_to_list</data></a></td>
+                <td>8</td>
+                <td>4</td>
+                <td>0</td>
+                <td class="right" data-ratio="4 8">50%</td>
+            </tr>
+            <tr class="region">
+                <td class="name left"><a href="z_833b0317e3c43dca_common_py.html">biobb_dna/utils/common.py</a></td>
+                <td class="name left"><a href="z_833b0317e3c43dca_common_py.html"><data value=''><span class='no-noun'>(no function)</span></data></a></td>
+                <td>2</td>
+                <td>0</td>
+                <td>0</td>
+                <td class="right" data-ratio="2 2">100%</td>
+            </tr>
             <tr class="region">
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             <tr class="region">
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-                <td>98</td>
+                <td>102</td>
                 <td>22</td>
                 <td>0</td>
-                <td class="right" data-ratio="76 98">78%</td>
+                <td class="right" data-ratio="80 102">78%</td>
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                 <td>0</td>
-                <td class="right" data-ratio="86 108">80%</td>
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-                <td>103</td>
+                <td>105</td>
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-                <td class="right" data-ratio="83 103">81%</td>
+                <td class="right" data-ratio="85 105">81%</td>
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-                <td>93</td>
-                <td>25</td>
+                <td>95</td>
+                <td>26</td>
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-                <td class="right" data-ratio="68 93">73%</td>
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-                <td class="right" data-ratio="99 130">76%</td>
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+                <td>4</td>
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diff --git a/coverage/z_020f76a90aa51c7b_test_bipopulations_py.html b/coverage/z_020f76a90aa51c7b_test_bipopulations_py.html
index 892aed2..a8be451 100644
--- a/coverage/z_020f76a90aa51c7b_test_bipopulations_py.html
+++ b/coverage/z_020f76a90aa51c7b_test_bipopulations_py.html
@@ -64,8 +64,8 @@ <h2>
             <a id="indexLink" class="nav" href="index.html">&Hat; index</a> &nbsp; &nbsp;
             <a id="nextFileLink" class="nav" href="z_020f76a90aa51c7b_test_canonical_alpha_gamma_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
-            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.4">coverage.py v7.6.4</a>,
-            created at 2024-11-04 11:05 +0000
+            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
+            created at 2024-11-15 12:07 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -81,26 +81,30 @@ <h2>
 </header>
 <main id="source">
     <p class="pln"><span class="n"><a id="t1" href="#t1">1</a></span><span class="t"><span class="com"># type: ignore</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t2" href="#t2">2</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_common</span><span class="op">.</span><span class="nam">tools</span> <span class="key">import</span> <span class="nam">test_fixtures</span> <span class="key">as</span> <span class="nam">fx</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t3" href="#t3">3</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_dna</span><span class="op">.</span><span class="nam">backbone</span><span class="op">.</span><span class="nam">bipopulations</span> <span class="key">import</span> <span class="nam">bipopulations</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t4" href="#t4">4</a></span><span class="t"><span class="key">import</span> <span class="nam">platform</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t2" href="#t2">2</a></span><span class="t"><span class="key">import</span> <span class="nam">platform</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t3" href="#t3">3</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t4" href="#t4">4</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_common</span><span class="op">.</span><span class="nam">tools</span> <span class="key">import</span> <span class="nam">test_fixtures</span> <span class="key">as</span> <span class="nam">fx</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t5" href="#t5">5</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t6" href="#t6">6</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t7" href="#t7">7</a></span><span class="t"><span class="key">class</span> <span class="nam">TestBIPopulations</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="t8" href="#t8">8</a></span><span class="t">    <span class="key">def</span> <span class="nam">setup_class</span><span class="op">(</span><span class="nam">self</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t9" href="#t9">9</a></span><span class="t">        <span class="nam">fx</span><span class="op">.</span><span class="nam">test_setup</span><span class="op">(</span><span class="nam">self</span><span class="op">,</span> <span class="str">'bipopulations'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t10" href="#t10">10</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t11" href="#t11">11</a></span><span class="t">    <span class="key">def</span> <span class="nam">teardown_class</span><span class="op">(</span><span class="nam">self</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t12" href="#t12">12</a></span><span class="t">        <span class="nam">fx</span><span class="op">.</span><span class="nam">test_teardown</span><span class="op">(</span><span class="nam">self</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t13" href="#t13">13</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t14" href="#t14">14</a></span><span class="t">    <span class="key">def</span> <span class="nam">test_bipopulations</span><span class="op">(</span><span class="nam">self</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t15" href="#t15">15</a></span><span class="t">        <span class="nam">returncode</span> <span class="op">=</span> <span class="nam">bipopulations</span><span class="op">(</span><span class="nam">properties</span><span class="op">=</span><span class="nam">self</span><span class="op">.</span><span class="nam">properties</span><span class="op">,</span> <span class="op">**</span><span class="nam">self</span><span class="op">.</span><span class="nam">paths</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t16" href="#t16">16</a></span><span class="t">        <span class="key">assert</span> <span class="nam">fx</span><span class="op">.</span><span class="nam">not_empty</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">paths</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="run"><span class="n"><a id="t17" href="#t17">17</a></span><span class="t">        <span class="key">assert</span> <span class="nam">fx</span><span class="op">.</span><span class="nam">not_empty</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">paths</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="run"><span class="n"><a id="t18" href="#t18">18</a></span><span class="t">        <span class="key">assert</span> <span class="nam">fx</span><span class="op">.</span><span class="nam">exe_success</span><span class="op">(</span><span class="nam">returncode</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t19" href="#t19">19</a></span><span class="t">        <span class="key">if</span> <span class="nam">platform</span><span class="op">.</span><span class="nam">system</span><span class="op">(</span><span class="op">)</span> <span class="op">==</span> <span class="str">'Darwin'</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t20" href="#t20">20</a></span><span class="t">            <span class="key">assert</span> <span class="nam">fx</span><span class="op">.</span><span class="nam">equal</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">paths</span><span class="op">[</span><span class="str">'output_csv_path'</span><span class="op">]</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">paths</span><span class="op">[</span><span class="str">'ref_csv_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="t21" href="#t21">21</a></span><span class="t">        <span class="key">assert</span> <span class="nam">fx</span><span class="op">.</span><span class="nam">equal</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">paths</span><span class="op">[</span><span class="str">'output_jpg_path'</span><span class="op">]</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">paths</span><span class="op">[</span><span class="str">'ref_jpg_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="t6" href="#t6">6</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_dna</span><span class="op">.</span><span class="nam">backbone</span><span class="op">.</span><span class="nam">bipopulations</span> <span class="key">import</span> <span class="nam">bipopulations</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t7" href="#t7">7</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t8" href="#t8">8</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t9" href="#t9">9</a></span><span class="t"><span class="key">class</span> <span class="nam">TestBIPopulations</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t10" href="#t10">10</a></span><span class="t">    <span class="key">def</span> <span class="nam">setup_class</span><span class="op">(</span><span class="nam">self</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t11" href="#t11">11</a></span><span class="t">        <span class="nam">fx</span><span class="op">.</span><span class="nam">test_setup</span><span class="op">(</span><span class="nam">self</span><span class="op">,</span> <span class="str">"bipopulations"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t12" href="#t12">12</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t13" href="#t13">13</a></span><span class="t">    <span class="key">def</span> <span class="nam">teardown_class</span><span class="op">(</span><span class="nam">self</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t14" href="#t14">14</a></span><span class="t">        <span class="key">pass</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t15" href="#t15">15</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t16" href="#t16">16</a></span><span class="t">    <span class="com"># fx.test_teardown(self)</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">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t18" href="#t18">18</a></span><span class="t">    <span class="key">def</span> <span class="nam">test_bipopulations</span><span class="op">(</span><span class="nam">self</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t19" href="#t19">19</a></span><span class="t">        <span class="nam">returncode</span> <span class="op">=</span> <span class="nam">bipopulations</span><span class="op">(</span><span class="nam">properties</span><span class="op">=</span><span class="nam">self</span><span class="op">.</span><span class="nam">properties</span><span class="op">,</span> <span class="op">**</span><span class="nam">self</span><span class="op">.</span><span class="nam">paths</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t20" href="#t20">20</a></span><span class="t">        <span class="key">assert</span> <span class="nam">fx</span><span class="op">.</span><span class="nam">not_empty</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">paths</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="run"><span class="n"><a id="t21" href="#t21">21</a></span><span class="t">        <span class="key">assert</span> <span class="nam">fx</span><span class="op">.</span><span class="nam">not_empty</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">paths</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="run"><span class="n"><a id="t22" href="#t22">22</a></span><span class="t">        <span class="key">assert</span> <span class="nam">fx</span><span class="op">.</span><span class="nam">exe_success</span><span class="op">(</span><span class="nam">returncode</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t23" href="#t23">23</a></span><span class="t">        <span class="key">if</span> <span class="nam">platform</span><span class="op">.</span><span class="nam">system</span><span class="op">(</span><span class="op">)</span> <span class="op">==</span> <span class="str">"Darwin"</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t24" href="#t24">24</a></span><span class="t">            <span class="key">assert</span> <span class="nam">fx</span><span class="op">.</span><span class="nam">equal</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">paths</span><span class="op">[</span><span class="str">"output_csv_path"</span><span class="op">]</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">paths</span><span class="op">[</span><span class="str">"ref_csv_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="t25" href="#t25">25</a></span><span class="t">        <span class="key">assert</span> <span class="nam">fx</span><span class="op">.</span><span class="nam">equal</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">paths</span><span class="op">[</span><span class="str">"output_jpg_path"</span><span class="op">]</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">paths</span><span class="op">[</span><span class="str">"ref_jpg_output"</span><span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
 </main>
 <footer>
     <div class="content">
@@ -109,8 +113,8 @@ <h2>
             <a class="nav" href="index.html">&Hat; index</a> &nbsp; &nbsp;
             <a class="nav" href="z_020f76a90aa51c7b_test_canonical_alpha_gamma_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
-            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.4">coverage.py v7.6.4</a>,
-            created at 2024-11-04 11:05 +0000
+            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
+            created at 2024-11-15 12:07 +0000
         </p>
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 </footer>
diff --git a/coverage/z_020f76a90aa51c7b_test_canonical_alpha_gamma_py.html b/coverage/z_020f76a90aa51c7b_test_canonical_alpha_gamma_py.html
index f95f53a..eb68f82 100644
--- a/coverage/z_020f76a90aa51c7b_test_canonical_alpha_gamma_py.html
+++ b/coverage/z_020f76a90aa51c7b_test_canonical_alpha_gamma_py.html
@@ -64,8 +64,8 @@ <h2>
             <a id="indexLink" class="nav" href="index.html">&Hat; index</a> &nbsp; &nbsp;
             <a id="nextFileLink" class="nav" href="z_020f76a90aa51c7b_test_puckering_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
-            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.4">coverage.py v7.6.4</a>,
-            created at 2024-11-04 11:05 +0000
+            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
+            created at 2024-11-15 12:07 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -109,8 +109,8 @@ <h2>
             <a class="nav" href="index.html">&Hat; index</a> &nbsp; &nbsp;
             <a class="nav" href="z_020f76a90aa51c7b_test_puckering_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
-            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.4">coverage.py v7.6.4</a>,
-            created at 2024-11-04 11:05 +0000
+            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
+            created at 2024-11-15 12:07 +0000
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 </footer>
diff --git a/coverage/z_020f76a90aa51c7b_test_puckering_py.html b/coverage/z_020f76a90aa51c7b_test_puckering_py.html
index 0f24d74..ad3c43c 100644
--- a/coverage/z_020f76a90aa51c7b_test_puckering_py.html
+++ b/coverage/z_020f76a90aa51c7b_test_puckering_py.html
@@ -64,8 +64,8 @@ <h2>
             <a id="indexLink" class="nav" href="index.html">&Hat; index</a> &nbsp; &nbsp;
             <a id="nextFileLink" class="nav" href="z_97f47455ed834d2d_test_correlation_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
-            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.4">coverage.py v7.6.4</a>,
-            created at 2024-11-04 11:05 +0000
+            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
+            created at 2024-11-15 12:07 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -109,8 +109,8 @@ <h2>
             <a class="nav" href="index.html">&Hat; index</a> &nbsp; &nbsp;
             <a class="nav" href="z_97f47455ed834d2d_test_correlation_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
-            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.4">coverage.py v7.6.4</a>,
-            created at 2024-11-04 11:05 +0000
+            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
+            created at 2024-11-15 12:07 +0000
         </p>
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 </footer>
diff --git a/coverage/z_100f5897bddc1993_test_averages_py.html b/coverage/z_100f5897bddc1993_test_averages_py.html
index d4bbaee..c98139c 100644
--- a/coverage/z_100f5897bddc1993_test_averages_py.html
+++ b/coverage/z_100f5897bddc1993_test_averages_py.html
@@ -64,8 +64,8 @@ <h2>
             <a id="indexLink" class="nav" href="index.html">&Hat; index</a> &nbsp; &nbsp;
             <a id="nextFileLink" class="nav" href="z_100f5897bddc1993_test_bimodality_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
-            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.4">coverage.py v7.6.4</a>,
-            created at 2024-11-04 11:05 +0000
+            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
+            created at 2024-11-15 12:07 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -113,8 +113,8 @@ <h2>
             <a class="nav" href="index.html">&Hat; index</a> &nbsp; &nbsp;
             <a class="nav" href="z_100f5897bddc1993_test_bimodality_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
-            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.4">coverage.py v7.6.4</a>,
-            created at 2024-11-04 11:05 +0000
+            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
+            created at 2024-11-15 12:07 +0000
         </p>
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 </footer>
diff --git a/coverage/z_100f5897bddc1993_test_bimodality_py.html b/coverage/z_100f5897bddc1993_test_bimodality_py.html
index febbcab..67d5512 100644
--- a/coverage/z_100f5897bddc1993_test_bimodality_py.html
+++ b/coverage/z_100f5897bddc1993_test_bimodality_py.html
@@ -64,8 +64,8 @@ <h2>
             <a id="indexLink" class="nav" href="index.html">&Hat; index</a> &nbsp; &nbsp;
             <a id="nextFileLink" class="nav" href="z_100f5897bddc1993_test_timeseries_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
-            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.4">coverage.py v7.6.4</a>,
-            created at 2024-11-04 11:05 +0000
+            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
+            created at 2024-11-15 12:07 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -109,8 +109,8 @@ <h2>
             <a class="nav" href="index.html">&Hat; index</a> &nbsp; &nbsp;
             <a class="nav" href="z_100f5897bddc1993_test_timeseries_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
-            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.4">coverage.py v7.6.4</a>,
-            created at 2024-11-04 11:05 +0000
+            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
+            created at 2024-11-15 12:07 +0000
         </p>
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 </footer>
diff --git a/coverage/z_100f5897bddc1993_test_timeseries_py.html b/coverage/z_100f5897bddc1993_test_timeseries_py.html
index 027f6ca..54b1800 100644
--- a/coverage/z_100f5897bddc1993_test_timeseries_py.html
+++ b/coverage/z_100f5897bddc1993_test_timeseries_py.html
@@ -64,8 +64,8 @@ <h2>
             <a id="indexLink" class="nav" href="index.html">&Hat; index</a> &nbsp; &nbsp;
             <a id="nextFileLink" class="nav" href="z_100f5897bddc1993_test_timeseries_unzip_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
-            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.4">coverage.py v7.6.4</a>,
-            created at 2024-11-04 11:05 +0000
+            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
+            created at 2024-11-15 12:07 +0000
         </p>
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@@ -111,8 +111,8 @@ <h2>
             <a class="nav" href="index.html">&Hat; index</a> &nbsp; &nbsp;
             <a class="nav" href="z_100f5897bddc1993_test_timeseries_unzip_py.html">&#xbb; next</a>
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-            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.4">coverage.py v7.6.4</a>,
-            created at 2024-11-04 11:05 +0000
+            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
+            created at 2024-11-15 12:07 +0000
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diff --git a/coverage/z_100f5897bddc1993_test_timeseries_unzip_py.html b/coverage/z_100f5897bddc1993_test_timeseries_unzip_py.html
index b4523f4..5727eeb 100644
--- a/coverage/z_100f5897bddc1993_test_timeseries_unzip_py.html
+++ b/coverage/z_100f5897bddc1993_test_timeseries_unzip_py.html
@@ -64,8 +64,8 @@ <h2>
             <a id="indexLink" class="nav" href="index.html">&Hat; index</a> &nbsp; &nbsp;
             <a id="nextFileLink" class="nav" href="z_cda7f8e8576a7189_test_stiffness_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
-            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.4">coverage.py v7.6.4</a>,
-            created at 2024-11-04 11:05 +0000
+            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
+            created at 2024-11-15 12:07 +0000
         </p>
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             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -114,8 +114,8 @@ <h2>
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-            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.4">coverage.py v7.6.4</a>,
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+            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
+            created at 2024-11-15 12:07 +0000
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diff --git a/coverage/z_159731231e5c9c9d___init___py.html b/coverage/z_159731231e5c9c9d___init___py.html
index a95ecd2..47b2f1b 100644
--- a/coverage/z_159731231e5c9c9d___init___py.html
+++ b/coverage/z_159731231e5c9c9d___init___py.html
@@ -64,8 +64,8 @@ <h2>
             <a id="indexLink" class="nav" href="index.html">&Hat; index</a> &nbsp; &nbsp;
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-            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.4">coverage.py v7.6.4</a>,
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+            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
+            created at 2024-11-15 12:07 +0000
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@@ -93,8 +93,8 @@ <h2>
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-            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.4">coverage.py v7.6.4</a>,
-            created at 2024-11-04 11:05 +0000
+            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
+            created at 2024-11-15 12:07 +0000
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 </footer>
diff --git a/coverage/z_159731231e5c9c9d_bipopulations_py.html b/coverage/z_159731231e5c9c9d_bipopulations_py.html
index 9b356a3..2d0e557 100644
--- a/coverage/z_159731231e5c9c9d_bipopulations_py.html
+++ b/coverage/z_159731231e5c9c9d_bipopulations_py.html
@@ -54,8 +54,8 @@ <h1>
             </div>
         </aside>
         <h2>
-            <span class="text">98 statements &nbsp;</span>
-            <button type="button" class="run button_toggle_run" value="run" data-shortcut="r" title="Toggle lines run">76<span class="text"> run</span></button>
+            <span class="text">102 statements &nbsp;</span>
+            <button type="button" class="run button_toggle_run" value="run" data-shortcut="r" title="Toggle lines run">80<span class="text"> run</span></button>
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+            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
+            created at 2024-11-15 12:07 +0000
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@@ -88,284 +88,295 @@ <h2>
     <p class="pln"><span class="n"><a id="t6" href="#t6">6</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t7" href="#t7">7</a></span><span class="t"><span class="key">import</span> <span class="nam">matplotlib</span><span class="op">.</span><span class="nam">pyplot</span> <span class="key">as</span> <span class="nam">plt</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t8" href="#t8">8</a></span><span class="t"><span class="key">import</span> <span class="nam">pandas</span> <span class="key">as</span> <span class="nam">pd</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t9" href="#t9">9</a></span><span class="t"><span class="key">from</span> <span class="nam">numpy</span> <span class="key">import</span> <span class="nam">nan</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t10" href="#t10">10</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_dna</span><span class="op">.</span><span class="nam">utils</span><span class="op">.</span><span class="nam">loader</span> <span class="key">import</span> <span class="nam">read_series</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t11" href="#t11">11</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_dna</span><span class="op">.</span><span class="nam">utils</span><span class="op">.</span><span class="nam">transform</span> <span class="key">import</span> <span class="nam">inverse_complement</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t12" href="#t12">12</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_common</span><span class="op">.</span><span class="nam">generic</span><span class="op">.</span><span class="nam">biobb_object</span> <span class="key">import</span> <span class="nam">BiobbObject</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t13" href="#t13">13</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_common</span><span class="op">.</span><span class="nam">tools</span><span class="op">.</span><span class="nam">file_utils</span> <span class="key">import</span> <span class="nam">launchlogger</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t14" href="#t14">14</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_common</span><span class="op">.</span><span class="nam">configuration</span> <span class="key">import</span> <span class="nam">settings</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t15" href="#t15">15</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t16" href="#t16">16</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t17" href="#t17">17</a></span><span class="t"><span class="key">class</span> <span class="nam">BIPopulations</span><span class="op">(</span><span class="nam">BiobbObject</span><span class="op">)</span><span class="op">:</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">"""</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 BIPopulations</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 BI/BII populations from epsilon and zeta parameters.</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"><span class="str">            * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory.</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="run"><span class="n"><a id="t9" href="#t9">9</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_common</span><span class="op">.</span><span class="nam">configuration</span> <span class="key">import</span> <span class="nam">settings</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t10" href="#t10">10</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_common</span><span class="op">.</span><span class="nam">generic</span><span class="op">.</span><span class="nam">biobb_object</span> <span class="key">import</span> <span class="nam">BiobbObject</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t11" href="#t11">11</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_common</span><span class="op">.</span><span class="nam">tools</span><span class="op">.</span><span class="nam">file_utils</span> <span class="key">import</span> <span class="nam">launchlogger</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t12" href="#t12">12</a></span><span class="t"><span class="key">from</span> <span class="nam">numpy</span> <span class="key">import</span> <span class="nam">nan</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t13" href="#t13">13</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t14" href="#t14">14</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_dna</span><span class="op">.</span><span class="nam">utils</span><span class="op">.</span><span class="nam">common</span> <span class="key">import</span> <span class="nam">_from_string_to_list</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t15" href="#t15">15</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_dna</span><span class="op">.</span><span class="nam">utils</span><span class="op">.</span><span class="nam">loader</span> <span class="key">import</span> <span class="nam">read_series</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t16" href="#t16">16</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_dna</span><span class="op">.</span><span class="nam">utils</span><span class="op">.</span><span class="nam">transform</span> <span class="key">import</span> <span class="nam">inverse_complement</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">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t18" href="#t18">18</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t19" href="#t19">19</a></span><span class="t"><span class="key">class</span> <span class="nam">BIPopulations</span><span class="op">(</span><span class="nam">BiobbObject</span><span class="op">)</span><span class="op">:</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">"""</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 BIPopulations</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 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"><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="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_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="t27" href="#t27">27</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="t28" href="#t28">28</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="t29" href="#t29">29</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="t30" href="#t30">30</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="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/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="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">            * **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="t34" href="#t34">34</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="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"><span class="str">            * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory.</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">            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="t42" href="#t42">42</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="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">                '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">            bipopulations(</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_epsilC_path='/path/to/epsilC.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_epsilW_path='/path/to/epsilW.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_zetaC_path='/path/to/zetaC.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_zetaW_path='/path/to/zetaW.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="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="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>&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_epsilC_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">input_epsilW_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">input_zetaC_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">input_zetaW_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">output_csv_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="nam">output_jpg_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="nam">properties</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="t74" href="#t74">74</a></span><span class="t">        <span class="op">**</span><span class="nam">kwargs</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="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="t76" href="#t76">76</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="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"># Call parent class constructor</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">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="t80" href="#t80">80</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="t81" href="#t81">81</a></span><span class="t">&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="com"># Input/Output files</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">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="t84" href="#t84">84</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="t85" href="#t85">85</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="t86" href="#t86">86</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="t87" href="#t87">87</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="t88" href="#t88">88</a></span><span class="t">                <span class="str">"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="t89" href="#t89">89</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="t90" href="#t90">90</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="t91" href="#t91">91</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="t92" href="#t92">92</a></span><span class="t">                <span class="str">"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="t93" href="#t93">93</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="t94" href="#t94">94</a></span><span class="t">        <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="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">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="t97" href="#t97">97</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="pln"><span class="n"><a id="t98" href="#t98">98</a></span><span class="t">        <span class="com"># self.seqpos = properties.get("seqpos", None)</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">seqpos</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">            <span class="nam">int</span><span class="op">(</span><span class="nam">elem</span><span class="op">)</span> <span class="key">for</span> <span class="nam">elem</span> <span class="key">in</span> <span class="nam">_from_string_to_list</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><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="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">print</span><span class="op">(</span><span class="str">"seqpos::::::::"</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">print</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="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="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="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:`BIPopulations &lt;backbone.bipopulations.BIPopulations>` 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="pln"><span class="n"><a id="t117" href="#t117">117</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="t118" href="#t118">118</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="t119" href="#t119">119</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="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="t120" href="#t120">120</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="t121" href="#t121">121</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="t122" href="#t122">122</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="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="t123" href="#t123">123</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="t124" href="#t124">124</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="t125" href="#t125">125</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="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="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">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="t128" href="#t128">128</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="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="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"># calculate difference between epsil and zeta parameters</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">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="t133" href="#t133">133</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="t134" href="#t134">134</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="t135" href="#t135">135</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="t136" href="#t136">136</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="t137" href="#t137">137</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="t138" href="#t138">138</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="t139" href="#t139">139</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="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 BI population</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">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="t143" href="#t143">143</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="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 table</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">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="t147" href="#t147">147</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="t148" href="#t148">148</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="t149" href="#t149">149</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="t150" href="#t150">150</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="t151" href="#t151">151</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="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">            <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="t117" href="#t117">117</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="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">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="t119" href="#t119">119</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="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"># check seqpos</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">seqpos</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">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="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">f"seqpos values must be between 1 and {len(self.sequence) - 2}"</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="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="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="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">"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="t129" href="#t129">129</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="t130" href="#t130">130</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="key">None</span>  <span class="com"># type: ignore</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">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="t134" href="#t134">134</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="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">usecols</span><span class="op">=</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</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>&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">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="t137" href="#t137">137</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="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">usecols</span><span class="op">=</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</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="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">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="t140" href="#t140">140</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="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">usecols</span><span class="op">=</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</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="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">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="t143" href="#t143">143</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="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">usecols</span><span class="op">=</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</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="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"># calculate difference between epsil and zeta parameters</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">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><span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span><span class="op">,</span> <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="t148" href="#t148">148</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><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>&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 plot</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">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="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">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="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="t160" href="#t160">160</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="t161" href="#t161">161</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="t162" href="#t162">162</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="t163" href="#t163">163</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="t164" href="#t164">164</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="t165" href="#t165">165</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="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="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="t168" href="#t168">168</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="t169" href="#t169">169</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="t170" href="#t170">170</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="t171" href="#t171">171</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="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> <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="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">"Nucleotide Sequence"</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">"BI/BII Population (%)"</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><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="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">stage_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"># Copy files to host</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">copy_to_host</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"># Remove temporary file(s)</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">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="t187" href="#t187">187</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="str">""</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="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">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="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="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="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">return</span> <span class="num">0</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="run"><span class="n"><a id="t195" href="#t195">195</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="t196" href="#t196">196</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="t197" href="#t197">197</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="t198" href="#t198">198</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="t199" href="#t199">199</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="t200" href="#t200">200</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="t201" href="#t201">201</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="t202" href="#t202">202</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="t203" href="#t203">203</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="t204" href="#t204">204</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="t205" href="#t205">205</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="t206" href="#t206">206</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="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">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="t209" href="#t209">209</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="t210" href="#t210">210</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="t211" href="#t211">211</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="t212" href="#t212">212</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="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">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="t215" href="#t215">215</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="t216" href="#t216">216</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="t217" href="#t217">217</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="t218" href="#t218">218</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="t219" href="#t219">219</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="t220" href="#t220">220</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="t221" href="#t221">221</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="t222" href="#t222">222</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="t223" href="#t223">223</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="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">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="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">&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"># difference between epsilon and zeta coordinates</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">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="t230" href="#t230">230</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="t231" href="#t231">231</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">bipopulations</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_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="t235" href="#t235">235</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="t236" href="#t236">236</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="t237" href="#t237">237</a></span><span class="t">        <span class="nam">properties</span><span class="op">:</span> <span class="nam">Optional</span><span class="op">[</span><span class="nam">dict</span><span class="op">]</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="t238" href="#t238">238</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="t239" href="#t239">239</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="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>&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="op">{</span><span class="str">"Nucleotide"</span><span class="op">:</span> <span class="nam">xlabels</span><span class="op">,</span> <span class="str">"BI population"</span><span class="op">:</span> <span class="nam">BI</span><span class="op">,</span> <span class="str">"BII population"</span><span class="op">:</span> <span class="nam">BII</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="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">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="t159" href="#t159">159</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="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="nam">index</span><span class="op">=</span><span class="key">False</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="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="pln"><span class="n"><a id="t162" href="#t162">162</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="t163" href="#t163">163</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="t164" href="#t164">164</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">bar</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> <span class="nam">BI</span><span class="op">,</span> <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="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><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> <span class="nam">BII</span><span class="op">,</span> <span class="nam">bottom</span><span class="op">=</span><span class="nam">BI</span><span class="op">,</span> <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="t166" href="#t166">166</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="t167" href="#t167">167</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">bar</span><span class="op">(</span><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> <span class="op">[</span><span class="num">100</span><span class="op">]</span><span class="op">,</span> <span class="nam">color</span><span class="op">=</span><span class="str">"white"</span><span class="op">,</span> <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">"BI/BII Population (%)"</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: BI/BII Population"</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><span class="nam">self</span><span class="op">.</span><span class="nam">stage_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="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="t175" href="#t175">175</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="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"># Copy files to host</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">copy_to_host</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"># Remove temporary file(s)</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">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><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="str">""</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">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="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="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="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="key">return</span> <span class="num">0</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">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="t189" href="#t189">189</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="t190" href="#t190">190</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="t191" href="#t191">191</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="t192" href="#t192">192</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="t193" href="#t193">193</a></span><span class="t">        <span class="nam">labelsW</span> <span class="op">=</span> <span class="op">[</span><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="t194" href="#t194">194</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="t195" href="#t195">195</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="t196" href="#t196">196</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="t197" href="#t197">197</a></span><span class="t">        <span class="nam">labelsC</span> <span class="op">=</span> <span class="op">[</span><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="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">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="t200" href="#t200">200</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="t201" href="#t201">201</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="t202" href="#t202">202</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="t203" href="#t203">203</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="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">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="t206" href="#t206">206</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="t207" href="#t207">207</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="t208" href="#t208">208</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><span class="nam">zetaW</span><span class="op">,</span> <span class="nam">separator_df</span><span class="op">,</span> <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> <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="t209" href="#t209">209</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><span class="nam">epsilW</span><span class="op">,</span> <span class="nam">separator_df</span><span class="op">,</span> <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> <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="t210" href="#t210">210</a></span><span class="t">&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="com"># difference between epsilon and zeta coordinates</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">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="t213" href="#t213">213</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="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">&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">bipopulations</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_epsilC_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="t218" href="#t218">218</a></span><span class="t">    <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="t219" href="#t219">219</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>&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">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="t221" href="#t221">221</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>&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">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">Optional</span><span class="op">[</span><span class="nam">dict</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="pln"><span class="n"><a id="t224" href="#t224">224</a></span><span class="t">    <span class="op">**</span><span class="nam">kwargs</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="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="t226" href="#t226">226</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="t227" href="#t227">227</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="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">BIPopulations</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_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="t231" href="#t231">231</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="t232" href="#t232">232</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="t233" href="#t233">233</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="t234" href="#t234">234</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="t235" href="#t235">235</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="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">        <span class="op">**</span><span class="nam">kwargs</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="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="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">&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">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">input_epsilC_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_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="t244" href="#t244">244</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="t245" href="#t245">245</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="t246" href="#t246">246</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="t247" href="#t247">247</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="t248" href="#t248">248</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="t249" href="#t249">249</a></span><span class="t">&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">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="t252" href="#t252">252</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="t253" href="#t253">253</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="t254" href="#t254">254</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="t255" href="#t255">255</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="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_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="t259" href="#t259">259</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="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">'--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="t261" href="#t261">261</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="t262" href="#t262">262</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="t263" href="#t263">263</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="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_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="t265" href="#t265">265</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="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">'--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="t267" href="#t267">267</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="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_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="t269" href="#t269">269</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="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">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="t272" href="#t272">272</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="t273" href="#t273">273</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="t274" href="#t274">274</a></span><span class="t">&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">bipopulations</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_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="t277" href="#t277">277</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="t278" href="#t278">278</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="t279" href="#t279">279</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="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="run"><span class="n"><a id="t241" href="#t241">241</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="t242" href="#t242">242</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="t243" href="#t243">243</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>&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">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="t245" href="#t245">245</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="pln"><span class="n"><a id="t246" href="#t246">246</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="t247" href="#t247">247</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="t248" href="#t248">248</a></span><span class="t">&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">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="t250" href="#t250">250</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>&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">"--input_epsilC_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">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="t253" href="#t253">253</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="pln"><span class="n"><a id="t254" href="#t254">254</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="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>&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">"--input_epsilW_path"</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">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 &lt;epsilW> input ser file path. Accepted formats: ser."</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="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>&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="str">"--input_zetaC_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">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="t263" href="#t263">263</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="pln"><span class="n"><a id="t264" href="#t264">264</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="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>&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">"--input_zetaW_path"</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">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;zetaW> input ser file path. Accepted formats: ser."</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="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>&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="str">"--output_csv_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">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">"Path to output csv file. Accepted formats: csv."</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="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>&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">"--output_jpg_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">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">"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="t279" href="#t279">279</a></span><span class="t">    <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="mis show_mis"><span class="n"><a id="t281" href="#t281">281</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="t282" href="#t282">282</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="t283" href="#t283">283</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="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="mis show_mis"><span class="n"><a id="t285" href="#t285">285</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="t286" href="#t286">286</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="t287" href="#t287">287</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="t288" href="#t288">288</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="t289" href="#t289">289</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="t290" href="#t290">290</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="t291" href="#t291">291</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="t292" href="#t292">292</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="t293" href="#t293">293</a></span><span class="t">    <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">&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="run"><span class="n"><a id="t296" href="#t296">296</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="t297" href="#t297">297</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">
@@ -374,8 +385,8 @@ <h2>
             <a class="nav" href="index.html">&Hat; index</a> &nbsp; &nbsp;
             <a class="nav" href="z_159731231e5c9c9d_canonicalag_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
-            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.4">coverage.py v7.6.4</a>,
-            created at 2024-11-04 11:05 +0000
+            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
+            created at 2024-11-15 12:07 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_159731231e5c9c9d_canonicalag_py.html b/coverage/z_159731231e5c9c9d_canonicalag_py.html
index 0cf2c18..f89e756 100644
--- a/coverage/z_159731231e5c9c9d_canonicalag_py.html
+++ b/coverage/z_159731231e5c9c9d_canonicalag_py.html
@@ -54,8 +54,8 @@ <h1>
             </div>
         </aside>
         <h2>
-            <span class="text">108 statements &nbsp;</span>
-            <button type="button" class="run button_toggle_run" value="run" data-shortcut="r" title="Toggle lines run">86<span class="text"> run</span></button>
+            <span class="text">110 statements &nbsp;</span>
+            <button type="button" class="run button_toggle_run" value="run" data-shortcut="r" title="Toggle lines run">88<span class="text"> run</span></button>
             <button type="button" class="mis show_mis button_toggle_mis" value="mis" data-shortcut="m" title="Toggle lines missing">22<span class="text"> missing</span></button>
             <button type="button" class="exc show_exc button_toggle_exc" value="exc" data-shortcut="x" title="Toggle lines excluded">0<span class="text"> excluded</span></button>
         </h2>
@@ -64,8 +64,8 @@ <h2>
             <a id="indexLink" class="nav" href="index.html">&Hat; index</a> &nbsp; &nbsp;
             <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/7.6.4">coverage.py v7.6.4</a>,
-            created at 2024-11-04 11:05 +0000
+            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
+            created at 2024-11-15 12:07 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -87,293 +87,311 @@ <h2>
     <p class="run"><span class="n"><a id="t5" href="#t5">5</a></span><span class="t"><span class="key">from</span> <span class="nam">typing</span> <span class="key">import</span> <span class="nam">Optional</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t6" href="#t6">6</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t7" href="#t7">7</a></span><span class="t"><span class="key">import</span> <span class="nam">matplotlib</span><span class="op">.</span><span class="nam">pyplot</span> <span class="key">as</span> <span class="nam">plt</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t8" href="#t8">8</a></span><span class="t"><span class="key">import</span> <span class="nam">pandas</span> <span class="key">as</span> <span class="nam">pd</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t9" href="#t9">9</a></span><span class="t"><span class="key">import</span> <span class="nam">numpy</span> <span class="key">as</span> <span class="nam">np</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t10" href="#t10">10</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_dna</span><span class="op">.</span><span class="nam">utils</span><span class="op">.</span><span class="nam">loader</span> <span class="key">import</span> <span class="nam">read_series</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t11" href="#t11">11</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_dna</span><span class="op">.</span><span class="nam">utils</span><span class="op">.</span><span class="nam">transform</span> <span class="key">import</span> <span class="nam">inverse_complement</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t12" href="#t12">12</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_common</span><span class="op">.</span><span class="nam">generic</span><span class="op">.</span><span class="nam">biobb_object</span> <span class="key">import</span> <span class="nam">BiobbObject</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t13" href="#t13">13</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_common</span><span class="op">.</span><span class="nam">tools</span><span class="op">.</span><span class="nam">file_utils</span> <span class="key">import</span> <span class="nam">launchlogger</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t14" href="#t14">14</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_common</span><span class="op">.</span><span class="nam">configuration</span> <span class="key">import</span> <span class="nam">settings</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t15" href="#t15">15</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t16" href="#t16">16</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t17" href="#t17">17</a></span><span class="t"><span class="key">class</span> <span class="nam">CanonicalAG</span><span class="op">(</span><span class="nam">BiobbObject</span><span class="op">)</span><span class="op">:</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">"""</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 CanonicalAG</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 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="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"><span class="str">            * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory.</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="run"><span class="n"><a id="t8" href="#t8">8</a></span><span class="t"><span class="key">import</span> <span class="nam">numpy</span> <span class="key">as</span> <span class="nam">np</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t9" href="#t9">9</a></span><span class="t"><span class="key">import</span> <span class="nam">pandas</span> <span class="key">as</span> <span class="nam">pd</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t10" href="#t10">10</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_common</span><span class="op">.</span><span class="nam">configuration</span> <span class="key">import</span> <span class="nam">settings</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t11" href="#t11">11</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_common</span><span class="op">.</span><span class="nam">generic</span><span class="op">.</span><span class="nam">biobb_object</span> <span class="key">import</span> <span class="nam">BiobbObject</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t12" href="#t12">12</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_common</span><span class="op">.</span><span class="nam">tools</span><span class="op">.</span><span class="nam">file_utils</span> <span class="key">import</span> <span class="nam">launchlogger</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t13" href="#t13">13</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t14" href="#t14">14</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_dna</span><span class="op">.</span><span class="nam">utils</span><span class="op">.</span><span class="nam">common</span> <span class="key">import</span> <span class="nam">_from_string_to_list</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t15" href="#t15">15</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_dna</span><span class="op">.</span><span class="nam">utils</span><span class="op">.</span><span class="nam">loader</span> <span class="key">import</span> <span class="nam">read_series</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t16" href="#t16">16</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_dna</span><span class="op">.</span><span class="nam">utils</span><span class="op">.</span><span class="nam">transform</span> <span class="key">import</span> <span class="nam">inverse_complement</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">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t18" href="#t18">18</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t19" href="#t19">19</a></span><span class="t"><span class="key">class</span> <span class="nam">CanonicalAG</span><span class="op">(</span><span class="nam">BiobbObject</span><span class="op">)</span><span class="op">:</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">"""</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 CanonicalAG</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 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"><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="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_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="t27" href="#t27">27</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="t28" href="#t28">28</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="t29" href="#t29">29</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="t30" href="#t30">30</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="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. 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="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">            * **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="t34" href="#t34">34</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="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"><span class="str">            * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory.</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">            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">                '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="t42" href="#t42">42</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="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">                'seqpos': [1,2],</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">                'sequence': 'GCAT',</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">            canonicalag(</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_alphaC_path='/path/to/alphaC.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_alphaW_path='/path/to/alphaW.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_gammaC_path='/path/to/gammaC.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_gammaW_path='/path/to/gammaW.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/table/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/table/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="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="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>&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_alphaC_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">input_alphaW_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">input_gammaC_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">input_gammaW_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="nam">output_csv_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="nam">output_jpg_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="nam">properties</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="t75" href="#t75">75</a></span><span class="t">        <span class="op">**</span><span class="nam">kwargs</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="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="t77" href="#t77">77</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="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"># Call parent class constructor</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">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="t81" href="#t81">81</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="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"># Input/Output files</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">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="t85" href="#t85">85</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="t86" href="#t86">86</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="t87" href="#t87">87</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="t88" href="#t88">88</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="t89" href="#t89">89</a></span><span class="t">                <span class="str">"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="t90" href="#t90">90</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="t91" href="#t91">91</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="t92" href="#t92">92</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="t93" href="#t93">93</a></span><span class="t">                <span class="str">"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="t94" href="#t94">94</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="t95" href="#t95">95</a></span><span class="t">        <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="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="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">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="t99" href="#t99">99</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><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="t100" href="#t100">100</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="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">int</span><span class="op">(</span><span class="nam">elem</span><span class="op">)</span> <span class="key">for</span> <span class="nam">elem</span> <span class="key">in</span> <span class="nam">_from_string_to_list</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><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="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 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="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="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:`CanonicalAG &lt;backbone.canonicalag.CanonicalAG>` 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"># 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="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="pln"><span class="n"><a id="t117" href="#t117">117</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="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">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="t119" href="#t119">119</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="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"># read input files</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">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="t123" href="#t123">123</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="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="t124" href="#t124">124</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="t125" href="#t125">125</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="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="t126" href="#t126">126</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="t127" href="#t127">127</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="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="t128" href="#t128">128</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="t129" href="#t129">129</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="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="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">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="t133" href="#t133">133</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="t134" href="#t134">134</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="t135" href="#t135">135</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="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"># calculate difference between epsil and zeta parameters</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">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="t139" href="#t139">139</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="t140" href="#t140">140</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="t141" href="#t141">141</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="t142" href="#t142">142</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="t143" href="#t143">143</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="t144" href="#t144">144</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="t145" href="#t145">145</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="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 table</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">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="t149" href="#t149">149</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="t150" href="#t150">150</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="t151" href="#t151">151</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="t152" href="#t152">152</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="t153" href="#t153">153</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="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="t154" href="#t154">154</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="t121" href="#t121">121</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="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">seqpos</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">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="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">f"seqpos values must be between 1 and {len(self.sequence) - 2}"</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="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="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="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">"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="t129" href="#t129">129</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="t130" href="#t130">130</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="key">None</span>  <span class="com"># type: ignore</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">stage_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>&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>&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">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="t137" href="#t137">137</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="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>&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="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">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="t140" href="#t140">140</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="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>&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="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">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="t143" href="#t143">143</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="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>&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="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"># fix angle range so its not negative</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">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="t148" href="#t148">148</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="t149" href="#t149">149</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="t150" href="#t150">150</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="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"># calculate difference between epsil and zeta parameters</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">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><span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span><span class="op">,</span> <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="t154" href="#t154">154</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><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>&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"># save plot</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">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="t158" href="#t158">158</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="t159" href="#t159">159</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="t160" href="#t160">160</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="t161" href="#t161">161</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="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="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="t164" href="#t164">164</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="t165" href="#t165">165</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="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="pln"><span class="n"><a id="t167" href="#t167">167</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="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="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="t170" href="#t170">170</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="t171" href="#t171">171</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="t172" href="#t172">172</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="t173" href="#t173">173</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="t174" href="#t174">174</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="t175" href="#t175">175</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="t176" href="#t176">176</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="t177" href="#t177">177</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="t178" href="#t178">178</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="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">stage_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="run"><span class="n"><a id="t182" href="#t182">182</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="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"># Copy files to host</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">self</span><span class="op">.</span><span class="nam">copy_to_host</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="com"># save table</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">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="t158" href="#t158">158</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>&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="op">{</span><span class="str">"Nucleotide"</span><span class="op">:</span> <span class="nam">xlabels</span><span class="op">,</span> <span class="str">"Canonical alpha/gamma"</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="t160" href="#t160">160</a></span><span class="t">        <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">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="t162" href="#t162">162</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="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="nam">index</span><span class="op">=</span><span class="key">False</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>&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">bar</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> <span class="nam">canonical_populations</span><span class="op">,</span> <span class="nam">label</span><span class="op">=</span><span class="str">"canonical alpha/gamma"</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="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="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="t173" href="#t173">173</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="t174" href="#t174">174</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="t175" href="#t175">175</a></span><span class="t">        <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"># empty bar to divide both sequences</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">axs</span><span class="op">.</span><span class="nam">bar</span><span class="op">(</span><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> <span class="op">[</span><span class="num">100</span><span class="op">]</span><span class="op">,</span> <span class="nam">color</span><span class="op">=</span><span class="str">"white"</span><span class="op">,</span> <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="t178" href="#t178">178</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="t179" href="#t179">179</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="t180" href="#t180">180</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="t181" href="#t181">181</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="t182" href="#t182">182</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="t183" href="#t183">183</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="t184" href="#t184">184</a></span><span class="t">        <span class="nam">fig</span><span class="op">.</span><span class="nam">savefig</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">stage_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="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="t185" href="#t185">185</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="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"># Remove temporary file(s)</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">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="t189" href="#t189">189</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="str">""</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="op">]</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">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="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">return</span> <span class="num">0</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="run"><span class="n"><a id="t195" href="#t195">195</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="t196" href="#t196">196</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="t197" href="#t197">197</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="t198" href="#t198">198</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="t199" href="#t199">199</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="t200" href="#t200">200</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="t201" href="#t201">201</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="pln"><span class="n"><a id="t187" href="#t187">187</a></span><span class="t">        <span class="com"># Copy files to host</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">self</span><span class="op">.</span><span class="nam">copy_to_host</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><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="str">""</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="t192" href="#t192">192</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="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">return</span> <span class="num">0</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">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="t197" href="#t197">197</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="t198" href="#t198">198</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="t199" href="#t199">199</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="t200" href="#t200">200</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="t201" href="#t201">201</a></span><span class="t">        <span class="nam">labelsW</span> <span class="op">=</span> <span class="op">[</span><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="t202" href="#t202">202</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="t203" href="#t203">203</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="t204" href="#t204">204</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="t205" href="#t205">205</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="t206" href="#t206">206</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="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">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="t209" href="#t209">209</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="t210" href="#t210">210</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="t211" href="#t211">211</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="t212" href="#t212">212</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="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">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="t215" href="#t215">215</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="t216" href="#t216">216</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="t217" href="#t217">217</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="t218" href="#t218">218</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="t219" href="#t219">219</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="t220" href="#t220">220</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="t221" href="#t221">221</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="t222" href="#t222">222</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="t223" href="#t223">223</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="t224" href="#t224">224</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="t225" href="#t225">225</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="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">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="t228" href="#t228">228</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="t229" href="#t229">229</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="t230" href="#t230">230</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="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">return</span> <span class="nam">canonical_alpha_gamma</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">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="t235" href="#t235">235</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="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">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="t237" href="#t237">237</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="t238" href="#t238">238</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="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">&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">canonicalag</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_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="t243" href="#t243">243</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="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">Optional</span><span class="op">[</span><span class="nam">dict</span><span class="op">]</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:`CanonicalAG &lt;dna.backbone.canonicalag.CanonicalAG>` 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.canonicalag.CanonicalAG.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">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">input_alphaC_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_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="t252" href="#t252">252</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="t253" href="#t253">253</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="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="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 Canonical Alpha/Gamma distributions.'</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_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="t267" href="#t267">267</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="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_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="t269" href="#t269">269</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="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_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="t271" href="#t271">271</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="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_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="t273" href="#t273">273</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="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">canonicalag</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_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="t285" href="#t285">285</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="t286" href="#t286">286</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="t287" href="#t287">287</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="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="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>
+    <p class="run"><span class="n"><a id="t203" href="#t203">203</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="t204" href="#t204">204</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="t205" href="#t205">205</a></span><span class="t">        <span class="nam">labelsC</span> <span class="op">=</span> <span class="op">[</span><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="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">if</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="t208" href="#t208">208</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="t209" href="#t209">209</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="t210" href="#t210">210</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="t211" href="#t211">211</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="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">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="t214" href="#t214">214</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="t215" href="#t215">215</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><span class="nam">gammaW</span><span class="op">,</span> <span class="nam">separator_df</span><span class="op">,</span> <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> <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="t216" href="#t216">216</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><span class="nam">alphaW</span><span class="op">,</span> <span class="nam">separator_df</span><span class="op">,</span> <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> <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="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="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="t219" href="#t219">219</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="t220" href="#t220">220</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><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="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">return</span> <span class="nam">canonical_alpha_gamma</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">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="t225" href="#t225">225</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="t226" href="#t226">226</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="t227" href="#t227">227</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="t228" href="#t228">228</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="t229" href="#t229">229</a></span><span class="t">&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">canonicalag</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">input_alphaC_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="t233" href="#t233">233</a></span><span class="t">    <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="t234" href="#t234">234</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>&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_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="t236" href="#t236">236</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>&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">str</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">Optional</span><span class="op">[</span><span class="nam">dict</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="pln"><span class="n"><a id="t239" href="#t239">239</a></span><span class="t">    <span class="op">**</span><span class="nam">kwargs</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="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:`CanonicalAG &lt;dna.backbone.canonicalag.CanonicalAG>` 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.backbone.canonicalag.CanonicalAG.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">CanonicalAG</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_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="t246" href="#t246">246</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="t247" href="#t247">247</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="t248" href="#t248">248</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="t249" href="#t249">249</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="t250" href="#t250">250</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="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">        <span class="op">**</span><span class="nam">kwargs</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="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="t254" href="#t254">254</a></span><span class="t">&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="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="t257" href="#t257">257</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="t258" href="#t258">258</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>&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">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="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="pln"><span class="n"><a id="t261" href="#t261">261</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="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>&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">"--input_alphaC_path"</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">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;alphaC> input ser file path. Accepted formats: ser."</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="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>&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="str">"--input_alphaW_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">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;alphaW> input ser file path. Accepted formats: ser."</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="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>&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">"--input_gammaC_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">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;gammaC> input ser file path. Accepted formats: ser."</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="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>&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="str">"--input_gammaW_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">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">"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="pln"><span class="n"><a id="t284" href="#t284">284</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="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>&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="str">"--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">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="t288" href="#t288">288</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="pln"><span class="n"><a id="t289" href="#t289">289</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="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>&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">"--output_jpg_path"</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">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 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="t294" href="#t294">294</a></span><span class="t">    <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">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="t297" href="#t297">297</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="t298" href="#t298">298</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="t299" href="#t299">299</a></span><span class="t">&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">canonicalag</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">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="t302" href="#t302">302</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="t303" href="#t303">303</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="t304" href="#t304">304</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="t305" href="#t305">305</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="t306" href="#t306">306</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="t307" href="#t307">307</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="t308" href="#t308">308</a></span><span class="t">    <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="pln"><span class="n"><a id="t310" href="#t310">310</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t311" href="#t311">311</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="t312" href="#t312">312</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">
@@ -382,8 +400,8 @@ <h2>
             <a class="nav" href="index.html">&Hat; index</a> &nbsp; &nbsp;
             <a class="nav" href="z_159731231e5c9c9d_puckering_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
-            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.4">coverage.py v7.6.4</a>,
-            created at 2024-11-04 11:05 +0000
+            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
+            created at 2024-11-15 12:07 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_159731231e5c9c9d_puckering_py.html b/coverage/z_159731231e5c9c9d_puckering_py.html
index d3f8858..75dff31 100644
--- a/coverage/z_159731231e5c9c9d_puckering_py.html
+++ b/coverage/z_159731231e5c9c9d_puckering_py.html
@@ -54,8 +54,8 @@ <h1>
             </div>
         </aside>
         <h2>
-            <span class="text">103 statements &nbsp;</span>
-            <button type="button" class="run button_toggle_run" value="run" data-shortcut="r" title="Toggle lines run">83<span class="text"> run</span></button>
+            <span class="text">105 statements &nbsp;</span>
+            <button type="button" class="run button_toggle_run" value="run" data-shortcut="r" title="Toggle lines run">85<span class="text"> run</span></button>
             <button type="button" class="mis show_mis button_toggle_mis" value="mis" data-shortcut="m" title="Toggle lines missing">20<span class="text"> missing</span></button>
             <button type="button" class="exc show_exc button_toggle_exc" value="exc" data-shortcut="x" title="Toggle lines excluded">0<span class="text"> excluded</span></button>
         </h2>
@@ -64,8 +64,8 @@ <h2>
             <a id="indexLink" class="nav" href="index.html">&Hat; index</a> &nbsp; &nbsp;
             <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/7.6.4">coverage.py v7.6.4</a>,
-            created at 2024-11-04 11:05 +0000
+            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
+            created at 2024-11-15 12:07 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -87,264 +87,264 @@ <h2>
     <p class="run"><span class="n"><a id="t5" href="#t5">5</a></span><span class="t"><span class="key">from</span> <span class="nam">typing</span> <span class="key">import</span> <span class="nam">Optional</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t6" href="#t6">6</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t7" href="#t7">7</a></span><span class="t"><span class="key">import</span> <span class="nam">matplotlib</span><span class="op">.</span><span class="nam">pyplot</span> <span class="key">as</span> <span class="nam">plt</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t8" href="#t8">8</a></span><span class="t"><span class="key">import</span> <span class="nam">pandas</span> <span class="key">as</span> <span class="nam">pd</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t9" href="#t9">9</a></span><span class="t"><span class="key">import</span> <span class="nam">numpy</span> <span class="key">as</span> <span class="nam">np</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t10" href="#t10">10</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_dna</span><span class="op">.</span><span class="nam">utils</span><span class="op">.</span><span class="nam">loader</span> <span class="key">import</span> <span class="nam">read_series</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t11" href="#t11">11</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_dna</span><span class="op">.</span><span class="nam">utils</span><span class="op">.</span><span class="nam">transform</span> <span class="key">import</span> <span class="nam">inverse_complement</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t12" href="#t12">12</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_common</span><span class="op">.</span><span class="nam">generic</span><span class="op">.</span><span class="nam">biobb_object</span> <span class="key">import</span> <span class="nam">BiobbObject</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t13" href="#t13">13</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_common</span><span class="op">.</span><span class="nam">tools</span><span class="op">.</span><span class="nam">file_utils</span> <span class="key">import</span> <span class="nam">launchlogger</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t14" href="#t14">14</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_common</span><span class="op">.</span><span class="nam">configuration</span> <span class="key">import</span> <span class="nam">settings</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t15" href="#t15">15</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t16" href="#t16">16</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t17" href="#t17">17</a></span><span class="t"><span class="key">class</span> <span class="nam">Puckering</span><span class="op">(</span><span class="nam">BiobbObject</span><span class="op">)</span><span class="op">:</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">"""</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 Puckering</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 Puckering from phase parameters.</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 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="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">            * **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">            * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory.</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="run"><span class="n"><a id="t8" href="#t8">8</a></span><span class="t"><span class="key">import</span> <span class="nam">numpy</span> <span class="key">as</span> <span class="nam">np</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t9" href="#t9">9</a></span><span class="t"><span class="key">import</span> <span class="nam">pandas</span> <span class="key">as</span> <span class="nam">pd</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t10" href="#t10">10</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_common</span><span class="op">.</span><span class="nam">configuration</span> <span class="key">import</span> <span class="nam">settings</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t11" href="#t11">11</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_common</span><span class="op">.</span><span class="nam">generic</span><span class="op">.</span><span class="nam">biobb_object</span> <span class="key">import</span> <span class="nam">BiobbObject</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t12" href="#t12">12</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_common</span><span class="op">.</span><span class="nam">tools</span><span class="op">.</span><span class="nam">file_utils</span> <span class="key">import</span> <span class="nam">launchlogger</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t13" href="#t13">13</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t14" href="#t14">14</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_dna</span><span class="op">.</span><span class="nam">utils</span><span class="op">.</span><span class="nam">common</span> <span class="key">import</span> <span class="nam">_from_string_to_list</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t15" href="#t15">15</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_dna</span><span class="op">.</span><span class="nam">utils</span><span class="op">.</span><span class="nam">loader</span> <span class="key">import</span> <span class="nam">read_series</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t16" href="#t16">16</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_dna</span><span class="op">.</span><span class="nam">utils</span><span class="op">.</span><span class="nam">transform</span> <span class="key">import</span> <span class="nam">inverse_complement</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">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t18" href="#t18">18</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t19" href="#t19">19</a></span><span class="t"><span class="key">class</span> <span class="nam">Puckering</span><span class="op">(</span><span class="nam">BiobbObject</span><span class="op">)</span><span class="op">:</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">"""</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 Puckering</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 Puckering from phase 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"><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="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_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="t27" href="#t27">27</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="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/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="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/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="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">            * **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"><span class="str">            * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory.</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">            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="t41" href="#t41">41</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="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">                '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">            puckering(</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_phaseC_path='/path/to/phaseC.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_phaseW_path='/path/to/phaseW.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="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="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>&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">self</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_phaseC_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_phaseW_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>&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>&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>&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="op">**</span><span class="nam">kwargs</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="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_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="t81" href="#t81">81</a></span><span class="t">                <span class="str">"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="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><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><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><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="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="nam">int</span><span class="op">(</span><span class="nam">elem</span><span class="op">)</span> <span class="key">for</span> <span class="nam">elem</span> <span class="key">in</span> <span class="nam">_from_string_to_list</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><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="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"># 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"># read input files</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">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="t116" href="#t116">116</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="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="t117" href="#t117">117</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="t118" href="#t118">118</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="t119" href="#t119">119</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="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="t120" href="#t120">120</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="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"># fix angle range so its not negative</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">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="t124" href="#t124">124</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="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"># calculate difference between epsil and zeta parameters</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">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="t128" href="#t128">128</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="t129" href="#t129">129</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="t130" href="#t130">130</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="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:`Puckering &lt;backbone.puckering.Puckering>` 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="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>&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="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="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="t120" href="#t120">120</a></span><span class="t">                <span class="key">raise</span> <span class="nam">ValueError</span><span class="op">(</span><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">        <span class="key">else</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">seqpos</span> <span class="op">=</span> <span class="key">None</span>  <span class="com"># type: ignore</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 files</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">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="t126" href="#t126">126</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="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">usecols</span><span class="op">=</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</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="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">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="t129" href="#t129">129</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="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">usecols</span><span class="op">=</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</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="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"># save plot</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">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="t134" href="#t134">134</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="t135" href="#t135">135</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="t136" href="#t136">136</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="t137" href="#t137">137</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="t138" href="#t138">138</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="t139" href="#t139">139</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="t140" href="#t140">140</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="t141" href="#t141">141</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="t142" href="#t142">142</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="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">Spop</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">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="t147" href="#t147">147</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="t148" href="#t148">148</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="t149" href="#t149">149</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="t150" href="#t150">150</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="t151" href="#t151">151</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="t152" href="#t152">152</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="t153" href="#t153">153</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="t154" href="#t154">154</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="t155" href="#t155">155</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="t156" href="#t156">156</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="t157" href="#t157">157</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="t158" href="#t158">158</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="t159" href="#t159">159</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="t160" href="#t160">160</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="t161" href="#t161">161</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="t162" href="#t162">162</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="t163" href="#t163">163</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="t164" href="#t164">164</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="t165" href="#t165">165</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="t166" href="#t166">166</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="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="t167" href="#t167">167</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="t168" href="#t168">168</a></span><span class="t">&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"># save table</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">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="t171" href="#t171">171</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="t172" href="#t172">172</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="t173" href="#t173">173</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="t174" href="#t174">174</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="t175" href="#t175">175</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="t176" href="#t176">176</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="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="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="t178" href="#t178">178</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="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">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"># Copy files to host</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">copy_to_host</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"># Remove temporary file(s)</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">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="t187" href="#t187">187</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="str">""</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="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">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="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="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="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">return</span> <span class="num">0</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="run"><span class="n"><a id="t195" href="#t195">195</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="t196" href="#t196">196</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="t197" href="#t197">197</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="t198" href="#t198">198</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="t199" href="#t199">199</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="t200" href="#t200">200</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="t201" href="#t201">201</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="t202" href="#t202">202</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="t203" href="#t203">203</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="t204" href="#t204">204</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="t205" href="#t205">205</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="t206" href="#t206">206</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="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">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="t209" href="#t209">209</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="t210" href="#t210">210</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="t211" href="#t211">211</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="t212" href="#t212">212</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="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">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="t215" href="#t215">215</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="t216" href="#t216">216</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="t217" href="#t217">217</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="t218" href="#t218">218</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="t219" href="#t219">219</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="t220" href="#t220">220</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="t221" href="#t221">221</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="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="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="t224" href="#t224">224</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="t225" href="#t225">225</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="t226" href="#t226">226</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="t227" href="#t227">227</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="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">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="t230" href="#t230">230</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="t231" href="#t231">231</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="t232" href="#t232">232</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="t233" href="#t233">233</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="t234" href="#t234">234</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"># fix angle range so its not negative</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">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="t134" href="#t134">134</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="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"># calculate difference between epsil and zeta parameters</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">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><span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span><span class="op">,</span> <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><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> <span class="nam">Npop</span><span class="op">,</span> <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="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><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> <span class="nam">Epop</span><span class="op">,</span> <span class="nam">bottom</span><span class="op">=</span><span class="nam">Npop</span><span class="op">,</span> <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="t144" href="#t144">144</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">bar</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> <span class="nam">Spop</span><span class="op">,</span> <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">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="t145" href="#t145">145</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">bar</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> <span class="nam">Wpop</span><span class="op">,</span> <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> <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="t146" href="#t146">146</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="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><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> <span class="op">[</span><span class="num">100</span><span class="op">]</span><span class="op">,</span> <span class="nam">color</span><span class="op">=</span><span class="str">"white"</span><span class="op">,</span> <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="t148" href="#t148">148</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="t149" href="#t149">149</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="t150" href="#t150">150</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="t151" href="#t151">151</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="t152" href="#t152">152</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="t153" href="#t153">153</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="t154" href="#t154">154</a></span><span class="t">        <span class="nam">fig</span><span class="op">.</span><span class="nam">savefig</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">stage_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="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="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"># save table</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">populations</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="t158" href="#t158">158</a></span><span class="t">            <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">"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="t160" href="#t160">160</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="t161" href="#t161">161</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="t162" href="#t162">162</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="t163" href="#t163">163</a></span><span class="t">                <span class="str">"South"</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="t164" href="#t164">164</a></span><span class="t">            <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>&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">populations</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">stage_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="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="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">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="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"># Copy files to host</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">self</span><span class="op">.</span><span class="nam">copy_to_host</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"># Remove temporary file(s)</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">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><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="str">""</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="t175" href="#t175">175</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="t176" href="#t176">176</a></span><span class="t">&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">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="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="key">return</span> <span class="num">0</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="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="t182" href="#t182">182</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="t183" href="#t183">183</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="t184" href="#t184">184</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="t185" href="#t185">185</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="t186" href="#t186">186</a></span><span class="t">        <span class="nam">labelsW</span> <span class="op">=</span> <span class="op">[</span><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="t187" href="#t187">187</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="t188" href="#t188">188</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="t189" href="#t189">189</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="t190" href="#t190">190</a></span><span class="t">        <span class="nam">labelsC</span> <span class="op">=</span> <span class="op">[</span><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="t191" href="#t191">191</a></span><span class="t">&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">if</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="t193" href="#t193">193</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="t194" href="#t194">194</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="t195" href="#t195">195</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="t196" href="#t196">196</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="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="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="t199" href="#t199">199</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="t200" href="#t200">200</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><span class="nam">phaseW</span><span class="op">,</span> <span class="nam">separator_df</span><span class="op">,</span> <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> <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="t201" href="#t201">201</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="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">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="t204" href="#t204">204</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="t205" href="#t205">205</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="t206" href="#t206">206</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="t207" href="#t207">207</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="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">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="t210" href="#t210">210</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="t211" href="#t211">211</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="t212" href="#t212">212</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="t213" href="#t213">213</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="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">&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">puckering</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_phaseC_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="t218" href="#t218">218</a></span><span class="t">    <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="t219" href="#t219">219</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>&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">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="t221" href="#t221">221</a></span><span class="t">    <span class="nam">properties</span><span class="op">:</span> <span class="nam">Optional</span><span class="op">[</span><span class="nam">dict</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="pln"><span class="n"><a id="t222" href="#t222">222</a></span><span class="t">    <span class="op">**</span><span class="nam">kwargs</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="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:`Puckering &lt;dna.backbone.puckering.Puckering>` 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.backbone.puckering.Puckering.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">Puckering</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">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="t229" href="#t229">229</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="t230" href="#t230">230</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="t231" href="#t231">231</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="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">        <span class="op">**</span><span class="nam">kwargs</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="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="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">puckering</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">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="t238" href="#t238">238</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="t239" href="#t239">239</a></span><span class="t">        <span class="nam">properties</span><span class="op">:</span> <span class="nam">Optional</span><span class="op">[</span><span class="nam">dict</span><span class="op">]</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:`Puckering &lt;dna.backbone.puckering.Puckering>` 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.backbone.puckering.Puckering.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">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">input_phaseC_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_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="t246" href="#t246">246</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="t247" href="#t247">247</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="t248" href="#t248">248</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="t249" href="#t249">249</a></span><span class="t">&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">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="t252" href="#t252">252</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="t253" href="#t253">253</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="t254" href="#t254">254</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="t255" href="#t255">255</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="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_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="t259" href="#t259">259</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="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">'--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="t261" href="#t261">261</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="t262" href="#t262">262</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="t263" href="#t263">263</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="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">'--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="t265" href="#t265">265</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="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">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="t238" href="#t238">238</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="t239" href="#t239">239</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>&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">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="t241" href="#t241">241</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="pln"><span class="n"><a id="t242" href="#t242">242</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="t243" href="#t243">243</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="t244" href="#t244">244</a></span><span class="t">&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">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="t246" href="#t246">246</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>&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">"--input_phaseC_path"</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">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="t249" href="#t249">249</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="pln"><span class="n"><a id="t250" href="#t250">250</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="t251" href="#t251">251</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>&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">"--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">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="t254" href="#t254">254</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="pln"><span class="n"><a id="t255" href="#t255">255</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="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>&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="str">"--output_csv_path"</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">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">"Path to output csv file. Accepted formats: csv."</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="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">required_args</span><span class="op">.</span><span class="nam">add_argument</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="str">"--output_jpg_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">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="t264" href="#t264">264</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="t265" href="#t265">265</a></span><span class="t">    <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>
@@ -355,11 +355,12 @@ <h2>
     <p class="pln"><span class="n"><a id="t273" href="#t273">273</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="t274" href="#t274">274</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="t275" href="#t275">275</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="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="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">    <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>
 </main>
 <footer>
     <div class="content">
@@ -368,8 +369,8 @@ <h2>
             <a class="nav" href="index.html">&Hat; index</a> &nbsp; &nbsp;
             <a class="nav" href="z_74fa14c6d0e940a4___init___py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
-            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.4">coverage.py v7.6.4</a>,
-            created at 2024-11-04 11:05 +0000
+            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
+            created at 2024-11-15 12:07 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_3afbcd666ed82c91___init___py.html b/coverage/z_3afbcd666ed82c91___init___py.html
index 2885186..f71e059 100644
--- a/coverage/z_3afbcd666ed82c91___init___py.html
+++ b/coverage/z_3afbcd666ed82c91___init___py.html
@@ -64,8 +64,8 @@ <h2>
             <a id="indexLink" class="nav" href="index.html">&Hat; index</a> &nbsp; &nbsp;
             <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/7.6.4">coverage.py v7.6.4</a>,
-            created at 2024-11-04 11:05 +0000
+            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
+            created at 2024-11-15 12:07 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -94,8 +94,8 @@ <h2>
             <a class="nav" href="index.html">&Hat; index</a> &nbsp; &nbsp;
             <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/7.6.4">coverage.py v7.6.4</a>,
-            created at 2024-11-04 11:05 +0000
+            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
+            created at 2024-11-15 12:07 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_3afbcd666ed82c91_dna_averages_py.html b/coverage/z_3afbcd666ed82c91_dna_averages_py.html
index 3c207cd..4aa7475 100644
--- a/coverage/z_3afbcd666ed82c91_dna_averages_py.html
+++ b/coverage/z_3afbcd666ed82c91_dna_averages_py.html
@@ -54,9 +54,9 @@ <h1>
             </div>
         </aside>
         <h2>
-            <span class="text">93 statements &nbsp;</span>
-            <button type="button" class="run button_toggle_run" value="run" data-shortcut="r" title="Toggle lines run">68<span class="text"> run</span></button>
-            <button type="button" class="mis show_mis button_toggle_mis" value="mis" data-shortcut="m" title="Toggle lines missing">25<span class="text"> missing</span></button>
+            <span class="text">95 statements &nbsp;</span>
+            <button type="button" class="run button_toggle_run" value="run" data-shortcut="r" title="Toggle lines run">69<span class="text"> run</span></button>
+            <button type="button" class="mis show_mis button_toggle_mis" value="mis" data-shortcut="m" title="Toggle lines missing">26<span class="text"> missing</span></button>
             <button type="button" class="exc show_exc button_toggle_exc" value="exc" data-shortcut="x" title="Toggle lines excluded">0<span class="text"> excluded</span></button>
         </h2>
         <p class="text">
@@ -64,8 +64,8 @@ <h2>
             <a id="indexLink" class="nav" href="index.html">&Hat; index</a> &nbsp; &nbsp;
             <a id="nextFileLink" class="nav" href="z_3afbcd666ed82c91_dna_bimodality_py.html">&#xbb; next</a>
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-            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.4">coverage.py v7.6.4</a>,
-            created at 2024-11-04 11:05 +0000
+            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
+            created at 2024-11-15 12:07 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -83,259 +83,283 @@ <h2>
     <p class="pln"><span class="n"><a id="t1" href="#t1">1</a></span><span class="t"><span class="com">#!/usr/bin/env python3</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t2" href="#t2">2</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t3" href="#t3">3</a></span><span class="t"><span class="str">"""Module containing the HelParAverages class and the command line interface."""</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t4" href="#t4">4</a></span><span class="t"><span class="key">import</span> <span class="nam">argparse</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t5" href="#t5">5</a></span><span class="t"><span class="key">from</span> <span class="nam">typing</span> <span class="key">import</span> <span class="nam">Optional</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t4" href="#t4">4</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t5" href="#t5">5</a></span><span class="t"><span class="key">import</span> <span class="nam">argparse</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t6" href="#t6">6</a></span><span class="t"><span class="key">from</span> <span class="nam">pathlib</span> <span class="key">import</span> <span class="nam">Path</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t7" href="#t7">7</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t8" href="#t8">8</a></span><span class="t"><span class="key">import</span> <span class="nam">matplotlib</span><span class="op">.</span><span class="nam">pyplot</span> <span class="key">as</span> <span class="nam">plt</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t9" href="#t9">9</a></span><span class="t"><span class="key">import</span> <span class="nam">pandas</span> <span class="key">as</span> <span class="nam">pd</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t10" href="#t10">10</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_dna</span><span class="op">.</span><span class="nam">utils</span> <span class="key">import</span> <span class="nam">constants</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t11" href="#t11">11</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_dna</span><span class="op">.</span><span class="nam">utils</span><span class="op">.</span><span class="nam">loader</span> <span class="key">import</span> <span class="nam">read_series</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t7" href="#t7">7</a></span><span class="t"><span class="key">from</span> <span class="nam">typing</span> <span class="key">import</span> <span class="nam">Optional</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t8" href="#t8">8</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t9" href="#t9">9</a></span><span class="t"><span class="key">import</span> <span class="nam">matplotlib</span><span class="op">.</span><span class="nam">pyplot</span> <span class="key">as</span> <span class="nam">plt</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t10" href="#t10">10</a></span><span class="t"><span class="key">import</span> <span class="nam">pandas</span> <span class="key">as</span> <span class="nam">pd</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t11" href="#t11">11</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_common</span><span class="op">.</span><span class="nam">configuration</span> <span class="key">import</span> <span class="nam">settings</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t12" href="#t12">12</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_common</span><span class="op">.</span><span class="nam">generic</span><span class="op">.</span><span class="nam">biobb_object</span> <span class="key">import</span> <span class="nam">BiobbObject</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t13" href="#t13">13</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_common</span><span class="op">.</span><span class="nam">tools</span><span class="op">.</span><span class="nam">file_utils</span> <span class="key">import</span> <span class="nam">launchlogger</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t14" href="#t14">14</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_common</span><span class="op">.</span><span class="nam">configuration</span> <span class="key">import</span> <span class="nam">settings</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t15" href="#t15">15</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t16" href="#t16">16</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t17" href="#t17">17</a></span><span class="t"><span class="key">class</span> <span class="nam">HelParAverages</span><span class="op">(</span><span class="nam">BiobbObject</span><span class="op">)</span><span class="op">:</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">"""</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 HelParAverages</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">    | 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="t21" href="#t21">21</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="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">            * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory.</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="t14" href="#t14">14</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t15" href="#t15">15</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_dna</span><span class="op">.</span><span class="nam">utils</span> <span class="key">import</span> <span class="nam">constants</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t16" href="#t16">16</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_dna</span><span class="op">.</span><span class="nam">utils</span><span class="op">.</span><span class="nam">common</span> <span class="key">import</span> <span class="nam">_from_string_to_list</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t17" href="#t17">17</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_dna</span><span class="op">.</span><span class="nam">utils</span><span class="op">.</span><span class="nam">loader</span> <span class="key">import</span> <span class="nam">read_series</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">&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="run"><span class="n"><a id="t20" href="#t20">20</a></span><span class="t"><span class="key">class</span> <span class="nam">HelParAverages</span><span class="op">(</span><span class="nam">BiobbObject</span><span class="op">)</span><span class="op">:</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">"""</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 HelParAverages</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">    | 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="t24" href="#t24">24</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="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_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="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/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="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/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="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">            * **helpar_name** (*str*) - (Optional) 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">            * **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="t34" href="#t34">34</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="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"><span class="str">            * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory.</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">    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.dna.dna_averages import dna_averages</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">                'helpar_name': 'twist',</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">                'seqpos': [1,2],</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">                'sequence': 'GCAT'</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">            dna_averages(</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_ser_path='/path/to/twist.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">&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>&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_ser_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>&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_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>&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="op">**</span><span class="nam">kwargs</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="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_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="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><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><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">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="t91" href="#t91">91</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="t92" href="#t92">92</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><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="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="nam">int</span><span class="op">(</span><span class="nam">elem</span><span class="op">)</span> <span class="key">for</span> <span class="nam">elem</span> <span class="key">in</span> <span class="nam">_from_string_to_list</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><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="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">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="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">stage_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="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:`HelParAverages &lt;dna.averages.HelParAverages>` 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"># get helical parameter from filename if not specified</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">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="t117" href="#t117">117</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="t118" href="#t118">118</a></span><span class="t">                <span class="nam">ser_name</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">stage_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="t119" href="#t119">119</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="t120" href="#t120">120</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="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="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="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">"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="t124" href="#t124">124</a></span><span class="t">                    <span class="str">"so it must be specified!"</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="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="mis show_mis"><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>&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="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 base length and 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="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="t135" href="#t135">135</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="t136" href="#t136">136</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="t137" href="#t137">137</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="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">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="t139" href="#t139">139</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="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="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">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="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">stage_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="mis show_mis"><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="mis show_mis"><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="mis show_mis"><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+1+self.baselen]}"</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="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="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="run"><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="run"><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">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"># rename duplicated subunits</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="key">while</span> <span class="nam">any</span><span class="op">(</span><span class="nam">pd</span><span class="op">.</span><span class="nam">Index</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">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="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="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">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="t164" href="#t164">164</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="t165" href="#t165">165</a></span><span class="t">                <span class="key">in</span> <span class="nam">zip</span><span class="op">(</span><span class="nam">pd</span><span class="op">.</span><span class="nam">Index</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">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="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"># write output files for all selected bases</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">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="t169" href="#t169">169</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="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"># save plot</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">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="t173" href="#t173">173</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="t174" href="#t174">174</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="t175" href="#t175">175</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="t176" href="#t176">176</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="t177" href="#t177">177</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="t178" href="#t178">178</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="t179" href="#t179">179</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="t180" href="#t180">180</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="t181" href="#t181">181</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="t182" href="#t182">182</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="t183" href="#t183">183</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="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">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="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>&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">"Base Pair "</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">f"{'Step' if self.baselen==1 else ''} "</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"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="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">stage_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="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"># save table</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">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="t195" href="#t195">195</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="t196" href="#t196">196</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="t197" href="#t197">197</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="t198" href="#t198">198</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="t199" href="#t199">199</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="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">            <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="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">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="t203" href="#t203">203</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">        <span class="com"># Copy files to host</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">self</span><span class="op">.</span><span class="nam">copy_to_host</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">&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="com"># Remove temporary file(s)</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">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="t209" href="#t209">209</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="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="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">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="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">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="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">return</span> <span class="num">0</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="pln"><span class="n"><a id="t143" href="#t143">143</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="t144" href="#t144">144</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="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="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="t146" href="#t146">146</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="t147" href="#t147">147</a></span><span class="t">                    <span class="str">f"seqpos values must be between 1 and {len(self.sequence) - 2}"</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="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="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="t150" href="#t150">150</a></span><span class="t">                <span class="key">raise</span> <span class="nam">ValueError</span><span class="op">(</span><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="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">self</span><span class="op">.</span><span class="nam">seqpos</span> <span class="op">=</span> <span class="key">None</span>  <span class="com"># type: ignore</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"># read input .ser file</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">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="t156" href="#t156">156</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="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">usecols</span><span class="op">=</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</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="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">if</span> <span class="key">not</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="t159" href="#t159">159</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="t160" href="#t160">160</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="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><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="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">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>&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>&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="key">else</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">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="t168" href="#t168">168</a></span><span class="t">            <span class="nam">xlabels</span> <span class="op">=</span> <span class="op">[</span><span class="str">f"{sequence[i:i+1+self.baselen]}"</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="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"># rename duplicated subunits</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">while</span> <span class="nam">any</span><span class="op">(</span><span class="nam">pd</span><span class="op">.</span><span class="nam">Index</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">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="t172" href="#t172">172</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="t173" href="#t173">173</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="t174" href="#t174">174</a></span><span class="t">                <span class="key">for</span> <span class="nam">duplicated</span><span class="op">,</span> <span class="nam">name</span> <span class="key">in</span> <span class="nam">zip</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">pd</span><span class="op">.</span><span class="nam">Index</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">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>&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>&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>&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"># write output files for all selected bases</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">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="t181" href="#t181">181</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="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 plot</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">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="t185" href="#t185">185</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="t186" href="#t186">186</a></span><span class="t">            <span class="nam">means</span><span class="op">.</span><span class="nam">index</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> <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> <span class="nam">marker</span><span class="op">=</span><span class="str">"o"</span><span class="op">,</span> <span class="nam">capsize</span><span class="op">=</span><span class="num">5</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="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_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="t189" href="#t189">189</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="t190" href="#t190">190</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="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="t191" href="#t191">191</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="t192" href="#t192">192</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="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 ''} "</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="str">f"Helical Parameter: {self.helpar_name.capitalize()}"</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>&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">fig</span><span class="op">.</span><span class="nam">savefig</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">stage_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="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>&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="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">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="t203" href="#t203">203</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="t204" href="#t204">204</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>&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="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="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">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">stage_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="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">&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">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="t210" href="#t210">210</a></span><span class="t">&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="com"># Copy files to host</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">self</span><span class="op">.</span><span class="nam">copy_to_host</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><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="str">""</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="t216" href="#t216">216</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="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">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="t219" href="#t219">219</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="t220" href="#t220">220</a></span><span class="t">        <span class="nam">properties</span><span class="op">:</span> <span class="nam">Optional</span><span class="op">[</span><span class="nam">dict</span><span class="op">]</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="t221" href="#t221">221</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="t222" href="#t222">222</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="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="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="t225" href="#t225">225</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="t226" href="#t226">226</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="t227" href="#t227">227</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="t228" href="#t228">228</a></span><span class="t">&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">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="t231" href="#t231">231</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="t232" href="#t232">232</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="t233" href="#t233">233</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="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">'--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="t235" href="#t235">235</a></span><span class="t">&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">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="t237" href="#t237">237</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="t238" href="#t238">238</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="t239" href="#t239">239</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="t240" href="#t240">240</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="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">'--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="t242" href="#t242">242</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="t243" href="#t243">243</a></span><span class="t">&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">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="t245" href="#t245">245</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="t246" href="#t246">246</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="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">dna_averages</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_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="t250" href="#t250">250</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="t251" href="#t251">251</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="t252" href="#t252">252</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="t253" href="#t253">253</a></span><span class="t">&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="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="t256" href="#t256">256</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="run"><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">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="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">return</span> <span class="num">0</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="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">dna_averages</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">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="t225" href="#t225">225</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>&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">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="t227" href="#t227">227</a></span><span class="t">    <span class="nam">properties</span><span class="op">:</span> <span class="nam">Optional</span><span class="op">[</span><span class="nam">dict</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="pln"><span class="n"><a id="t228" href="#t228">228</a></span><span class="t">    <span class="op">**</span><span class="nam">kwargs</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="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="t230" href="#t230">230</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="t231" href="#t231">231</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="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">return</span> <span class="nam">HelParAverages</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">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">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">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">        <span class="op">**</span><span class="nam">kwargs</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="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="t240" href="#t240">240</a></span><span class="t">&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">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="t243" href="#t243">243</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="t244" href="#t244">244</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>&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">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="t246" href="#t246">246</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="pln"><span class="n"><a id="t247" href="#t247">247</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="t248" href="#t248">248</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="t249" href="#t249">249</a></span><span class="t">&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">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="t251" href="#t251">251</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>&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">"--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">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="t254" href="#t254">254</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="pln"><span class="n"><a id="t255" href="#t255">255</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="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>&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="str">"--output_csv_path"</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">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">"Path to output csv file. Accepted formats: csv."</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="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">required_args</span><span class="op">.</span><span class="nam">add_argument</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="str">"--output_jpg_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">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="t264" href="#t264">264</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="t265" href="#t265">265</a></span><span class="t">    <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">dna_averages</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_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="t273" href="#t273">273</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="t274" href="#t274">274</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="t275" href="#t275">275</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="t276" href="#t276">276</a></span><span class="t">    <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="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>
 </main>
 <footer>
     <div class="content">
@@ -344,8 +368,8 @@ <h2>
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             <a class="nav" href="z_3afbcd666ed82c91_dna_bimodality_py.html">&#xbb; next</a>
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-            created at 2024-11-04 11:05 +0000
+            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
+            created at 2024-11-15 12:07 +0000
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index d3a5f78..83dc1da 100644
--- a/coverage/z_3afbcd666ed82c91_dna_bimodality_py.html
+++ b/coverage/z_3afbcd666ed82c91_dna_bimodality_py.html
@@ -64,8 +64,8 @@ <h2>
             <a id="indexLink" class="nav" href="index.html">&Hat; index</a> &nbsp; &nbsp;
             <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/7.6.4">coverage.py v7.6.4</a>,
-            created at 2024-11-04 11:05 +0000
+            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
+            created at 2024-11-15 12:07 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -425,8 +425,8 @@ <h2>
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             <a class="nav" href="z_3afbcd666ed82c91_dna_timeseries_py.html">&#xbb; next</a>
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-            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.4">coverage.py v7.6.4</a>,
-            created at 2024-11-04 11:05 +0000
+            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
+            created at 2024-11-15 12:07 +0000
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 </footer>
diff --git a/coverage/z_3afbcd666ed82c91_dna_timeseries_py.html b/coverage/z_3afbcd666ed82c91_dna_timeseries_py.html
index 184e4b2..a21951a 100644
--- a/coverage/z_3afbcd666ed82c91_dna_timeseries_py.html
+++ b/coverage/z_3afbcd666ed82c91_dna_timeseries_py.html
@@ -54,8 +54,8 @@ <h1>
             </div>
         </aside>
         <h2>
-            <span class="text">130 statements &nbsp;</span>
-            <button type="button" class="run button_toggle_run" value="run" data-shortcut="r" title="Toggle lines run">99<span class="text"> run</span></button>
+            <span class="text">131 statements &nbsp;</span>
+            <button type="button" class="run button_toggle_run" value="run" data-shortcut="r" title="Toggle lines run">100<span class="text"> run</span></button>
             <button type="button" class="mis show_mis button_toggle_mis" value="mis" data-shortcut="m" title="Toggle lines missing">31<span class="text"> missing</span></button>
             <button type="button" class="exc show_exc button_toggle_exc" value="exc" data-shortcut="x" title="Toggle lines excluded">0<span class="text"> excluded</span></button>
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@@ -64,8 +64,8 @@ <h2>
             <a id="indexLink" class="nav" href="index.html">&Hat; index</a> &nbsp; &nbsp;
             <a id="nextFileLink" class="nav" href="z_3afbcd666ed82c91_dna_timeseries_unzip_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
-            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.4">coverage.py v7.6.4</a>,
-            created at 2024-11-04 11:05 +0000
+            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
+            created at 2024-11-15 12:07 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -83,315 +83,338 @@ <h2>
     <p class="pln"><span class="n"><a id="t1" href="#t1">1</a></span><span class="t"><span class="com">#!/usr/bin/env python3</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t2" href="#t2">2</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t3" href="#t3">3</a></span><span class="t"><span class="str">"""Module containing the HelParTimeSeries class and the command line interface."""</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t4" href="#t4">4</a></span><span class="t"><span class="key">import</span> <span class="nam">argparse</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t5" href="#t5">5</a></span><span class="t"><span class="key">from</span> <span class="nam">typing</span> <span class="key">import</span> <span class="nam">Optional</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t6" href="#t6">6</a></span><span class="t"><span class="key">import</span> <span class="nam">zipfile</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t7" href="#t7">7</a></span><span class="t"><span class="key">import</span> <span class="nam">re</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t4" href="#t4">4</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t5" href="#t5">5</a></span><span class="t"><span class="key">import</span> <span class="nam">argparse</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t6" href="#t6">6</a></span><span class="t"><span class="key">import</span> <span class="nam">re</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t7" href="#t7">7</a></span><span class="t"><span class="key">import</span> <span class="nam">zipfile</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t8" href="#t8">8</a></span><span class="t"><span class="key">from</span> <span class="nam">pathlib</span> <span class="key">import</span> <span class="nam">Path</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t9" href="#t9">9</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t10" href="#t10">10</a></span><span class="t"><span class="key">import</span> <span class="nam">pandas</span> <span class="key">as</span> <span class="nam">pd</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t9" href="#t9">9</a></span><span class="t"><span class="key">from</span> <span class="nam">typing</span> <span class="key">import</span> <span class="nam">Optional</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t10" href="#t10">10</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t11" href="#t11">11</a></span><span class="t"><span class="key">import</span> <span class="nam">matplotlib</span><span class="op">.</span><span class="nam">pyplot</span> <span class="key">as</span> <span class="nam">plt</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t12" href="#t12">12</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_dna</span><span class="op">.</span><span class="nam">utils</span> <span class="key">import</span> <span class="nam">constants</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t13" href="#t13">13</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_dna</span><span class="op">.</span><span class="nam">utils</span><span class="op">.</span><span class="nam">loader</span> <span class="key">import</span> <span class="nam">read_series</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t12" href="#t12">12</a></span><span class="t"><span class="key">import</span> <span class="nam">pandas</span> <span class="key">as</span> <span class="nam">pd</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t13" href="#t13">13</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_common</span><span class="op">.</span><span class="nam">configuration</span> <span class="key">import</span> <span class="nam">settings</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t14" href="#t14">14</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_common</span><span class="op">.</span><span class="nam">generic</span><span class="op">.</span><span class="nam">biobb_object</span> <span class="key">import</span> <span class="nam">BiobbObject</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t15" href="#t15">15</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_common</span><span class="op">.</span><span class="nam">configuration</span> <span class="key">import</span> <span class="nam">settings</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t16" href="#t16">16</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_common</span><span class="op">.</span><span class="nam">tools</span> <span class="key">import</span> <span class="nam">file_utils</span> <span class="key">as</span> <span class="nam">fu</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t17" href="#t17">17</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_common</span><span class="op">.</span><span class="nam">tools</span><span class="op">.</span><span class="nam">file_utils</span> <span class="key">import</span> <span class="nam">launchlogger</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">&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="run"><span class="n"><a id="t20" href="#t20">20</a></span><span class="t"><span class="key">class</span> <span class="nam">HelParTimeSeries</span><span class="op">(</span><span class="nam">BiobbObject</span><span class="op">)</span><span class="op">:</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">"""</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 HelParTimeSeries</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">    | 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="t24" href="#t24">24</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="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_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="t28" href="#t28">28</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="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 *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">            * **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="t32" href="#t32">32</a></span><span class="t"><span class="str">            * **helpar_name** (*str*) - (None) Helical parameter name. It must match the name of the helical parameter in the .ser input file. Values: majd, majw, mind, minw, inclin, tip, xdisp, ydisp, shear, stretch, stagger, buckle, propel, opening, rise, roll, twist, shift, slide, tilt, alphaC, alphaW, betaC, betaW, gammaC, gammaW, deltaC, deltaW, epsilC, epsilW, zetaC, zetaW, chiC, chiW, phaseC, phaseW.</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">            * **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="t34" href="#t34">34</a></span><span class="t"><span class="str">            * **seqpos** (*list*) - (None) list of sequence positions (columns indices starting by 1) 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="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"><span class="str">            * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory.</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="run"><span class="n"><a id="t15" href="#t15">15</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_common</span><span class="op">.</span><span class="nam">tools</span> <span class="key">import</span> <span class="nam">file_utils</span> <span class="key">as</span> <span class="nam">fu</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t16" href="#t16">16</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_common</span><span class="op">.</span><span class="nam">tools</span><span class="op">.</span><span class="nam">file_utils</span> <span class="key">import</span> <span class="nam">launchlogger</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">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t18" href="#t18">18</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_dna</span><span class="op">.</span><span class="nam">utils</span> <span class="key">import</span> <span class="nam">constants</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t19" href="#t19">19</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_dna</span><span class="op">.</span><span class="nam">utils</span><span class="op">.</span><span class="nam">common</span> <span class="key">import</span> <span class="nam">_from_string_to_list</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t20" href="#t20">20</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_dna</span><span class="op">.</span><span class="nam">utils</span><span class="op">.</span><span class="nam">loader</span> <span class="key">import</span> <span class="nam">read_series</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">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t23" href="#t23">23</a></span><span class="t"><span class="key">class</span> <span class="nam">HelParTimeSeries</span><span class="op">(</span><span class="nam">BiobbObject</span><span class="op">)</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">"""</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 HelParTimeSeries</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">    | 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="t27" href="#t27">27</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="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_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="t31" href="#t31">31</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="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">            * **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="t34" href="#t34">34</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="t35" href="#t35">35</a></span><span class="t"><span class="str">            * **helpar_name** (*str*) - (None) Helical parameter name. It must match the name of the helical parameter in the .ser input file. Values: majd, majw, mind, minw, inclin, tip, xdisp, ydisp, shear, stretch, stagger, buckle, propel, opening, rise, roll, twist, shift, slide, tilt, alphaC, alphaW, betaC, betaW, gammaC, gammaW, deltaC, deltaW, epsilC, epsilW, zetaC, zetaW, chiC, chiW, phaseC, phaseW.</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">            * **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="t37" href="#t37">37</a></span><span class="t"><span class="str">            * **seqpos** (*list*) - (None) list of sequence positions (columns indices starting by 1) 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"><span class="str">            * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory.</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.dna.dna_timeseries import dna_timeseries</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">                'helpar_name': 'twist',</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">                'seqpos': [1,2,3,4,5],</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">                'sequence': 'GCAACGTGCTATGGAAGC',</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_timeseries(</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_ser_path='/path/to/twist.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_zip_path='/path/to/output/file.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">                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_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="t64" href="#t64">64</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="t65" href="#t65">65</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="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"># Call parent class constructor</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">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="t69" href="#t69">69</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="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_timeseries import dna_timeseries</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">                'helpar_name': 'twist',</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">                'seqpos': [1,2,3,4,5],</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">                'sequence': 'GCAACGTGCTATGGAAGC',</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">            }</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">            dna_timeseries(</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_ser_path='/path/to/twist.ser',</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/file.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: 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_ser_path</span><span class="op">,</span> <span class="nam">output_zip_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>&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> <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"># Input/Output files</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">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="t73" href="#t73">73</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="t74" href="#t74">74</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="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_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="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> <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">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="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">10</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="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">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="t89" href="#t89">89</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="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"># get helical parameter from filename if not specified</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">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="t93" href="#t93">93</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="t94" href="#t94">94</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="t95" href="#t95">95</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="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">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="t97" href="#t97">97</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="t98" href="#t98">98</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="t99" href="#t99">99</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="t100" href="#t100">100</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="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">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="t102" href="#t102">102</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="t103" href="#t103">103</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="t104" href="#t104">104</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="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 base length from helical parameter name</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="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="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">0</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="key">else</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">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="pln"><span class="n"><a id="t111" href="#t111">111</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="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">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="t113" href="#t113">113</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="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="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">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="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"># Check the properties</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">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="t119" href="#t119">119</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="t120" href="#t120">120</a></span><span class="t">&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="op">@</span><span class="nam">launchlogger</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">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="t123" href="#t123">123</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="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"># Setup Biobb</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">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="t127" href="#t127">127</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="t128" href="#t128">128</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="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 sequence</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">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="t132" href="#t132">132</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="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 cols with 0 index</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="nam">cols</span> <span class="op">=</span> <span class="op">[</span><span class="nam">i</span><span class="op">-</span><span class="num">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="pln"><span class="n"><a id="t137" href="#t137">137</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="t138" href="#t138">138</a></span><span class="t">            <span class="nam">cols</span> <span class="op">=</span> <span class="nam">list</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">self</span><span class="op">.</span><span class="nam">sequence</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">&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"># sort cols in ascending order</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">cols</span><span class="op">.</span><span class="nam">sort</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="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_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="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><span class="str">"output_zip_path"</span><span class="op">:</span> <span class="nam">output_zip_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="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="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">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="t84" href="#t84">84</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="t85" href="#t85">85</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="t86" href="#t86">86</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><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="t87" href="#t87">87</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="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="nam">int</span><span class="op">(</span><span class="nam">elem</span><span class="op">)</span> <span class="key">for</span> <span class="nam">elem</span> <span class="key">in</span> <span class="nam">_from_string_to_list</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><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="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">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="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"># get helical parameter from filename if not specified</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="run"><span class="n"><a id="t94" href="#t94">94</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="t95" href="#t95">95</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="t96" href="#t96">96</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="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="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>&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="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="t100" href="#t100">100</a></span><span class="t">                    <span class="str">"so it must be specified!"</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="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="key">else</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">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="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 is invalid! "</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">f"Options: {constants.helical_parameters}"</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="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 base length from helical parameter name</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="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="t111" href="#t111">111</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="t112" href="#t112">112</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="t113" href="#t113">113</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="pln"><span class="n"><a id="t114" href="#t114">114</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="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">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="t116" href="#t116">116</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="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="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">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="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"># Check the properties</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">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="t122" href="#t122">122</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="t123" href="#t123">123</a></span><span class="t">&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="op">@</span><span class="nam">launchlogger</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">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="t126" href="#t126">126</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="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"># Setup Biobb</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">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="t130" href="#t130">130</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="t131" href="#t131">131</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="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 sequence</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">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="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="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="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"># calculate cols with 0 index</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">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">cols</span> <span class="op">=</span> <span class="op">[</span><span class="nam">i</span> <span class="op">-</span> <span class="num">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="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="nam">cols</span> <span class="op">=</span> <span class="nam">list</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">self</span><span class="op">.</span><span class="nam">sequence</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">&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"># check seqpos for base pairs</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="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="key">and</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_basepairs</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="key">if</span> <span class="op">(</span><span class="nam">max</span><span class="op">(</span><span class="nam">cols</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">cols</span><span class="op">)</span> <span class="op">&lt;</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="t146" href="#t146">146</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="t147" href="#t147">147</a></span><span class="t">                    <span class="str">f"seqpos values must be between 1 and {len(self.sequence) - 1}"</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="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="pln"><span class="n"><a id="t143" href="#t143">143</a></span><span class="t">        <span class="com"># sort cols in ascending order</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">cols</span><span class="op">.</span><span class="nam">sort</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">&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"># check seqpos for base pairs</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">and</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_basepairs</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="op">(</span><span class="nam">max</span><span class="op">(</span><span class="nam">cols</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">cols</span><span class="op">)</span> <span class="op">&lt;</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="t149" href="#t149">149</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="t150" href="#t150">150</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="t151" href="#t151">151</a></span><span class="t">        <span class="com"># check seqpos for non base pairs</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="key">elif</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="key">and</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">hp_basepairs</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="key">if</span> <span class="op">(</span><span class="nam">max</span><span class="op">(</span><span class="nam">cols</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">1</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">cols</span><span class="op">)</span> <span class="op">&lt;</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="t154" href="#t154">154</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="t155" href="#t155">155</a></span><span class="t">                    <span class="str">f"seqpos values must be between 1 and {len(self.sequence)}"</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="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="pln"><span class="n"><a id="t150" href="#t150">150</a></span><span class="t">                    <span class="str">f"seqpos values must be between 1 and {len(self.sequence) - 1}"</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="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="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="t153" href="#t153">153</a></span><span class="t">                <span class="key">raise</span> <span class="nam">ValueError</span><span class="op">(</span><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="t154" href="#t154">154</a></span><span class="t">        <span class="com"># check seqpos for non base pairs</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="key">elif</span> <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span> <span class="key">and</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">hp_basepairs</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="key">if</span> <span class="op">(</span><span class="nam">max</span><span class="op">(</span><span class="nam">cols</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">1</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">cols</span><span class="op">)</span> <span class="op">&lt;</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="t157" href="#t157">157</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="t158" href="#t158">158</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="t159" href="#t159">159</a></span><span class="t">&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="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_basepairs</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"># remove first and last base pairs from cols if they match 0 and len(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="key">if</span> <span class="nam">min</span><span class="op">(</span><span class="nam">cols</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="mis show_mis"><span class="n"><a id="t163" href="#t163">163</a></span><span class="t">                <span class="nam">cols</span><span class="op">.</span><span class="nam">pop</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="t164" href="#t164">164</a></span><span class="t">            <span class="key">if</span> <span class="nam">max</span><span class="op">(</span><span class="nam">cols</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">1</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t165" href="#t165">165</a></span><span class="t">                <span class="nam">cols</span><span class="op">.</span><span class="nam">pop</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="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"># discard first and last base(pairs) from sequence</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">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><span class="num">1</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"># create indices list</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">indices</span> <span class="op">=</span> <span class="nam">cols</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="t171" href="#t171">171</a></span><span class="t">            <span class="com"># create subunits list from cols</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">subunits</span> <span class="op">=</span> <span class="op">[</span><span class="str">f"{i+1}_{sequence[i-1:i+self.baselen]}"</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">cols</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="com"># clean subunits (leave only basepairs)</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">pattern</span> <span class="op">=</span> <span class="nam">re</span><span class="op">.</span><span class="nam">compile</span><span class="op">(</span><span class="str">r'\d+_[A-Za-z]{2}'</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"># get removed items</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">removed_items</span> <span class="op">=</span> <span class="op">[</span><span class="nam">s</span> <span class="key">for</span> <span class="nam">s</span> <span class="key">in</span> <span class="nam">subunits</span> <span class="key">if</span> <span class="key">not</span> <span class="nam">pattern</span><span class="op">.</span><span class="nam">fullmatch</span><span class="op">(</span><span class="nam">s</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="com"># get indices of removed items (in integer format and starting from 0)</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">removed_numbers</span> <span class="op">=</span> <span class="op">[</span><span class="nam">int</span><span class="op">(</span><span class="nam">match</span><span class="op">.</span><span class="nam">group</span><span class="op">(</span><span class="op">)</span><span class="op">)</span> <span class="key">for</span> <span class="nam">item</span> <span class="key">in</span> <span class="nam">removed_items</span> <span class="key">if</span> <span class="op">(</span><span class="nam">match</span> <span class="op">:=</span> <span class="nam">re</span><span class="op">.</span><span class="nam">match</span><span class="op">(</span><span class="str">r'\d+'</span><span class="op">,</span> <span class="nam">item</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="t179" href="#t179">179</a></span><span class="t">            <span class="nam">removed_numbers</span> <span class="op">=</span> <span class="nam">list</span><span class="op">(</span><span class="nam">map</span><span class="op">(</span><span class="nam">int</span><span class="op">,</span> <span class="nam">removed_numbers</span><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">removed_numbers</span> <span class="op">=</span> <span class="op">[</span><span class="nam">int</span><span class="op">(</span><span class="nam">i</span><span class="op">)</span><span class="op">-</span><span class="num">1</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">removed_numbers</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"># remove non basepairs from subunits and indices</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">subunits</span> <span class="op">=</span> <span class="op">[</span><span class="nam">s</span> <span class="key">for</span> <span class="nam">s</span> <span class="key">in</span> <span class="nam">subunits</span> <span class="key">if</span> <span class="nam">pattern</span><span class="op">.</span><span class="nam">fullmatch</span><span class="op">(</span><span class="nam">s</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">indices</span> <span class="op">=</span> <span class="op">[</span><span class="nam">i</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">indices</span> <span class="key">if</span> <span class="nam">i</span> <span class="key">not</span> <span class="key">in</span> <span class="nam">removed_numbers</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="key">else</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t185" href="#t185">185</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="pln"><span class="n"><a id="t186" href="#t186">186</a></span><span class="t">            <span class="com"># create indices list</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">indices</span> <span class="op">=</span> <span class="nam">cols</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="t188" href="#t188">188</a></span><span class="t">            <span class="com"># trick for getting the index column from the .ser file</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">indices</span><span class="op">.</span><span class="nam">insert</span><span class="op">(</span><span class="num">0</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="t190" href="#t190">190</a></span><span class="t">            <span class="com"># create subunits list from cols</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">subunits</span> <span class="op">=</span> <span class="op">[</span><span class="str">f"{i+1}_{sequence[i:i+1+self.baselen]}"</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">cols</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"># read input .ser file</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">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="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="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="t196" href="#t196">196</a></span><span class="t">            <span class="nam">usecols</span><span class="op">=</span><span class="nam">indices</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"># get columns for selected bases</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">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="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"># 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="t202" href="#t202">202</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="t203" href="#t203">203</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">stage_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="t204" href="#t204">204</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="t205" href="#t205">205</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="t206" href="#t206">206</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="t207" href="#t207">207</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="t208" href="#t208">208</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="t209" href="#t209">209</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="t210" href="#t210">210</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="t211" href="#t211">211</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="t212" href="#t212">212</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="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"># column series</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">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="t216" href="#t216">216</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="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">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="str">""</span><span class="op">)</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="t218" href="#t218">218</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="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">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="str">""</span><span class="op">)</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="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">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="t223" href="#t223">223</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="t224" href="#t224">224</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="t225" href="#t225">225</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="t226" href="#t226">226</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="t227" href="#t227">227</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="t228" href="#t228">228</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="t229" href="#t229">229</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="t230" href="#t230">230</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="t231" href="#t231">231</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="t232" href="#t232">232</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">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="str">""</span><span class="op">)</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="t233" href="#t233">233</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="t234" href="#t234">234</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="t235" href="#t235">235</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">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="str">""</span><span class="op">)</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="t236" href="#t236">236</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="t237" href="#t237">237</a></span><span class="t">&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"># columns histogram</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">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="t240" href="#t240">240</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="t241" href="#t241">241</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="t242" href="#t242">242</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="t243" href="#t243">243</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">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="str">""</span><span class="op">)</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="t244" href="#t244">244</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="t245" href="#t245">245</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="t246" href="#t246">246</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="t247" href="#t247">247</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">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="str">""</span><span class="op">)</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="t248" href="#t248">248</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="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="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="t251" href="#t251">251</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="t252" href="#t252">252</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="t253" href="#t253">253</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">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="str">""</span><span class="op">)</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="t254" href="#t254">254</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="t255" href="#t255">255</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="t256" href="#t256">256</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="t257" href="#t257">257</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">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="str">""</span><span class="op">)</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="t258" href="#t258">258</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="t259" href="#t259">259</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="t260" href="#t260">260</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="t158" href="#t158">158</a></span><span class="t">                    <span class="str">f"seqpos values must be between 1 and {len(self.sequence)}"</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="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="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="t161" href="#t161">161</a></span><span class="t">                <span class="key">raise</span> <span class="nam">ValueError</span><span class="op">(</span><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="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="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_basepairs</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="com"># remove first and last base pairs from cols if they match 0 and len(sequence)</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="key">if</span> <span class="nam">min</span><span class="op">(</span><span class="nam">cols</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="mis show_mis"><span class="n"><a id="t166" href="#t166">166</a></span><span class="t">                <span class="nam">cols</span><span class="op">.</span><span class="nam">pop</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="t167" href="#t167">167</a></span><span class="t">            <span class="key">if</span> <span class="nam">max</span><span class="op">(</span><span class="nam">cols</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">1</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">cols</span><span class="op">.</span><span class="nam">pop</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="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"># discard first and last base(pairs) from sequence</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">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><span class="num">1</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"># create indices list</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">indices</span> <span class="op">=</span> <span class="nam">cols</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="t174" href="#t174">174</a></span><span class="t">            <span class="com"># create subunits list from cols</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">subunits</span> <span class="op">=</span> <span class="op">[</span><span class="str">f"{i+1}_{sequence[i-1:i+self.baselen]}"</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">cols</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"># clean subunits (leave only basepairs)</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">pattern</span> <span class="op">=</span> <span class="nam">re</span><span class="op">.</span><span class="nam">compile</span><span class="op">(</span><span class="str">r"\d+_[A-Za-z]{2}"</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"># get removed items</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">removed_items</span> <span class="op">=</span> <span class="op">[</span><span class="nam">s</span> <span class="key">for</span> <span class="nam">s</span> <span class="key">in</span> <span class="nam">subunits</span> <span class="key">if</span> <span class="key">not</span> <span class="nam">pattern</span><span class="op">.</span><span class="nam">fullmatch</span><span class="op">(</span><span class="nam">s</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="com"># get indices of removed items (in integer format and starting from 0)</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">removed_numbers</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">int</span><span class="op">(</span><span class="nam">match</span><span class="op">.</span><span class="nam">group</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="key">for</span> <span class="nam">item</span> <span class="key">in</span> <span class="nam">removed_items</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="key">if</span> <span class="op">(</span><span class="nam">match</span> <span class="op">:=</span> <span class="nam">re</span><span class="op">.</span><span class="nam">match</span><span class="op">(</span><span class="str">r"\d+"</span><span class="op">,</span> <span class="nam">item</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="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">removed_numbers</span> <span class="op">=</span> <span class="nam">list</span><span class="op">(</span><span class="nam">map</span><span class="op">(</span><span class="nam">int</span><span class="op">,</span> <span class="nam">removed_numbers</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">removed_numbers</span> <span class="op">=</span> <span class="op">[</span><span class="nam">int</span><span class="op">(</span><span class="nam">i</span><span class="op">)</span> <span class="op">-</span> <span class="num">1</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">removed_numbers</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"># remove non basepairs from subunits and indices</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">subunits</span> <span class="op">=</span> <span class="op">[</span><span class="nam">s</span> <span class="key">for</span> <span class="nam">s</span> <span class="key">in</span> <span class="nam">subunits</span> <span class="key">if</span> <span class="nam">pattern</span><span class="op">.</span><span class="nam">fullmatch</span><span class="op">(</span><span class="nam">s</span><span class="op">)</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">indices</span> <span class="op">=</span> <span class="op">[</span><span class="nam">i</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">indices</span> <span class="key">if</span> <span class="nam">i</span> <span class="key">not</span> <span class="key">in</span> <span class="nam">removed_numbers</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="key">else</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">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="pln"><span class="n"><a id="t193" href="#t193">193</a></span><span class="t">            <span class="com"># create indices list</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">indices</span> <span class="op">=</span> <span class="nam">cols</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="t195" href="#t195">195</a></span><span class="t">            <span class="com"># trick for getting the index column from the .ser file</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">indices</span><span class="op">.</span><span class="nam">insert</span><span class="op">(</span><span class="num">0</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="t197" href="#t197">197</a></span><span class="t">            <span class="com"># create subunits list from cols</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="nam">subunits</span> <span class="op">=</span> <span class="op">[</span><span class="str">f"{i+1}_{sequence[i:i+1+self.baselen]}"</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">cols</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"># read input .ser file</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">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="t202" href="#t202">202</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="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">usecols</span><span class="op">=</span><span class="nam">indices</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="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="pln"><span class="n"><a id="t205" href="#t205">205</a></span><span class="t">        <span class="com"># get columns for selected 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">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="t207" href="#t207">207</a></span><span class="t">&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"># 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="t209" href="#t209">209</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><span class="nam">Path</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">stage_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="t210" href="#t210">210</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="t211" href="#t211">211</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="t212" href="#t212">212</a></span><span class="t">            <span class="nam">column_data</span> <span class="op">=</span> <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><span class="op">.</span><span class="nam">unstack</span><span class="op">(</span><span class="op">)</span><span class="op">.</span><span class="nam">dropna</span><span class="op">(</span><span class="op">)</span><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>&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">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="t214" href="#t214">214</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="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"># column series</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">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="t218" href="#t218">218</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="t219" href="#t219">219</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">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="str">""</span><span class="op">)</span><span class="op">)</span> <span class="op">/</span> <span class="str">f"{series_colfn}.csv"</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="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="com"># save table</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">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="t223" href="#t223">223</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">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="str">""</span><span class="op">)</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="t224" href="#t224">224</a></span><span class="t">                <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="t225" href="#t225">225</a></span><span class="t">            <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">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="t228" href="#t228">228</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="t229" href="#t229">229</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="t230" href="#t230">230</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="t231" href="#t231">231</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="t232" href="#t232">232</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="t233" href="#t233">233</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="t234" href="#t234">234</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="t235" href="#t235">235</a></span><span class="t">                <span class="str">f"{'step' if self.baselen==1 else ''} {col})"</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="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">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="t238" href="#t238">238</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">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="str">""</span><span class="op">)</span><span class="op">)</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="pln"><span class="n"><a id="t239" href="#t239">239</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="t240" href="#t240">240</a></span><span class="t">            <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="com"># save plot</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">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="t243" href="#t243">243</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">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="str">""</span><span class="op">)</span><span class="op">)</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="pln"><span class="n"><a id="t244" href="#t244">244</a></span><span class="t">                <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="pln"><span class="n"><a id="t245" href="#t245">245</a></span><span class="t">            <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">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="t247" href="#t247">247</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">            <span class="com"># columns histogram</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">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="t250" href="#t250">250</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="t251" href="#t251">251</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="t252" href="#t252">252</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="t253" href="#t253">253</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">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="str">""</span><span class="op">)</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="t254" href="#t254">254</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="t255" href="#t255">255</a></span><span class="t">            <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="com"># save table</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">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="t258" href="#t258">258</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">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="str">""</span><span class="op">)</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="t259" href="#t259">259</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="t260" href="#t260">260</a></span><span class="t">            <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="pln"><span class="n"><a id="t262" href="#t262">262</a></span><span class="t">        <span class="com"># Copy files to host</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">self</span><span class="op">.</span><span class="nam">copy_to_host</span><span class="op">(</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="pln"><span class="n"><a id="t265" href="#t265">265</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="t266" href="#t266">266</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="t267" href="#t267">267</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="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="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">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="t270" href="#t270">270</a></span><span class="t">&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">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="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">return</span> <span class="num">0</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="t262" href="#t262">262</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="t263" href="#t263">263</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="t264" href="#t264">264</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="t265" href="#t265">265</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">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="str">""</span><span class="op">)</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="t266" href="#t266">266</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="t267" href="#t267">267</a></span><span class="t">            <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="com"># save plot</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">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="t270" href="#t270">270</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">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="str">""</span><span class="op">)</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="t271" href="#t271">271</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="pln"><span class="n"><a id="t272" href="#t272">272</a></span><span class="t">            <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">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="t274" href="#t274">274</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="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">dna_timeseries</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_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="t278" href="#t278">278</a></span><span class="t">        <span class="nam">properties</span><span class="op">:</span> <span class="nam">Optional</span><span class="op">[</span><span class="nam">dict</span><span class="op">]</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="t279" href="#t279">279</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="t280" href="#t280">280</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="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">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="t283" href="#t283">283</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="t284" href="#t284">284</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="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="t276" href="#t276">276</a></span><span class="t">        <span class="com"># Copy files to host</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">self</span><span class="op">.</span><span class="nam">copy_to_host</span><span class="op">(</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="pln"><span class="n"><a id="t279" href="#t279">279</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="t280" href="#t280">280</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><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="str">""</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="t281" href="#t281">281</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="t282" href="#t282">282</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t283" href="#t283">283</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="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">return</span> <span class="num">0</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="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">'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="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>&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">'Configuration file'</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">&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">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="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_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="t297" href="#t297">297</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="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">'--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="t299" href="#t299">299</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="t300" href="#t300">300</a></span><span class="t">&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">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="t302" href="#t302">302</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="t303" href="#t303">303</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="run"><span class="n"><a id="t288" href="#t288">288</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="t289" href="#t289">289</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="t290" href="#t290">290</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="t291" href="#t291">291</a></span><span class="t">    <span class="nam">properties</span><span class="op">:</span> <span class="nam">Optional</span><span class="op">[</span><span class="nam">dict</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="pln"><span class="n"><a id="t292" href="#t292">292</a></span><span class="t">    <span class="op">**</span><span class="nam">kwargs</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="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="t294" href="#t294">294</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="t295" href="#t295">295</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="t296" href="#t296">296</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t297" href="#t297">297</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="t298" href="#t298">298</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="t299" href="#t299">299</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="t300" href="#t300">300</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="t301" href="#t301">301</a></span><span class="t">        <span class="op">**</span><span class="nam">kwargs</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="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="t303" href="#t303">303</a></span><span class="t">&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">dna_timeseries</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">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="t307" href="#t307">307</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="t308" href="#t308">308</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="t309" href="#t309">309</a></span><span class="t">&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="run"><span class="n"><a id="t311" href="#t311">311</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="t312" href="#t312">312</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="run"><span class="n"><a id="t305" href="#t305">305</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="t306" href="#t306">306</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="t307" href="#t307">307</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>&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">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="t309" href="#t309">309</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="pln"><span class="n"><a id="t310" href="#t310">310</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="t311" href="#t311">311</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="t312" href="#t312">312</a></span><span class="t">&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">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="t314" href="#t314">314</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>&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="str">"--input_ser_path"</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">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="t317" href="#t317">317</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="pln"><span class="n"><a id="t318" href="#t318">318</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="t319" href="#t319">319</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>&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="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> <span class="nam">help</span><span class="op">=</span><span class="str">"Path to output directory."</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="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">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="t324" href="#t324">324</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="t325" href="#t325">325</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="t326" href="#t326">326</a></span><span class="t">&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">dna_timeseries</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">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="t329" href="#t329">329</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="t330" href="#t330">330</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="t331" href="#t331">331</a></span><span class="t">    <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="pln"><span class="n"><a id="t333" href="#t333">333</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t334" href="#t334">334</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="t335" href="#t335">335</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">
@@ -400,8 +423,8 @@ <h2>
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-            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.4">coverage.py v7.6.4</a>,
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+            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
+            created at 2024-11-15 12:07 +0000
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diff --git a/coverage/z_3afbcd666ed82c91_dna_timeseries_unzip_py.html b/coverage/z_3afbcd666ed82c91_dna_timeseries_unzip_py.html
index 1eabc4e..7494a49 100644
--- a/coverage/z_3afbcd666ed82c91_dna_timeseries_unzip_py.html
+++ b/coverage/z_3afbcd666ed82c91_dna_timeseries_unzip_py.html
@@ -64,8 +64,8 @@ <h2>
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+            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
+            created at 2024-11-15 12:07 +0000
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@@ -321,8 +321,8 @@ <h2>
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+            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
+            created at 2024-11-15 12:07 +0000
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index d607f9f..b3201a4 100644
--- a/coverage/z_64e03be4370b7ecc___init___py.html
+++ b/coverage/z_64e03be4370b7ecc___init___py.html
@@ -64,8 +64,8 @@ <h2>
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+            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
+            created at 2024-11-15 12:07 +0000
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@@ -97,8 +97,8 @@ <h2>
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+            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
+            created at 2024-11-15 12:07 +0000
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index cc3b58e..4f315fd 100644
--- a/coverage/z_64e03be4370b7ecc_intrabpcorr_py.html
+++ b/coverage/z_64e03be4370b7ecc_intrabpcorr_py.html
@@ -54,8 +54,8 @@ <h1>
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+            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
+            created at 2024-11-15 12:07 +0000
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@@ -83,334 +83,378 @@ <h2>
     <p class="pln"><span class="n"><a id="t1" href="#t1">1</a></span><span class="t"><span class="com">#!/usr/bin/env python3</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t2" href="#t2">2</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t3" href="#t3">3</a></span><span class="t"><span class="str">"""Module containing the IntraBasePairCorrelation class and the command line interface."""</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t4" href="#t4">4</a></span><span class="t"><span class="key">import</span> <span class="nam">argparse</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t5" href="#t5">5</a></span><span class="t"><span class="key">from</span> <span class="nam">typing</span> <span class="key">import</span> <span class="nam">Optional</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t4" href="#t4">4</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t5" href="#t5">5</a></span><span class="t"><span class="key">import</span> <span class="nam">argparse</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t6" href="#t6">6</a></span><span class="t"><span class="key">from</span> <span class="nam">itertools</span> <span class="key">import</span> <span class="nam">product</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t7" href="#t7">7</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t8" href="#t8">8</a></span><span class="t"><span class="key">import</span> <span class="nam">numpy</span> <span class="key">as</span> <span class="nam">np</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t9" href="#t9">9</a></span><span class="t"><span class="key">import</span> <span class="nam">pandas</span> <span class="key">as</span> <span class="nam">pd</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t10" href="#t10">10</a></span><span class="t"><span class="key">import</span> <span class="nam">matplotlib</span> <span class="key">as</span> <span class="nam">mpl</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t11" href="#t11">11</a></span><span class="t"><span class="key">import</span> <span class="nam">matplotlib</span><span class="op">.</span><span class="nam">pyplot</span> <span class="key">as</span> <span class="nam">plt</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t12" href="#t12">12</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t13" href="#t13">13</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_common</span><span class="op">.</span><span class="nam">generic</span><span class="op">.</span><span class="nam">biobb_object</span> <span class="key">import</span> <span class="nam">BiobbObject</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t14" href="#t14">14</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_common</span><span class="op">.</span><span class="nam">configuration</span> <span class="key">import</span> <span class="nam">settings</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t7" href="#t7">7</a></span><span class="t"><span class="key">from</span> <span class="nam">typing</span> <span class="key">import</span> <span class="nam">Optional</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t8" href="#t8">8</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t9" href="#t9">9</a></span><span class="t"><span class="key">import</span> <span class="nam">matplotlib</span> <span class="key">as</span> <span class="nam">mpl</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t10" href="#t10">10</a></span><span class="t"><span class="key">import</span> <span class="nam">matplotlib</span><span class="op">.</span><span class="nam">pyplot</span> <span class="key">as</span> <span class="nam">plt</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t11" href="#t11">11</a></span><span class="t"><span class="key">import</span> <span class="nam">numpy</span> <span class="key">as</span> <span class="nam">np</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t12" href="#t12">12</a></span><span class="t"><span class="key">import</span> <span class="nam">pandas</span> <span class="key">as</span> <span class="nam">pd</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t13" href="#t13">13</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_common</span><span class="op">.</span><span class="nam">configuration</span> <span class="key">import</span> <span class="nam">settings</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t14" href="#t14">14</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_common</span><span class="op">.</span><span class="nam">generic</span><span class="op">.</span><span class="nam">biobb_object</span> <span class="key">import</span> <span class="nam">BiobbObject</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t15" href="#t15">15</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_common</span><span class="op">.</span><span class="nam">tools</span><span class="op">.</span><span class="nam">file_utils</span> <span class="key">import</span> <span class="nam">launchlogger</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t16" href="#t16">16</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_dna</span><span class="op">.</span><span class="nam">utils</span><span class="op">.</span><span class="nam">loader</span> <span class="key">import</span> <span class="nam">read_series</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t16" href="#t16">16</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t17" href="#t17">17</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_dna</span><span class="op">.</span><span class="nam">utils</span> <span class="key">import</span> <span class="nam">constants</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">&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="run"><span class="n"><a id="t20" href="#t20">20</a></span><span class="t"><span class="key">class</span> <span class="nam">IntraBasePairCorrelation</span><span class="op">(</span><span class="nam">BiobbObject</span><span class="op">)</span><span class="op">:</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">"""</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"><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"><span class="str">            * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory.</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.intrabp_correlations.intrabpcorr import intrabpcorr</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t18" href="#t18">18</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_dna</span><span class="op">.</span><span class="nam">utils</span><span class="op">.</span><span class="nam">common</span> <span class="key">import</span> <span class="nam">_from_string_to_list</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t19" href="#t19">19</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_dna</span><span class="op">.</span><span class="nam">utils</span><span class="op">.</span><span class="nam">loader</span> <span class="key">import</span> <span class="nam">read_series</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">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t22" href="#t22">22</a></span><span class="t"><span class="key">class</span> <span class="nam">IntraBasePairCorrelation</span><span class="op">(</span><span class="nam">BiobbObject</span><span class="op">)</span><span class="op">:</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">"""</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">    | biobb_dna IntraBasePairCorrelation</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">    | 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="t26" href="#t26">26</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="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_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="t30" href="#t30">30</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="t31" href="#t31">31</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="t32" href="#t32">32</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="t33" href="#t33">33</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="t34" href="#t34">34</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="t35" href="#t35">35</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="t36" href="#t36">36</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="t37" href="#t37">37</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="t38" href="#t38">38</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="t39" href="#t39">39</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="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">            * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory.</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">    Examples:</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">        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="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">            intrabpcorr(</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_shear='path/to/input/shear.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_stretch='path/to/input/stretch.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_stagger='path/to/input/stagger.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_buckle='path/to/input/buckle.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_propel='path/to/input/propel.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">                input_filename_opening='path/to/input/opening.ser',</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="t47" href="#t47">47</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="t48" href="#t48">48</a></span><span class="t">&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">            intrabpcorr(</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_shear='path/to/input/shear.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_stretch='path/to/input/stretch.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_stagger='path/to/input/stagger.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">                input_filename_buckle='path/to/input/buckle.ser',</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_propel='path/to/input/propel.ser',</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">                input_filename_opening='path/to/input/opening.ser',</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_csv_path='path/to/output/file.csv',</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">                output_jpg_path='path/to/output/plot.jpg',</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">                properties=prop)</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">    Info:</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">        * wrapped_software:</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: In house</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">            * license: Apache-2.0</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">        * ontology:</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">            * name: EDAM</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">            * schema: http://edamontology.org/EDAM.owl</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_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="t69" href="#t69">69</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="t70" href="#t70">70</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="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>&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="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="t73" href="#t73">73</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="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"># Call parent class constructor</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">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="t77" href="#t77">77</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="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"># Input/Output files</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">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="t81" href="#t81">81</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="t82" href="#t82">82</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="t83" href="#t83">83</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="t84" href="#t84">84</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="t85" href="#t85">85</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="t86" href="#t86">86</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="t87" href="#t87">87</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="t88" href="#t88">88</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="t89" href="#t89">89</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="t90" href="#t90">90</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="t91" href="#t91">91</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="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">        <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="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="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">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="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:`HelParCorrelation &lt;intrabp_correlations.intrabpcorr.IntraBasePairCorrelation>` 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"># check sequence</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">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="t114" href="#t114">114</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="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"># check seqpos</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">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="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"># read input</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">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="t124" href="#t124">124</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="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="t125" href="#t125">125</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="t126" href="#t126">126</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="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="t127" href="#t127">127</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="t128" href="#t128">128</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="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="t129" href="#t129">129</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="t130" href="#t130">130</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="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="t131" href="#t131">131</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="t132" href="#t132">132</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="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="t133" href="#t133">133</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="t134" href="#t134">134</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="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="t135" href="#t135">135</a></span><span class="t">&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="pln"><span class="n"><a id="t137" href="#t137">137</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="t138" href="#t138">138</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="t139" href="#t139">139</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="t140" href="#t140">140</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="t141" href="#t141">141</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="t142" href="#t142">142</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="t143" href="#t143">143</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="t144" href="#t144">144</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="t145" href="#t145">145</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="t146" href="#t146">146</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="t147" href="#t147">147</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="t148" href="#t148">148</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="t149" href="#t149">149</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="t150" href="#t150">150</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="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"># rename duplicated subunits</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">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="t154" href="#t154">154</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="t155" href="#t155">155</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="t156" href="#t156">156</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="t157" href="#t157">157</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="t158" href="#t158">158</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="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"># set names to each dataset</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">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="t162" href="#t162">162</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="t163" href="#t163">163</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="t164" href="#t164">164</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="t165" href="#t165">165</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="t166" href="#t166">166</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="t167" href="#t167">167</a></span><span class="t">&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"># 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="t169" href="#t169">169</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="t170" href="#t170">170</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="t171" href="#t171">171</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="t172" href="#t172">172</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="t173" href="#t173">173</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="t174" href="#t174">174</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="t175" href="#t175">175</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="t176" href="#t176">176</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="t177" href="#t177">177</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="t178" href="#t178">178</a></span><span class="t">                <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">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="t180" href="#t180">180</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="t181" href="#t181">181</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="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="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">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="t184" href="#t184">184</a></span><span class="t">                <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="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">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="t187" href="#t187">187</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="t188" href="#t188">188</a></span><span class="t">                <span class="nam">method</span> <span class="op">=</span> <span class="str">"pearson"</span>  <span class="com"># type: ignore</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_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="t190" href="#t190">190</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="t191" href="#t191">191</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="t192" href="#t192">192</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="t193" href="#t193">193</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>  <span class="com"># type: ignore</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"># save csv data</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">to_csv</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">stage_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="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"># create heatmap</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">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="t200" href="#t200">200</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="t201" href="#t201">201</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="t202" href="#t202">202</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>  <span class="com"># type: ignore</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">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="t204" href="#t204">204</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="t205" href="#t205">205</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="t206" href="#t206">206</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="t207" href="#t207">207</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="t208" href="#t208">208</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="t209" href="#t209">209</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="t210" href="#t210">210</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="t211" href="#t211">211</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="t67" href="#t67">67</a></span><span class="t"><span class="str">    """</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="run"><span class="n"><a id="t69" href="#t69">69</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="t70" href="#t70">70</a></span><span class="t">        <span class="nam">self</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">input_filename_shear</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="nam">input_filename_stretch</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="nam">input_filename_stagger</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="nam">input_filename_buckle</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="nam">input_filename_propel</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="nam">input_filename_opening</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="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="nam">output_jpg_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="nam">properties</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="t80" href="#t80">80</a></span><span class="t">        <span class="op">**</span><span class="nam">kwargs</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> <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">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="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"># Call parent class constructor</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">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="t86" href="#t86">86</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="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"># Input/Output files</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">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="t90" href="#t90">90</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="t91" href="#t91">91</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="t92" href="#t92">92</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="t93" href="#t93">93</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="t94" href="#t94">94</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="t95" href="#t95">95</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="t96" href="#t96">96</a></span><span class="t">                <span class="str">"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="t97" href="#t97">97</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="t98" href="#t98">98</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="t99" href="#t99">99</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="t100" href="#t100">100</a></span><span class="t">                <span class="str">"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="t101" href="#t101">101</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="t102" href="#t102">102</a></span><span class="t">        <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="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="t105" href="#t105">105</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="t106" href="#t106">106</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="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">int</span><span class="op">(</span><span class="nam">elem</span><span class="op">)</span> <span class="key">for</span> <span class="nam">elem</span> <span class="key">in</span> <span class="nam">_from_string_to_list</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><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="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 the properties</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">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="t112" href="#t112">112</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="t113" href="#t113">113</a></span><span class="t">&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="op">@</span><span class="nam">launchlogger</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">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="t116" href="#t116">116</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="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"># Setup Biobb</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">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="t120" href="#t120">120</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="t121" href="#t121">121</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="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 sequence</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">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="t125" href="#t125">125</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="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="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="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="t130" href="#t130">130</a></span><span class="t">                <span class="key">raise</span> <span class="nam">ValueError</span><span class="op">(</span><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="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">seqpos</span> <span class="op">=</span> <span class="key">None</span>  <span class="com"># type: ignore</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"># read input</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">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="t136" href="#t136">136</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="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>&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="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">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="t139" href="#t139">139</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="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>&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="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">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="t142" href="#t142">142</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="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>&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="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">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">stage_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>&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="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">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="t148" href="#t148">148</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="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>&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="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">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="t151" href="#t151">151</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="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>&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="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="run"><span class="n"><a id="t154" href="#t154">154</a></span><span class="t">        <span class="key">if</span> <span class="key">not</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="t155" href="#t155">155</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="t156" href="#t156">156</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="t157" href="#t157">157</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="t158" href="#t158">158</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="t159" href="#t159">159</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="t160" href="#t160">160</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="t161" href="#t161">161</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="t162" href="#t162">162</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="t163" href="#t163">163</a></span><span class="t">                <span class="str">f"{i+1}_{self.sequence[i:i+1]}"</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">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>&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>&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_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="t167" href="#t167">167</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>&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="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="key">else</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t170" href="#t170">170</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="t171" href="#t171">171</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="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"># rename duplicated subunits</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">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="t175" href="#t175">175</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="t176" href="#t176">176</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="t177" href="#t177">177</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="t178" href="#t178">178</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="t179" href="#t179">179</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="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"># set names to each dataset</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">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="t183" href="#t183">183</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="t184" href="#t184">184</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="t185" href="#t185">185</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="t186" href="#t186">186</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="t187" href="#t187">187</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="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"># 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="t190" href="#t190">190</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="t191" href="#t191">191</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="t192" href="#t192">192</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="t193" href="#t193">193</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="t194" href="#t194">194</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="t195" href="#t195">195</a></span><span class="t">            <span class="key">if</span> <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>&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">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="t197" href="#t197">197</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="t198" href="#t198">198</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>&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="key">and</span> <span class="nam">ser2</span><span class="op">.</span><span class="nam">name</span> <span class="key">not</span> <span class="key">in</span> <span class="nam">constants</span><span class="op">.</span><span class="nam">hp_angular</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="key">or</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">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>&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="key">and</span> <span class="nam">ser1</span><span class="op">.</span><span class="nam">name</span> <span class="key">not</span> <span class="key">in</span> <span class="nam">constants</span><span class="op">.</span><span class="nam">hp_angular</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="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">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="t205" href="#t205">205</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="t206" href="#t206">206</a></span><span class="t">                <span class="nam">method</span> <span class="op">=</span> <span class="str">"pearson"</span>  <span class="com"># type: ignore</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">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="t208" href="#t208">208</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="t209" href="#t209">209</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="t210" href="#t210">210</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="t211" href="#t211">211</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>  <span class="com"># type: ignore</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="t213" href="#t213">213</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="t214" href="#t214">214</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="t215" href="#t215">215</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="t216" href="#t216">216</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="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="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="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_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="t220" href="#t220">220</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>  <span class="com"># type: ignore</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">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="t223" href="#t223">223</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="t224" href="#t224">224</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="t213" href="#t213">213</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="t214" href="#t214">214</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">stage_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="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"># create heatmap</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">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="t218" href="#t218">218</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">0.8</span><span class="op">,</span> <span class="op">-</span><span class="num">0.6</span><span class="op">,</span> <span class="op">-</span><span class="num">0.4</span><span class="op">,</span> <span class="op">-</span><span class="num">0.2</span><span class="op">,</span> <span class="num">0.2</span><span class="op">,</span> <span class="num">0.4</span><span class="op">,</span> <span class="num">0.6</span><span class="op">,</span> <span class="num">0.8</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="t219" href="#t219">219</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="t220" href="#t220">220</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>  <span class="com"># type: ignore</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">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="t222" href="#t222">222</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><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">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> <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="t223" href="#t223">223</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="t224" href="#t224">224</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">0.8</span><span class="op">,</span> <span class="op">-</span><span class="num">0.6</span><span class="op">,</span> <span class="op">-</span><span class="num">0.4</span><span class="op">,</span> <span class="op">-</span><span class="num">0.2</span><span class="op">,</span> <span class="num">0.2</span><span class="op">,</span> <span class="num">0.4</span><span class="op">,</span> <span class="num">0.6</span><span class="op">,</span> <span class="num">0.8</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="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="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="t227" href="#t227">227</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="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="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="t229" href="#t229">229</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="t230" href="#t230">230</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="t231" href="#t231">231</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">        <span class="com"># Copy files to host</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">self</span><span class="op">.</span><span class="nam">copy_to_host</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="com"># axes</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">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="t228" href="#t228">228</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="t229" href="#t229">229</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="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="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="t232" href="#t232">232</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="t233" href="#t233">233</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>  <span class="com"># type: ignore</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="str">""</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="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="run"><span class="n"><a id="t235" href="#t235">235</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="t236" href="#t236">236</a></span><span class="t">            <span class="str">"Correlation for neighboring basepairs "</span> <span class="str">"and pairs of helical parameters"</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="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="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="t240" href="#t240">240</a></span><span class="t">        <span class="nam">fig</span><span class="op">.</span><span class="nam">savefig</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">stage_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="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="t241" href="#t241">241</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="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="pln"><span class="n"><a id="t243" href="#t243">243</a></span><span class="t">        <span class="com"># Copy files to host</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">copy_to_host</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="pln"><span class="n"><a id="t246" href="#t246">246</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="t247" href="#t247">247</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><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="str">""</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">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="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="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="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="key">return</span> <span class="num">0</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="op">@</span><span class="nam">staticmethod</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">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="t256" href="#t256">256</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="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="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">Optional</span><span class="op">[</span><span class="nam">dict</span><span class="op">]</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="run"><span class="n"><a id="t258" href="#t258">258</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="t259" href="#t259">259</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="t260" href="#t260">260</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="t261" href="#t261">261</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="t262" href="#t262">262</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="t263" href="#t263">263</a></span><span class="t">&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="op">@</span><span class="nam">staticmethod</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">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="t266" href="#t266">266</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="t267" href="#t267">267</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="t268" href="#t268">268</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="t269" href="#t269">269</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="t270" href="#t270">270</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="t271" href="#t271">271</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="t272" href="#t272">272</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="t273" href="#t273">273</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="t274" href="#t274">274</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="t275" href="#t275">275</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="t276" href="#t276">276</a></span><span class="t">&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="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="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="run"><span class="n"><a id="t278" href="#t278">278</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="t279" href="#t279">279</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>&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">str</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">str</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">str</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">str</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">str</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">str</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">str</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">Optional</span><span class="op">[</span><span class="nam">dict</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="pln"><span class="n"><a id="t288" href="#t288">288</a></span><span class="t">    <span class="op">**</span><span class="nam">kwargs</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="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="t290" href="#t290">290</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="t291" href="#t291">291</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="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">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="t294" href="#t294">294</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="t295" href="#t295">295</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="t296" href="#t296">296</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="t297" href="#t297">297</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="t298" href="#t298">298</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="t299" href="#t299">299</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="t300" href="#t300">300</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="t301" href="#t301">301</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="t302" href="#t302">302</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="t303" href="#t303">303</a></span><span class="t">        <span class="op">**</span><span class="nam">kwargs</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="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="t305" href="#t305">305</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t306" href="#t306">306</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t307" href="#t307">307</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="t308" href="#t308">308</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="t309" href="#t309">309</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>&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">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="t311" href="#t311">311</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="pln"><span class="n"><a id="t312" href="#t312">312</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="t313" href="#t313">313</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="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">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="t316" href="#t316">316</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>&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">"--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">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="t319" href="#t319">319</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="pln"><span class="n"><a id="t320" href="#t320">320</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="t321" href="#t321">321</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>&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="str">"--input_filename_stretch"</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">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 ser file for helical parameter stretch. Accepted formats: ser."</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="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">required_args</span><span class="op">.</span><span class="nam">add_argument</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="str">"--input_filename_stagger"</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">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">"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="pln"><span class="n"><a id="t330" href="#t330">330</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="t331" href="#t331">331</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>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t332" href="#t332">332</a></span><span class="t">        <span class="str">"--input_filename_buckle"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t333" href="#t333">333</a></span><span class="t">        <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="t334" href="#t334">334</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="pln"><span class="n"><a id="t335" href="#t335">335</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="t336" href="#t336">336</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>&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="str">"--input_filename_propel"</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">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="t339" href="#t339">339</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="pln"><span class="n"><a id="t340" href="#t340">340</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="t341" href="#t341">341</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>&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="str">"--input_filename_opening"</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">        <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="t344" href="#t344">344</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="pln"><span class="n"><a id="t345" href="#t345">345</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="t346" href="#t346">346</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>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t347" href="#t347">347</a></span><span class="t">        <span class="str">"--output_csv_path"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t348" href="#t348">348</a></span><span class="t">        <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="t349" href="#t349">349</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="t350" href="#t350">350</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="t351" href="#t351">351</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>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t352" href="#t352">352</a></span><span class="t">        <span class="str">"--output_jpg_path"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t353" href="#t353">353</a></span><span class="t">        <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="t354" href="#t354">354</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="t355" href="#t355">355</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t356" href="#t356">356</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t357" href="#t357">357</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="t358" href="#t358">358</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="t359" href="#t359">359</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="t360" href="#t360">360</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t361" href="#t361">361</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="t362" href="#t362">362</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="t363" href="#t363">363</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="t364" href="#t364">364</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="t365" href="#t365">365</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="t366" href="#t366">366</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="t367" href="#t367">367</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="t368" href="#t368">368</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="t369" href="#t369">369</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="t370" href="#t370">370</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="t371" href="#t371">371</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t372" href="#t372">372</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t373" href="#t373">373</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t374" href="#t374">374</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="t375" href="#t375">375</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">
@@ -419,8 +463,8 @@ <h2>
             <a class="nav" href="index.html">&Hat; index</a> &nbsp; &nbsp;
             <a class="nav" href="z_64e03be4370b7ecc_intrahpcorr_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
-            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.4">coverage.py v7.6.4</a>,
-            created at 2024-11-04 11:05 +0000
+            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
+            created at 2024-11-15 12:07 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_64e03be4370b7ecc_intrahpcorr_py.html b/coverage/z_64e03be4370b7ecc_intrahpcorr_py.html
index 62bb88a..6871722 100644
--- a/coverage/z_64e03be4370b7ecc_intrahpcorr_py.html
+++ b/coverage/z_64e03be4370b7ecc_intrahpcorr_py.html
@@ -64,8 +64,8 @@ <h2>
             <a id="indexLink" class="nav" href="index.html">&Hat; index</a> &nbsp; &nbsp;
             <a id="nextFileLink" class="nav" href="z_64e03be4370b7ecc_intraseqcorr_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
-            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.4">coverage.py v7.6.4</a>,
-            created at 2024-11-04 11:05 +0000
+            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
+            created at 2024-11-15 12:07 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -431,8 +431,8 @@ <h2>
             <a class="nav" href="index.html">&Hat; index</a> &nbsp; &nbsp;
             <a class="nav" href="z_64e03be4370b7ecc_intraseqcorr_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
-            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.4">coverage.py v7.6.4</a>,
-            created at 2024-11-04 11:05 +0000
+            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
+            created at 2024-11-15 12:07 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_64e03be4370b7ecc_intraseqcorr_py.html b/coverage/z_64e03be4370b7ecc_intraseqcorr_py.html
index 4ff3a81..489bb80 100644
--- a/coverage/z_64e03be4370b7ecc_intraseqcorr_py.html
+++ b/coverage/z_64e03be4370b7ecc_intraseqcorr_py.html
@@ -2,7 +2,7 @@
 <html lang="en">
 <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8">
-    <title>Coverage for biobb_dna/intrabp_correlations/intraseqcorr.py: 71%</title>
+    <title>Coverage for biobb_dna/intrabp_correlations/intraseqcorr.py: 72%</title>
     <link rel="icon" sizes="32x32" href="favicon_32_cb_58284776.png">
     <link rel="stylesheet" href="style_cb_8e611ae1.css" type="text/css">
     <script src="coverage_html_cb_6fb7b396.js" defer></script>
@@ -12,7 +12,7 @@
     <div class="content">
         <h1>
             <span class="text">Coverage for </span><b>biobb_dna/intrabp_correlations/intraseqcorr.py</b>:
-            <span class="pc_cov">71%</span>
+            <span class="pc_cov">72%</span>
         </h1>
         <aside id="help_panel_wrapper">
             <input id="help_panel_state" type="checkbox">
@@ -54,8 +54,8 @@ <h1>
             </div>
         </aside>
         <h2>
-            <span class="text">94 statements &nbsp;</span>
-            <button type="button" class="run button_toggle_run" value="run" data-shortcut="r" title="Toggle lines run">67<span class="text"> run</span></button>
+            <span class="text">96 statements &nbsp;</span>
+            <button type="button" class="run button_toggle_run" value="run" data-shortcut="r" title="Toggle lines run">69<span class="text"> run</span></button>
             <button type="button" class="mis show_mis button_toggle_mis" value="mis" data-shortcut="m" title="Toggle lines missing">27<span class="text"> missing</span></button>
             <button type="button" class="exc show_exc button_toggle_exc" value="exc" data-shortcut="x" title="Toggle lines excluded">0<span class="text"> excluded</span></button>
         </h2>
@@ -64,8 +64,8 @@ <h2>
             <a id="indexLink" class="nav" href="index.html">&Hat; index</a> &nbsp; &nbsp;
             <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/7.6.4">coverage.py v7.6.4</a>,
-            created at 2024-11-04 11:05 +0000
+            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
+            created at 2024-11-15 12:07 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -83,239 +83,264 @@ <h2>
     <p class="pln"><span class="n"><a id="t1" href="#t1">1</a></span><span class="t"><span class="com">#!/usr/bin/env python3</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t2" href="#t2">2</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t3" href="#t3">3</a></span><span class="t"><span class="str">"""Module containing the IntraSequenceCorrelation class and the command line interface."""</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t4" href="#t4">4</a></span><span class="t"><span class="key">import</span> <span class="nam">argparse</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t5" href="#t5">5</a></span><span class="t"><span class="key">from</span> <span class="nam">typing</span> <span class="key">import</span> <span class="nam">Optional</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t4" href="#t4">4</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t5" href="#t5">5</a></span><span class="t"><span class="key">import</span> <span class="nam">argparse</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t6" href="#t6">6</a></span><span class="t"><span class="key">from</span> <span class="nam">pathlib</span> <span class="key">import</span> <span class="nam">Path</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t7" href="#t7">7</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t8" href="#t8">8</a></span><span class="t"><span class="key">import</span> <span class="nam">numpy</span> <span class="key">as</span> <span class="nam">np</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t7" href="#t7">7</a></span><span class="t"><span class="key">from</span> <span class="nam">typing</span> <span class="key">import</span> <span class="nam">Optional</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t8" href="#t8">8</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t9" href="#t9">9</a></span><span class="t"><span class="key">import</span> <span class="nam">matplotlib</span><span class="op">.</span><span class="nam">pyplot</span> <span class="key">as</span> <span class="nam">plt</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t10" href="#t10">10</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t11" href="#t11">11</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_common</span><span class="op">.</span><span class="nam">generic</span><span class="op">.</span><span class="nam">biobb_object</span> <span class="key">import</span> <span class="nam">BiobbObject</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t12" href="#t12">12</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_common</span><span class="op">.</span><span class="nam">configuration</span> <span class="key">import</span> <span class="nam">settings</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t10" href="#t10">10</a></span><span class="t"><span class="key">import</span> <span class="nam">numpy</span> <span class="key">as</span> <span class="nam">np</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t11" href="#t11">11</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_common</span><span class="op">.</span><span class="nam">configuration</span> <span class="key">import</span> <span class="nam">settings</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t12" href="#t12">12</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_common</span><span class="op">.</span><span class="nam">generic</span><span class="op">.</span><span class="nam">biobb_object</span> <span class="key">import</span> <span class="nam">BiobbObject</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t13" href="#t13">13</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_common</span><span class="op">.</span><span class="nam">tools</span><span class="op">.</span><span class="nam">file_utils</span> <span class="key">import</span> <span class="nam">launchlogger</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t14" href="#t14">14</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_dna</span><span class="op">.</span><span class="nam">utils</span><span class="op">.</span><span class="nam">loader</span> <span class="key">import</span> <span class="nam">read_series</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t14" href="#t14">14</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t15" href="#t15">15</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_dna</span><span class="op">.</span><span class="nam">utils</span> <span class="key">import</span> <span class="nam">constants</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t16" href="#t16">16</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t17" href="#t17">17</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t18" href="#t18">18</a></span><span class="t"><span class="key">class</span> <span class="nam">IntraSequenceCorrelation</span><span class="op">(</span><span class="nam">BiobbObject</span><span class="op">)</span><span class="op">:</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">"""</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"><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"><span class="str">            * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory.</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.intraseqcorr import intraseqcorr</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t16" href="#t16">16</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_dna</span><span class="op">.</span><span class="nam">utils</span><span class="op">.</span><span class="nam">common</span> <span class="key">import</span> <span class="nam">_from_string_to_list</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t17" href="#t17">17</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_dna</span><span class="op">.</span><span class="nam">utils</span><span class="op">.</span><span class="nam">loader</span> <span class="key">import</span> <span class="nam">read_series</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">&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="run"><span class="n"><a id="t20" href="#t20">20</a></span><span class="t"><span class="key">class</span> <span class="nam">IntraSequenceCorrelation</span><span class="op">(</span><span class="nam">BiobbObject</span><span class="op">)</span><span class="op">:</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">"""</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 IntraSequenceCorrelation</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"><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="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_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="t28" href="#t28">28</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="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/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="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 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="t32" href="#t32">32</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="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"><span class="str">            * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory.</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">            intraseqcorr(</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">                input_ser_path='path/to/input/file.ser',</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_csv_path='path/to/output/file.csv',</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">                output_jpg_path='path/to/output/plot.jpg',</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">                properties=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">    Info:</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">        * wrapped_software:</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">            * name: In house</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">            * license: Apache-2.0</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">        * ontology:</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: EDAM</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">            * schema: http://edamontology.org/EDAM.owl</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="pln"><span class="n"><a id="t54" href="#t54">54</a></span><span class="t"><span class="str">    """</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">            from biobb_dna.intrabp_correlations.intraseqcorr import intraseqcorr</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">            intraseqcorr(</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="run"><span class="n"><a id="t56" href="#t56">56</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="t57" href="#t57">57</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="t58" href="#t58">58</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="t59" href="#t59">59</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="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="com"># Call parent class constructor</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">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="t63" href="#t63">63</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="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"># Input/Output files</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">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="t67" href="#t67">67</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="t68" href="#t68">68</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="t69" href="#t69">69</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="t70" href="#t70">70</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="t71" href="#t71">71</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="t72" href="#t72">72</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="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">        <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="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">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="t77" href="#t77">77</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="t78" href="#t78">78</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="t79" href="#t79">79</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="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>&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">input_ser_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>&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_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>&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="op">**</span><span class="nam">kwargs</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="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><span class="str">"input_ser_path"</span><span class="op">:</span> <span class="nam">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="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><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="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="pln"><span class="n"><a id="t81" href="#t81">81</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="t82" href="#t82">82</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="t83" href="#t83">83</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="t84" href="#t84">84</a></span><span class="t">&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="op">@</span><span class="nam">launchlogger</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="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="t87" href="#t87">87</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="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"># Setup Biobb</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">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="t91" href="#t91">91</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="t92" href="#t92">92</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="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"># check sequence</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">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="t96" href="#t96">96</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="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"># get helical parameter from filename if not specified</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">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="t100" href="#t100">100</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="t101" href="#t101">101</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="t102" href="#t102">102</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="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="t103" href="#t103">103</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="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="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>&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">"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="t107" href="#t107">107</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="t108" href="#t108">108</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="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">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="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 is invalid! "</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"Options: {constants.helical_parameters}"</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"># 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="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">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="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="str">"pearson"</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">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="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"># check seqpos</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">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="t122" href="#t122">122</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="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">"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="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 .ser file</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">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="t128" href="#t128">128</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="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="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="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="t131" href="#t131">131</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="t132" href="#t132">132</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="t133" href="#t133">133</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="t134" href="#t134">134</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="t135" href="#t135">135</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="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="mis show_mis"><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><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="t138" href="#t138">138</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="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"># make matrix</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_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="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"># save csv data</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">to_csv</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">stage_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="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 heatmap</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">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="t148" href="#t148">148</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="t149" href="#t149">149</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="t150" href="#t150">150</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="t151" href="#t151">151</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="t152" href="#t152">152</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="t153" href="#t153">153</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="t154" href="#t154">154</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="t155" href="#t155">155</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="t156" href="#t156">156</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="t157" href="#t157">157</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="t158" href="#t158">158</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="t159" href="#t159">159</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="t160" href="#t160">160</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="t161" href="#t161">161</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="t162" href="#t162">162</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="t163" href="#t163">163</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="t164" href="#t164">164</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="t165" href="#t165">165</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="t166" href="#t166">166</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="t167" href="#t167">167</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="t168" href="#t168">168</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="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="t169" href="#t169">169</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="t170" href="#t170">170</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="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"># Copy files to host</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">self</span><span class="op">.</span><span class="nam">copy_to_host</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="str">""</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="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="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">seqpos</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="nam">int</span><span class="op">(</span><span class="nam">elem</span><span class="op">)</span> <span class="key">for</span> <span class="nam">elem</span> <span class="key">in</span> <span class="nam">_from_string_to_list</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><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="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><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"># 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:`HelParCorrelation &lt;intrabp_correlations.intraseqcorr.IntraSequenceCorrelation>` 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"># get helical parameter from filename if not specified</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="run"><span class="n"><a id="t107" href="#t107">107</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="t108" href="#t108">108</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="t109" href="#t109">109</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>&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">in</span> <span class="nam">Path</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">stage_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="pln"><span class="n"><a id="t111" href="#t111">111</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="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>&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="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>&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="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"># 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="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">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="t127" href="#t127">127</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="t128" href="#t128">128</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="t129" href="#t129">129</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>  <span class="com"># type: ignore</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="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><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">        <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">seqpos</span> <span class="op">=</span> <span class="key">None</span>  <span class="com"># type: ignore</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"># read input .ser file</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">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="t140" href="#t140">140</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="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">usecols</span><span class="op">=</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</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="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="key">if</span> <span class="key">not</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="t143" href="#t143">143</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="t144" href="#t144">144</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="t145" href="#t145">145</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="t146" href="#t146">146</a></span><span class="t">            <span class="nam">labels</span> <span class="op">=</span> <span class="op">[</span><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="t147" href="#t147">147</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="t148" href="#t148">148</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="t149" href="#t149">149</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="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"># make matrix</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_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="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 csv data</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_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">stage_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="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"># create heatmap</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">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="t159" href="#t159">159</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="t160" href="#t160">160</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="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">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="t162" href="#t162">162</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="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="nam">j</span> <span class="op">+</span> <span class="num">0.5</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">i</span> <span class="op">+</span> <span class="num">0.5</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"{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="t167" href="#t167">167</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="t168" href="#t168">168</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="t169" href="#t169">169</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="pln"><span class="n"><a id="t170" href="#t170">170</a></span><span class="t">                <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="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="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">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="t173" href="#t173">173</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="t174" href="#t174">174</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="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 Correlation "</span> <span class="str">f"for Helical Parameter '{self.helpar_name}'"</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>&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">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="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><span class="nam">self</span><span class="op">.</span><span class="nam">stage_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="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"># Copy files to host</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">copy_to_host</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="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="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">Optional</span><span class="op">[</span><span class="nam">dict</span><span class="op">]</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="t185" href="#t185">185</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="t186" href="#t186">186</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><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="str">""</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="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="op">@</span><span class="nam">staticmethod</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">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="t195" href="#t195">195</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="t196" href="#t196">196</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="t197" href="#t197">197</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="t198" href="#t198">198</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="t199" href="#t199">199</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="t200" href="#t200">200</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="t201" href="#t201">201</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="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="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="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="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">intraseqcorr</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>&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">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_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="t208" href="#t208">208</a></span><span class="t">    <span class="nam">properties</span><span class="op">:</span> <span class="nam">Optional</span><span class="op">[</span><span class="nam">dict</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="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>&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="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:`HelParCorrelation &lt;intrabp_correlations.intraseqcorr.IntraSequenceCorrelation>` 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;intrabp_correlations.intraseqcorr.IntraSequenceCorrelation.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">IntraSequenceCorrelation</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_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="t216" href="#t216">216</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="t217" href="#t217">217</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="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>&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="nam">kwargs</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="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="t221" href="#t221">221</a></span><span class="t">&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">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="t224" href="#t224">224</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="t225" href="#t225">225</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>&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">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="t227" href="#t227">227</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="pln"><span class="n"><a id="t228" href="#t228">228</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="t229" href="#t229">229</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="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">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="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>&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="str">"--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">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 ser file with inputs. Accepted formats: ser."</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="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">required_args</span><span class="op">.</span><span class="nam">add_argument</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="str">"--output_csv_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">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="t240" href="#t240">240</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="t241" href="#t241">241</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="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>&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="str">"--output_jpg_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">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 plot. 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">    <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">intraseqcorr</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">    <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="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">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="t261" href="#t261">261</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">
@@ -324,8 +349,8 @@ <h2>
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+            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
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+            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
+            created at 2024-11-15 12:07 +0000
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+            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
+            created at 2024-11-15 12:07 +0000
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@@ -64,8 +64,8 @@ <h2>
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+            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
+            created at 2024-11-15 12:07 +0000
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+            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
+            created at 2024-11-15 12:07 +0000
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+++ b/coverage/z_74fa14c6d0e940a4_biobb_canion_py.html
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             &nbsp; &nbsp; &nbsp;
-            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.4">coverage.py v7.6.4</a>,
-            created at 2024-11-04 11:05 +0000
+            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
+            created at 2024-11-15 12:07 +0000
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-            created at 2024-11-04 11:05 +0000
+            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
+            created at 2024-11-15 12:07 +0000
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     </div>
 </footer>
diff --git a/coverage/z_74fa14c6d0e940a4_biobb_curves_py.html b/coverage/z_74fa14c6d0e940a4_biobb_curves_py.html
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-            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.4">coverage.py v7.6.4</a>,
-            created at 2024-11-04 11:05 +0000
+            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
+            created at 2024-11-15 12:07 +0000
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-            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.4">coverage.py v7.6.4</a>,
-            created at 2024-11-04 11:05 +0000
+            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
+            created at 2024-11-15 12:07 +0000
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diff --git a/coverage/z_74fa14c6d0e940a4_canal_unzip_py.html b/coverage/z_74fa14c6d0e940a4_canal_unzip_py.html
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             <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/7.6.4">coverage.py v7.6.4</a>,
-            created at 2024-11-04 11:05 +0000
+            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
+            created at 2024-11-15 12:07 +0000
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@@ -314,8 +314,8 @@ <h2>
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             <a class="nav" href="z_3afbcd666ed82c91___init___py.html">&#xbb; next</a>
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-            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.4">coverage.py v7.6.4</a>,
-            created at 2024-11-04 11:05 +0000
+            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
+            created at 2024-11-15 12:07 +0000
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index b4dbdff..f9e9ca0 100644
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             <a id="nextFileLink" class="nav" href="z_159731231e5c9c9d___init___py.html">&#xbb; next</a>
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-            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.4">coverage.py v7.6.4</a>,
-            created at 2024-11-04 11:05 +0000
+            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
+            created at 2024-11-15 12:07 +0000
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@@ -98,8 +98,8 @@ <h2>
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-            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.4">coverage.py v7.6.4</a>,
-            created at 2024-11-04 11:05 +0000
+            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
+            created at 2024-11-15 12:07 +0000
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+++ b/coverage/z_8030ef0ea5bfd6aa_test_canal_py.html
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-            created at 2024-11-04 11:05 +0000
+            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
+            created at 2024-11-15 12:07 +0000
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-            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.4">coverage.py v7.6.4</a>,
-            created at 2024-11-04 11:05 +0000
+            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
+            created at 2024-11-15 12:07 +0000
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@@ -64,8 +64,8 @@ <h2>
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             <a id="nextFileLink" class="nav" href="z_8030ef0ea5bfd6aa_test_canion_py.html">&#xbb; next</a>
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-            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.4">coverage.py v7.6.4</a>,
-            created at 2024-11-04 11:05 +0000
+            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
+            created at 2024-11-15 12:07 +0000
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-            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.4">coverage.py v7.6.4</a>,
-            created at 2024-11-04 11:05 +0000
+            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
+            created at 2024-11-15 12:07 +0000
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-            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.4">coverage.py v7.6.4</a>,
-            created at 2024-11-04 11:05 +0000
+            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
+            created at 2024-11-15 12:07 +0000
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-            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.4">coverage.py v7.6.4</a>,
-            created at 2024-11-04 11:05 +0000
+            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
+            created at 2024-11-15 12:07 +0000
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-            created at 2024-11-04 11:05 +0000
+            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
+            created at 2024-11-15 12:07 +0000
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-            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.4">coverage.py v7.6.4</a>,
-            created at 2024-11-04 11:05 +0000
+            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
+            created at 2024-11-15 12:07 +0000
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index d8c1ea3..5507c35 100644
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+++ b/coverage/z_833b0317e3c43dca___init___py.html
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             <a id="indexLink" class="nav" href="index.html">&Hat; index</a> &nbsp; &nbsp;
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+            <a id="nextFileLink" class="nav" href="z_833b0317e3c43dca_common_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
-            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.4">coverage.py v7.6.4</a>,
-            created at 2024-11-04 11:05 +0000
+            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
+            created at 2024-11-15 12:07 +0000
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+            <a class="nav" href="z_833b0317e3c43dca_common_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
-            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.4">coverage.py v7.6.4</a>,
-            created at 2024-11-04 11:05 +0000
+            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
+            created at 2024-11-15 12:07 +0000
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diff --git a/coverage/z_833b0317e3c43dca_common_py.html b/coverage/z_833b0317e3c43dca_common_py.html
new file mode 100644
index 0000000..e2e2a6c
--- /dev/null
+++ b/coverage/z_833b0317e3c43dca_common_py.html
@@ -0,0 +1,127 @@
+<!DOCTYPE html>
+<html lang="en">
+<head>
+    <meta http-equiv="Content-Type" content="text/html; charset=utf-8">
+    <title>Coverage for biobb_dna/utils/common.py: 60%</title>
+    <link rel="icon" sizes="32x32" href="favicon_32_cb_58284776.png">
+    <link rel="stylesheet" href="style_cb_8e611ae1.css" type="text/css">
+    <script src="coverage_html_cb_6fb7b396.js" defer></script>
+</head>
+<body class="pyfile">
+<header>
+    <div class="content">
+        <h1>
+            <span class="text">Coverage for </span><b>biobb_dna/utils/common.py</b>:
+            <span class="pc_cov">60%</span>
+        </h1>
+        <aside id="help_panel_wrapper">
+            <input id="help_panel_state" type="checkbox">
+            <label for="help_panel_state">
+                <img id="keyboard_icon" src="keybd_closed_cb_ce680311.png" alt="Show/hide keyboard shortcuts">
+            </label>
+            <div id="help_panel">
+                <p class="legend">Shortcuts on this page</p>
+                <div class="keyhelp">
+                    <p>
+                        <kbd>r</kbd>
+                        <kbd>m</kbd>
+                        <kbd>x</kbd>
+                        &nbsp; toggle line displays
+                    </p>
+                    <p>
+                        <kbd>j</kbd>
+                        <kbd>k</kbd>
+                        &nbsp; next/prev highlighted chunk
+                    </p>
+                    <p>
+                        <kbd>0</kbd> &nbsp; (zero) top of page
+                    </p>
+                    <p>
+                        <kbd>1</kbd> &nbsp; (one) first highlighted chunk
+                    </p>
+                    <p>
+                        <kbd>[</kbd>
+                        <kbd>]</kbd>
+                        &nbsp; prev/next file
+                    </p>
+                    <p>
+                        <kbd>u</kbd> &nbsp; up to the index
+                    </p>
+                    <p>
+                        <kbd>?</kbd> &nbsp; show/hide this help
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+                </div>
+            </div>
+        </aside>
+        <h2>
+            <span class="text">10 statements &nbsp;</span>
+            <button type="button" class="run button_toggle_run" value="run" data-shortcut="r" title="Toggle lines run">6<span class="text"> run</span></button>
+            <button type="button" class="mis show_mis button_toggle_mis" value="mis" data-shortcut="m" title="Toggle lines missing">4<span class="text"> missing</span></button>
+            <button type="button" class="exc show_exc button_toggle_exc" value="exc" data-shortcut="x" title="Toggle lines excluded">0<span class="text"> excluded</span></button>
+        </h2>
+        <p class="text">
+            <a id="prevFileLink" class="nav" href="z_833b0317e3c43dca___init___py.html">&#xab; prev</a> &nbsp; &nbsp;
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+            &nbsp; &nbsp; &nbsp;
+            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
+            created at 2024-11-15 12:07 +0000
+        </p>
+        <aside class="hidden">
+            <button type="button" class="button_next_chunk" data-shortcut="j"></button>
+            <button type="button" class="button_prev_chunk" data-shortcut="k"></button>
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+            <button type="button" class="button_prev_file" data-shortcut="["></button>
+            <button type="button" class="button_next_file" data-shortcut="]"></button>
+            <button type="button" class="button_to_index" data-shortcut="u"></button>
+            <button type="button" class="button_show_hide_help" data-shortcut="?"></button>
+        </aside>
+    </div>
+</header>
+<main id="source">
+    <p class="run"><span class="n"><a id="t1" href="#t1">1</a></span><span class="t"><span class="key">from</span> <span class="nam">typing</span> <span class="key">import</span> <span class="nam">Optional</span><span class="op">,</span> <span class="nam">Union</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t2" href="#t2">2</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t3" href="#t3">3</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t4" href="#t4">4</a></span><span class="t"><span class="com"># TODO: Move this function to biobb_common.tools.file_utils</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t5" href="#t5">5</a></span><span class="t"><span class="key">def</span> <span class="nam">_from_string_to_list</span><span class="op">(</span><span class="nam">input_data</span><span class="op">:</span> <span class="nam">Optional</span><span class="op">[</span><span class="nam">Union</span><span class="op">[</span><span class="nam">str</span><span class="op">,</span> <span class="nam">list</span><span class="op">[</span><span class="nam">str</span><span class="op">]</span><span class="op">]</span><span class="op">]</span><span class="op">)</span> <span class="op">-></span> <span class="nam">list</span><span class="op">[</span><span class="nam">str</span><span class="op">]</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t6" href="#t6">6</a></span><span class="t">    <span class="str">"""</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t7" href="#t7">7</a></span><span class="t"><span class="str">    Converts a string to a list, splitting by commas or spaces. If the input is already a list, returns it as is.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t8" href="#t8">8</a></span><span class="t"><span class="str">    Returns an empty list if input_data is None.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t9" href="#t9">9</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t10" href="#t10">10</a></span><span class="t"><span class="str">    Parameters:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t11" href="#t11">11</a></span><span class="t"><span class="str">        input_data (str, list, or None): The string, list, or None value to convert.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t12" href="#t12">12</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t13" href="#t13">13</a></span><span class="t"><span class="str">    Returns:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t14" href="#t14">14</a></span><span class="t"><span class="str">        list: A list of string elements or an empty list if input_data is None.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t15" href="#t15">15</a></span><span class="t"><span class="str">    """</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t16" href="#t16">16</a></span><span class="t">    <span class="key">if</span> <span class="nam">input_data</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="t17" href="#t17">17</a></span><span class="t">        <span class="key">return</span> <span class="op">[</span><span class="op">]</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">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t19" href="#t19">19</a></span><span class="t">    <span class="key">if</span> <span class="nam">isinstance</span><span class="op">(</span><span class="nam">input_data</span><span class="op">,</span> <span class="nam">list</span><span class="op">)</span><span class="op">:</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="com"># If input is already a list, return it</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t21" href="#t21">21</a></span><span class="t">        <span class="key">return</span> <span class="nam">input_data</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="com"># If input is a string, determine the delimiter based on presence of commas</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t24" href="#t24">24</a></span><span class="t">    <span class="nam">delimiter</span> <span class="op">=</span> <span class="str">","</span> <span class="key">if</span> <span class="str">","</span> <span class="key">in</span> <span class="nam">input_data</span> <span class="key">else</span> <span class="str">" "</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t25" href="#t25">25</a></span><span class="t">    <span class="nam">items</span> <span class="op">=</span> <span class="nam">input_data</span><span class="op">.</span><span class="nam">split</span><span class="op">(</span><span class="nam">delimiter</span><span class="op">)</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">&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="com"># Remove whitespace from each item and ignore empty strings</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t28" href="#t28">28</a></span><span class="t">    <span class="nam">processed_items</span> <span class="op">=</span> <span class="op">[</span><span class="nam">item</span><span class="op">.</span><span class="nam">strip</span><span class="op">(</span><span class="op">)</span> <span class="key">for</span> <span class="nam">item</span> <span class="key">in</span> <span class="nam">items</span> <span class="key">if</span> <span class="nam">item</span><span class="op">.</span><span class="nam">strip</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="t29" href="#t29">29</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t30" href="#t30">30</a></span><span class="t">    <span class="key">return</span> <span class="nam">processed_items</span>&nbsp;</span><span class="r"></span></p>
+</main>
+<footer>
+    <div class="content">
+        <p>
+            <a class="nav" href="z_833b0317e3c43dca___init___py.html">&#xab; prev</a> &nbsp; &nbsp;
+            <a class="nav" href="index.html">&Hat; index</a> &nbsp; &nbsp;
+            <a class="nav" href="z_833b0317e3c43dca_constants_py.html">&#xbb; next</a>
+            &nbsp; &nbsp; &nbsp;
+            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
+            created at 2024-11-15 12:07 +0000
+        </p>
+    </div>
+</footer>
+</body>
+</html>
diff --git a/coverage/z_833b0317e3c43dca_constants_py.html b/coverage/z_833b0317e3c43dca_constants_py.html
index ee2ccf5..a6aecb4 100644
--- a/coverage/z_833b0317e3c43dca_constants_py.html
+++ b/coverage/z_833b0317e3c43dca_constants_py.html
@@ -60,12 +60,12 @@ <h2>
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         </h2>
         <p class="text">
-            <a id="prevFileLink" class="nav" href="z_833b0317e3c43dca___init___py.html">&#xab; prev</a> &nbsp; &nbsp;
+            <a id="prevFileLink" class="nav" href="z_833b0317e3c43dca_common_py.html">&#xab; prev</a> &nbsp; &nbsp;
             <a id="indexLink" class="nav" href="index.html">&Hat; index</a> &nbsp; &nbsp;
             <a id="nextFileLink" class="nav" href="z_833b0317e3c43dca_loader_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
-            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.4">coverage.py v7.6.4</a>,
-            created at 2024-11-04 11:05 +0000
+            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
+            created at 2024-11-15 12:07 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -157,12 +157,12 @@ <h2>
 <footer>
     <div class="content">
         <p>
-            <a class="nav" href="z_833b0317e3c43dca___init___py.html">&#xab; prev</a> &nbsp; &nbsp;
+            <a class="nav" href="z_833b0317e3c43dca_common_py.html">&#xab; prev</a> &nbsp; &nbsp;
             <a class="nav" href="index.html">&Hat; index</a> &nbsp; &nbsp;
             <a class="nav" href="z_833b0317e3c43dca_loader_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
-            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.4">coverage.py v7.6.4</a>,
-            created at 2024-11-04 11:05 +0000
+            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
+            created at 2024-11-15 12:07 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_833b0317e3c43dca_loader_py.html b/coverage/z_833b0317e3c43dca_loader_py.html
index 19c7347..dee6078 100644
--- a/coverage/z_833b0317e3c43dca_loader_py.html
+++ b/coverage/z_833b0317e3c43dca_loader_py.html
@@ -64,8 +64,8 @@ <h2>
             <a id="indexLink" class="nav" href="index.html">&Hat; index</a> &nbsp; &nbsp;
             <a id="nextFileLink" class="nav" href="z_833b0317e3c43dca_transform_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
-            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.4">coverage.py v7.6.4</a>,
-            created at 2024-11-04 11:05 +0000
+            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
+            created at 2024-11-15 12:07 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -132,8 +132,8 @@ <h2>
             <a class="nav" href="index.html">&Hat; index</a> &nbsp; &nbsp;
             <a class="nav" href="z_833b0317e3c43dca_transform_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
-            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.4">coverage.py v7.6.4</a>,
-            created at 2024-11-04 11:05 +0000
+            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
+            created at 2024-11-15 12:07 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_833b0317e3c43dca_transform_py.html b/coverage/z_833b0317e3c43dca_transform_py.html
index ce9764f..5a32e3c 100644
--- a/coverage/z_833b0317e3c43dca_transform_py.html
+++ b/coverage/z_833b0317e3c43dca_transform_py.html
@@ -64,8 +64,8 @@ <h2>
             <a id="indexLink" class="nav" href="index.html">&Hat; index</a> &nbsp; &nbsp;
             <a id="nextFileLink" class="nav" href="index.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
-            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.4">coverage.py v7.6.4</a>,
-            created at 2024-11-04 11:05 +0000
+            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
+            created at 2024-11-15 12:07 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -101,8 +101,8 @@ <h2>
             <a class="nav" href="index.html">&Hat; index</a> &nbsp; &nbsp;
             <a class="nav" href="index.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
-            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.4">coverage.py v7.6.4</a>,
-            created at 2024-11-04 11:05 +0000
+            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
+            created at 2024-11-15 12:07 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_8a2a7f872cf1434f___init___py.html b/coverage/z_8a2a7f872cf1434f___init___py.html
index 81a58db..dddc868 100644
--- a/coverage/z_8a2a7f872cf1434f___init___py.html
+++ b/coverage/z_8a2a7f872cf1434f___init___py.html
@@ -64,8 +64,8 @@ <h2>
             <a id="indexLink" class="nav" href="index.html">&Hat; index</a> &nbsp; &nbsp;
             <a id="nextFileLink" class="nav" href="z_8a2a7f872cf1434f_interbpcorr_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
-            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.4">coverage.py v7.6.4</a>,
-            created at 2024-11-04 11:05 +0000
+            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
+            created at 2024-11-15 12:07 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -96,8 +96,8 @@ <h2>
             <a class="nav" href="index.html">&Hat; index</a> &nbsp; &nbsp;
             <a class="nav" href="z_8a2a7f872cf1434f_interbpcorr_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
-            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.4">coverage.py v7.6.4</a>,
-            created at 2024-11-04 11:05 +0000
+            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
+            created at 2024-11-15 12:07 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_8a2a7f872cf1434f_interbpcorr_py.html b/coverage/z_8a2a7f872cf1434f_interbpcorr_py.html
index e3ec3c0..82134f1 100644
--- a/coverage/z_8a2a7f872cf1434f_interbpcorr_py.html
+++ b/coverage/z_8a2a7f872cf1434f_interbpcorr_py.html
@@ -54,8 +54,8 @@ <h1>
             </div>
         </aside>
         <h2>
-            <span class="text">142 statements &nbsp;</span>
-            <button type="button" class="run button_toggle_run" value="run" data-shortcut="r" title="Toggle lines run">120<span class="text"> run</span></button>
+            <span class="text">144 statements &nbsp;</span>
+            <button type="button" class="run button_toggle_run" value="run" data-shortcut="r" title="Toggle lines run">122<span class="text"> run</span></button>
             <button type="button" class="mis show_mis button_toggle_mis" value="mis" data-shortcut="m" title="Toggle lines missing">22<span class="text"> missing</span></button>
             <button type="button" class="exc show_exc button_toggle_exc" value="exc" data-shortcut="x" title="Toggle lines excluded">0<span class="text"> excluded</span></button>
         </h2>
@@ -64,8 +64,8 @@ <h2>
             <a id="indexLink" class="nav" href="index.html">&Hat; index</a> &nbsp; &nbsp;
             <a id="nextFileLink" class="nav" href="z_8a2a7f872cf1434f_interhpcorr_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
-            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.4">coverage.py v7.6.4</a>,
-            created at 2024-11-04 11:05 +0000
+            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
+            created at 2024-11-15 12:07 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -83,334 +83,382 @@ <h2>
     <p class="pln"><span class="n"><a id="t1" href="#t1">1</a></span><span class="t"><span class="com">#!/usr/bin/env python3</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t2" href="#t2">2</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t3" href="#t3">3</a></span><span class="t"><span class="str">"""Module containing the InterBasePairCorrelation class and the command line interface."""</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t4" href="#t4">4</a></span><span class="t"><span class="key">import</span> <span class="nam">argparse</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t5" href="#t5">5</a></span><span class="t"><span class="key">from</span> <span class="nam">typing</span> <span class="key">import</span> <span class="nam">Optional</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t4" href="#t4">4</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t5" href="#t5">5</a></span><span class="t"><span class="key">import</span> <span class="nam">argparse</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t6" href="#t6">6</a></span><span class="t"><span class="key">from</span> <span class="nam">itertools</span> <span class="key">import</span> <span class="nam">product</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t7" href="#t7">7</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t8" href="#t8">8</a></span><span class="t"><span class="key">import</span> <span class="nam">numpy</span> <span class="key">as</span> <span class="nam">np</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t9" href="#t9">9</a></span><span class="t"><span class="key">import</span> <span class="nam">pandas</span> <span class="key">as</span> <span class="nam">pd</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t10" href="#t10">10</a></span><span class="t"><span class="key">import</span> <span class="nam">matplotlib</span> <span class="key">as</span> <span class="nam">mpl</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t11" href="#t11">11</a></span><span class="t"><span class="key">import</span> <span class="nam">matplotlib</span><span class="op">.</span><span class="nam">pyplot</span> <span class="key">as</span> <span class="nam">plt</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t12" href="#t12">12</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t13" href="#t13">13</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_common</span><span class="op">.</span><span class="nam">generic</span><span class="op">.</span><span class="nam">biobb_object</span> <span class="key">import</span> <span class="nam">BiobbObject</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t14" href="#t14">14</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_common</span><span class="op">.</span><span class="nam">configuration</span> <span class="key">import</span> <span class="nam">settings</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t7" href="#t7">7</a></span><span class="t"><span class="key">from</span> <span class="nam">typing</span> <span class="key">import</span> <span class="nam">Optional</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t8" href="#t8">8</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t9" href="#t9">9</a></span><span class="t"><span class="key">import</span> <span class="nam">matplotlib</span> <span class="key">as</span> <span class="nam">mpl</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t10" href="#t10">10</a></span><span class="t"><span class="key">import</span> <span class="nam">matplotlib</span><span class="op">.</span><span class="nam">pyplot</span> <span class="key">as</span> <span class="nam">plt</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t11" href="#t11">11</a></span><span class="t"><span class="key">import</span> <span class="nam">numpy</span> <span class="key">as</span> <span class="nam">np</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t12" href="#t12">12</a></span><span class="t"><span class="key">import</span> <span class="nam">pandas</span> <span class="key">as</span> <span class="nam">pd</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t13" href="#t13">13</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_common</span><span class="op">.</span><span class="nam">configuration</span> <span class="key">import</span> <span class="nam">settings</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t14" href="#t14">14</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_common</span><span class="op">.</span><span class="nam">generic</span><span class="op">.</span><span class="nam">biobb_object</span> <span class="key">import</span> <span class="nam">BiobbObject</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t15" href="#t15">15</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_common</span><span class="op">.</span><span class="nam">tools</span><span class="op">.</span><span class="nam">file_utils</span> <span class="key">import</span> <span class="nam">launchlogger</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t16" href="#t16">16</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_dna</span><span class="op">.</span><span class="nam">utils</span><span class="op">.</span><span class="nam">loader</span> <span class="key">import</span> <span class="nam">read_series</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t16" href="#t16">16</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t17" href="#t17">17</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_dna</span><span class="op">.</span><span class="nam">utils</span> <span class="key">import</span> <span class="nam">constants</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">&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="run"><span class="n"><a id="t20" href="#t20">20</a></span><span class="t"><span class="key">class</span> <span class="nam">InterBasePairCorrelation</span><span class="op">(</span><span class="nam">BiobbObject</span><span class="op">)</span><span class="op">:</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">"""</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"><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"><span class="str">            * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory.</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.interbp_correlations.interbpcorr import interbpcorr</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t18" href="#t18">18</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_dna</span><span class="op">.</span><span class="nam">utils</span><span class="op">.</span><span class="nam">common</span> <span class="key">import</span> <span class="nam">_from_string_to_list</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t19" href="#t19">19</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_dna</span><span class="op">.</span><span class="nam">utils</span><span class="op">.</span><span class="nam">loader</span> <span class="key">import</span> <span class="nam">read_series</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">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t22" href="#t22">22</a></span><span class="t"><span class="key">class</span> <span class="nam">InterBasePairCorrelation</span><span class="op">(</span><span class="nam">BiobbObject</span><span class="op">)</span><span class="op">:</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">"""</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">    | biobb_dna InterBasePairCorrelation</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">    | 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="t26" href="#t26">26</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="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_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="t30" href="#t30">30</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="t31" href="#t31">31</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="t32" href="#t32">32</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="t33" href="#t33">33</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="t34" href="#t34">34</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="t35" href="#t35">35</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="t36" href="#t36">36</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="t37" href="#t37">37</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="t38" href="#t38">38</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="t39" href="#t39">39</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="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">            * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory.</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">    Examples:</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">        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="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">            interbpcorr(</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/input/shift.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_slide='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_rise='path/to/input/slide.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_tilt='path/to/input/tilt.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_roll='path/to/input/roll.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">                input_filename_twist='path/to/input/twist.ser',</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="t47" href="#t47">47</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="t48" href="#t48">48</a></span><span class="t">&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">            interbpcorr(</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_shift='path/to/input/shift.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_slide='path/to/input/slide.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_rise='path/to/input/slide.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">                input_filename_tilt='path/to/input/tilt.ser',</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_roll='path/to/input/roll.ser',</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">                input_filename_twist='path/to/input/twist.ser',</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_csv_path='path/to/output/file.csv',</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">                output_jpg_path='path/to/output/plot.jpg',</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">                properties=prop)</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">    Info:</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">        * wrapped_software:</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: In house</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">            * license: Apache-2.0</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">        * ontology:</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">            * name: EDAM</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">            * schema: http://edamontology.org/EDAM.owl</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_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>&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="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="t73" href="#t73">73</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="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"># Call parent class constructor</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">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="t77" href="#t77">77</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="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"># Input/Output files</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">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="t81" href="#t81">81</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="t82" href="#t82">82</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="t83" href="#t83">83</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="t84" href="#t84">84</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="t85" href="#t85">85</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="t86" href="#t86">86</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="t87" href="#t87">87</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="t88" href="#t88">88</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="t89" href="#t89">89</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="t90" href="#t90">90</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="t91" href="#t91">91</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="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">        <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="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="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">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="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:`HelParCorrelation &lt;correlations.interbpcorr.InterBasePairCorrelation>` 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"># check sequence</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">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="t114" href="#t114">114</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="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"># check seqpos</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">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="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"># read input</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">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="t124" href="#t124">124</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="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="t125" href="#t125">125</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="t126" href="#t126">126</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="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="t127" href="#t127">127</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="t128" href="#t128">128</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="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="t129" href="#t129">129</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="t130" href="#t130">130</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="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="t131" href="#t131">131</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="t132" href="#t132">132</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="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="t133" href="#t133">133</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="t134" href="#t134">134</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="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="t135" href="#t135">135</a></span><span class="t">&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="pln"><span class="n"><a id="t137" href="#t137">137</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="t138" href="#t138">138</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="t139" href="#t139">139</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="t140" href="#t140">140</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="t141" href="#t141">141</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="t142" href="#t142">142</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="t143" href="#t143">143</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="t144" href="#t144">144</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="t145" href="#t145">145</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="t146" href="#t146">146</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="t147" href="#t147">147</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="t148" href="#t148">148</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="t149" href="#t149">149</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="t150" href="#t150">150</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="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"># rename duplicated subunits</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">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="t154" href="#t154">154</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="t155" href="#t155">155</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="t156" href="#t156">156</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="t157" href="#t157">157</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="t158" href="#t158">158</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="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"># set names to each dataset</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">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="t162" href="#t162">162</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="t163" href="#t163">163</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="t164" href="#t164">164</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="t165" href="#t165">165</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="t166" href="#t166">166</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="t167" href="#t167">167</a></span><span class="t">&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"># 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="t169" href="#t169">169</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="t170" href="#t170">170</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="t171" href="#t171">171</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="t172" href="#t172">172</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="t173" href="#t173">173</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="t174" href="#t174">174</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="t175" href="#t175">175</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="t176" href="#t176">176</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="t177" href="#t177">177</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="t178" href="#t178">178</a></span><span class="t">                <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">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="t180" href="#t180">180</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="t181" href="#t181">181</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="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="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">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="t184" href="#t184">184</a></span><span class="t">                <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="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">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="t187" href="#t187">187</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="t188" href="#t188">188</a></span><span class="t">                <span class="nam">method</span> <span class="op">=</span> <span class="str">"pearson"</span>  <span class="com"># type: ignore</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_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="t190" href="#t190">190</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="t191" href="#t191">191</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="t192" href="#t192">192</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="t193" href="#t193">193</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>  <span class="com"># type: ignore</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"># save csv data</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">to_csv</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">stage_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="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"># create heatmap</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">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="t200" href="#t200">200</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="t201" href="#t201">201</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="t202" href="#t202">202</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>  <span class="com"># type: ignore</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">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="t204" href="#t204">204</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="t205" href="#t205">205</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="t206" href="#t206">206</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="t207" href="#t207">207</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="t208" href="#t208">208</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="t209" href="#t209">209</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="t210" href="#t210">210</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="t211" href="#t211">211</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="t67" href="#t67">67</a></span><span class="t"><span class="str">    """</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="run"><span class="n"><a id="t69" href="#t69">69</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="t70" href="#t70">70</a></span><span class="t">        <span class="nam">self</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">input_filename_shift</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="nam">input_filename_slide</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="nam">input_filename_rise</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="nam">input_filename_tilt</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="nam">input_filename_roll</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="nam">input_filename_twist</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="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="nam">output_jpg_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="nam">properties</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="t80" href="#t80">80</a></span><span class="t">        <span class="op">**</span><span class="nam">kwargs</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> <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">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="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"># Call parent class constructor</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">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="t86" href="#t86">86</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="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"># Input/Output files</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">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="t90" href="#t90">90</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="t91" href="#t91">91</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="t92" href="#t92">92</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="t93" href="#t93">93</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="t94" href="#t94">94</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="t95" href="#t95">95</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="t96" href="#t96">96</a></span><span class="t">                <span class="str">"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="t97" href="#t97">97</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="t98" href="#t98">98</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="t99" href="#t99">99</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="t100" href="#t100">100</a></span><span class="t">                <span class="str">"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="t101" href="#t101">101</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="t102" href="#t102">102</a></span><span class="t">        <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="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="t105" href="#t105">105</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="t106" href="#t106">106</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="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">int</span><span class="op">(</span><span class="nam">elem</span><span class="op">)</span> <span class="key">for</span> <span class="nam">elem</span> <span class="key">in</span> <span class="nam">_from_string_to_list</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><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="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 the properties</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">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="t112" href="#t112">112</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="t113" href="#t113">113</a></span><span class="t">&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="op">@</span><span class="nam">launchlogger</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">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="t116" href="#t116">116</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="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"># Setup Biobb</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">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="t120" href="#t120">120</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="t121" href="#t121">121</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="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 sequence</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">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="t125" href="#t125">125</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="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="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="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="t130" href="#t130">130</a></span><span class="t">                <span class="key">raise</span> <span class="nam">ValueError</span><span class="op">(</span><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="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">seqpos</span> <span class="op">=</span> <span class="key">None</span>  <span class="com"># type: ignore</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"># read input</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">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="t136" href="#t136">136</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="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>&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="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">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="t139" href="#t139">139</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="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>&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="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">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="t142" href="#t142">142</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="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>&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="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">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">stage_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>&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="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">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="t148" href="#t148">148</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="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>&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="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">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="t151" href="#t151">151</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="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>&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="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="run"><span class="n"><a id="t154" href="#t154">154</a></span><span class="t">        <span class="key">if</span> <span class="key">not</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="t155" href="#t155">155</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="t156" href="#t156">156</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="t157" href="#t157">157</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="t158" href="#t158">158</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="t159" href="#t159">159</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="t160" href="#t160">160</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="t161" href="#t161">161</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="t162" href="#t162">162</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="t163" href="#t163">163</a></span><span class="t">                <span class="str">f"{i+1}_{self.sequence[i:i+2]}"</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">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>&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>&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_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="t167" href="#t167">167</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>&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="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="key">else</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t170" href="#t170">170</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="t171" href="#t171">171</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="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"># rename duplicated subunits</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">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="t175" href="#t175">175</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="t176" href="#t176">176</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="t177" href="#t177">177</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="t178" href="#t178">178</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="t179" href="#t179">179</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="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"># set names to each dataset</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">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="t183" href="#t183">183</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="t184" href="#t184">184</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="t185" href="#t185">185</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="t186" href="#t186">186</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="t187" href="#t187">187</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="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"># 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="t190" href="#t190">190</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="t191" href="#t191">191</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="t192" href="#t192">192</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="t193" href="#t193">193</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="t194" href="#t194">194</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="t195" href="#t195">195</a></span><span class="t">            <span class="key">if</span> <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>&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">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="t197" href="#t197">197</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="t198" href="#t198">198</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>&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="key">and</span> <span class="nam">ser2</span><span class="op">.</span><span class="nam">name</span> <span class="key">not</span> <span class="key">in</span> <span class="nam">constants</span><span class="op">.</span><span class="nam">hp_angular</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="key">or</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">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>&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="key">and</span> <span class="nam">ser1</span><span class="op">.</span><span class="nam">name</span> <span class="key">not</span> <span class="key">in</span> <span class="nam">constants</span><span class="op">.</span><span class="nam">hp_angular</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="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">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="t205" href="#t205">205</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="t206" href="#t206">206</a></span><span class="t">                <span class="nam">method</span> <span class="op">=</span> <span class="str">"pearson"</span>  <span class="com"># type: ignore</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">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="t208" href="#t208">208</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="t209" href="#t209">209</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="t210" href="#t210">210</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="t211" href="#t211">211</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>  <span class="com"># type: ignore</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="t213" href="#t213">213</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="t214" href="#t214">214</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="t215" href="#t215">215</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="t216" href="#t216">216</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="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="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="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_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="t220" href="#t220">220</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>  <span class="com"># type: ignore</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">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="t223" href="#t223">223</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="t224" href="#t224">224</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="t213" href="#t213">213</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="t214" href="#t214">214</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">stage_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="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"># create heatmap</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">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="t218" href="#t218">218</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">0.8</span><span class="op">,</span> <span class="op">-</span><span class="num">0.6</span><span class="op">,</span> <span class="op">-</span><span class="num">0.4</span><span class="op">,</span> <span class="op">-</span><span class="num">0.2</span><span class="op">,</span> <span class="num">0.2</span><span class="op">,</span> <span class="num">0.4</span><span class="op">,</span> <span class="num">0.6</span><span class="op">,</span> <span class="num">0.8</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="t219" href="#t219">219</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="t220" href="#t220">220</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>  <span class="com"># type: ignore</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">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="t222" href="#t222">222</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><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">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> <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="t223" href="#t223">223</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="t224" href="#t224">224</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">0.8</span><span class="op">,</span> <span class="op">-</span><span class="num">0.6</span><span class="op">,</span> <span class="op">-</span><span class="num">0.4</span><span class="op">,</span> <span class="op">-</span><span class="num">0.2</span><span class="op">,</span> <span class="num">0.2</span><span class="op">,</span> <span class="num">0.4</span><span class="op">,</span> <span class="num">0.6</span><span class="op">,</span> <span class="num">0.8</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="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="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="t227" href="#t227">227</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="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="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="t229" href="#t229">229</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="t230" href="#t230">230</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="t231" href="#t231">231</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">        <span class="com"># Copy files to host</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">self</span><span class="op">.</span><span class="nam">copy_to_host</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="com"># axes</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">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="t228" href="#t228">228</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="t229" href="#t229">229</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="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="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="t232" href="#t232">232</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="t233" href="#t233">233</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>  <span class="com"># type: ignore</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="str">""</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="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="run"><span class="n"><a id="t235" href="#t235">235</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="t236" href="#t236">236</a></span><span class="t">            <span class="str">"Correlation for neighboring basepairs "</span> <span class="str">"and pairs of helical parameters"</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="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="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="t240" href="#t240">240</a></span><span class="t">        <span class="nam">fig</span><span class="op">.</span><span class="nam">savefig</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">stage_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="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="t241" href="#t241">241</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="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="t243" href="#t243">243</a></span><span class="t">        <span class="com"># Copy files to host</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">copy_to_host</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="pln"><span class="n"><a id="t246" href="#t246">246</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="t247" href="#t247">247</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>&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="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">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="str">""</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="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="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">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="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="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="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="key">return</span> <span class="num">0</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="op">@</span><span class="nam">staticmethod</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">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="t260" href="#t260">260</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="t261" href="#t261">261</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="t262" href="#t262">262</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="t263" href="#t263">263</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="t264" href="#t264">264</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="t265" href="#t265">265</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="t266" href="#t266">266</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="t267" href="#t267">267</a></span><span class="t">&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">Optional</span><span class="op">[</span><span class="nam">dict</span><span class="op">]</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="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="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="run"><span class="n"><a id="t268" href="#t268">268</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="t269" href="#t269">269</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="t270" href="#t270">270</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="t271" href="#t271">271</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="t272" href="#t272">272</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="t273" href="#t273">273</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="t274" href="#t274">274</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="t275" href="#t275">275</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="t276" href="#t276">276</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="t277" href="#t277">277</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="t278" href="#t278">278</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="t279" href="#t279">279</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="t280" href="#t280">280</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">interbpcorr</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_shift</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="t284" href="#t284">284</a></span><span class="t">    <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="t285" href="#t285">285</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>&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_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="t287" href="#t287">287</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>&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">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="t289" href="#t289">289</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>&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">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="t291" href="#t291">291</a></span><span class="t">    <span class="nam">properties</span><span class="op">:</span> <span class="nam">Optional</span><span class="op">[</span><span class="nam">dict</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="pln"><span class="n"><a id="t292" href="#t292">292</a></span><span class="t">    <span class="op">**</span><span class="nam">kwargs</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="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="t294" href="#t294">294</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="t295" href="#t295">295</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="t296" href="#t296">296</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t297" href="#t297">297</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="t298" href="#t298">298</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="t299" href="#t299">299</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="t300" href="#t300">300</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="t301" href="#t301">301</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="t302" href="#t302">302</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="t303" href="#t303">303</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="t304" href="#t304">304</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="t305" href="#t305">305</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="t306" href="#t306">306</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="t307" href="#t307">307</a></span><span class="t">        <span class="op">**</span><span class="nam">kwargs</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="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="t309" href="#t309">309</a></span><span class="t">&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="run"><span class="n"><a id="t311" href="#t311">311</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="t312" href="#t312">312</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="t313" href="#t313">313</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>&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">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="t315" href="#t315">315</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="pln"><span class="n"><a id="t316" href="#t316">316</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="t317" href="#t317">317</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="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">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="t320" href="#t320">320</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>&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="str">"--input_filename_shift"</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">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="t323" href="#t323">323</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="pln"><span class="n"><a id="t324" href="#t324">324</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="t325" href="#t325">325</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>&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="str">"--input_filename_slide"</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">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">"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="pln"><span class="n"><a id="t329" href="#t329">329</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="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>&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="str">"--input_filename_rise"</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">        <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="t333" href="#t333">333</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="pln"><span class="n"><a id="t334" href="#t334">334</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="t335" href="#t335">335</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>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t336" href="#t336">336</a></span><span class="t">        <span class="str">"--input_filename_tilt"</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">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="t338" href="#t338">338</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="pln"><span class="n"><a id="t339" href="#t339">339</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="t340" href="#t340">340</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>&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="str">"--input_filename_roll"</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">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="t343" href="#t343">343</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="pln"><span class="n"><a id="t344" href="#t344">344</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="t345" href="#t345">345</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>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t346" href="#t346">346</a></span><span class="t">        <span class="str">"--input_filename_twist"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t347" href="#t347">347</a></span><span class="t">        <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="t348" href="#t348">348</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="pln"><span class="n"><a id="t349" href="#t349">349</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="t350" href="#t350">350</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>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t351" href="#t351">351</a></span><span class="t">        <span class="str">"--output_csv_path"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t352" href="#t352">352</a></span><span class="t">        <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="t353" href="#t353">353</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="t354" href="#t354">354</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="t355" href="#t355">355</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>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t356" href="#t356">356</a></span><span class="t">        <span class="str">"--output_jpg_path"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t357" href="#t357">357</a></span><span class="t">        <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="t358" href="#t358">358</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="t359" href="#t359">359</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t360" href="#t360">360</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t361" href="#t361">361</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="t362" href="#t362">362</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="t363" href="#t363">363</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="t364" href="#t364">364</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t365" href="#t365">365</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="t366" href="#t366">366</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="t367" href="#t367">367</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="t368" href="#t368">368</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="t369" href="#t369">369</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="t370" href="#t370">370</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="t371" href="#t371">371</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="t372" href="#t372">372</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="t373" href="#t373">373</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="t374" href="#t374">374</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="t375" href="#t375">375</a></span><span class="t">    <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t376" href="#t376">376</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t377" href="#t377">377</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t378" href="#t378">378</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="t379" href="#t379">379</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">
@@ -419,8 +467,8 @@ <h2>
             <a class="nav" href="index.html">&Hat; index</a> &nbsp; &nbsp;
             <a class="nav" href="z_8a2a7f872cf1434f_interhpcorr_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
-            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.4">coverage.py v7.6.4</a>,
-            created at 2024-11-04 11:05 +0000
+            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
+            created at 2024-11-15 12:07 +0000
         </p>
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 </footer>
diff --git a/coverage/z_8a2a7f872cf1434f_interhpcorr_py.html b/coverage/z_8a2a7f872cf1434f_interhpcorr_py.html
index dc16568..60546bc 100644
--- a/coverage/z_8a2a7f872cf1434f_interhpcorr_py.html
+++ b/coverage/z_8a2a7f872cf1434f_interhpcorr_py.html
@@ -64,8 +64,8 @@ <h2>
             <a id="indexLink" class="nav" href="index.html">&Hat; index</a> &nbsp; &nbsp;
             <a id="nextFileLink" class="nav" href="z_8a2a7f872cf1434f_interseqcorr_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
-            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.4">coverage.py v7.6.4</a>,
-            created at 2024-11-04 11:05 +0000
+            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
+            created at 2024-11-15 12:07 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -429,8 +429,8 @@ <h2>
             <a class="nav" href="index.html">&Hat; index</a> &nbsp; &nbsp;
             <a class="nav" href="z_8a2a7f872cf1434f_interseqcorr_py.html">&#xbb; next</a>
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-            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.4">coverage.py v7.6.4</a>,
-            created at 2024-11-04 11:05 +0000
+            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
+            created at 2024-11-15 12:07 +0000
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 </footer>
diff --git a/coverage/z_8a2a7f872cf1434f_interseqcorr_py.html b/coverage/z_8a2a7f872cf1434f_interseqcorr_py.html
index 96519bd..09ec63e 100644
--- a/coverage/z_8a2a7f872cf1434f_interseqcorr_py.html
+++ b/coverage/z_8a2a7f872cf1434f_interseqcorr_py.html
@@ -2,7 +2,7 @@
 <html lang="en">
 <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8">
-    <title>Coverage for biobb_dna/interbp_correlations/interseqcorr.py: 71%</title>
+    <title>Coverage for biobb_dna/interbp_correlations/interseqcorr.py: 72%</title>
     <link rel="icon" sizes="32x32" href="favicon_32_cb_58284776.png">
     <link rel="stylesheet" href="style_cb_8e611ae1.css" type="text/css">
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@@ -12,7 +12,7 @@
     <div class="content">
         <h1>
             <span class="text">Coverage for </span><b>biobb_dna/interbp_correlations/interseqcorr.py</b>:
-            <span class="pc_cov">71%</span>
+            <span class="pc_cov">72%</span>
         </h1>
         <aside id="help_panel_wrapper">
             <input id="help_panel_state" type="checkbox">
@@ -54,8 +54,8 @@ <h1>
             </div>
         </aside>
         <h2>
-            <span class="text">94 statements &nbsp;</span>
-            <button type="button" class="run button_toggle_run" value="run" data-shortcut="r" title="Toggle lines run">67<span class="text"> run</span></button>
+            <span class="text">96 statements &nbsp;</span>
+            <button type="button" class="run button_toggle_run" value="run" data-shortcut="r" title="Toggle lines run">69<span class="text"> run</span></button>
             <button type="button" class="mis show_mis button_toggle_mis" value="mis" data-shortcut="m" title="Toggle lines missing">27<span class="text"> missing</span></button>
             <button type="button" class="exc show_exc button_toggle_exc" value="exc" data-shortcut="x" title="Toggle lines excluded">0<span class="text"> excluded</span></button>
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@@ -64,8 +64,8 @@ <h2>
             <a id="indexLink" class="nav" href="index.html">&Hat; index</a> &nbsp; &nbsp;
             <a id="nextFileLink" class="nav" href="z_64e03be4370b7ecc___init___py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
-            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.4">coverage.py v7.6.4</a>,
-            created at 2024-11-04 11:05 +0000
+            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
+            created at 2024-11-15 12:07 +0000
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             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -83,243 +83,268 @@ <h2>
     <p class="pln"><span class="n"><a id="t1" href="#t1">1</a></span><span class="t"><span class="com">#!/usr/bin/env python3</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t2" href="#t2">2</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t3" href="#t3">3</a></span><span class="t"><span class="str">"""Module containing the InterSequenceCorrelation class and the command line interface."""</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t4" href="#t4">4</a></span><span class="t"><span class="key">import</span> <span class="nam">argparse</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t5" href="#t5">5</a></span><span class="t"><span class="key">from</span> <span class="nam">typing</span> <span class="key">import</span> <span class="nam">Optional</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t4" href="#t4">4</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t5" href="#t5">5</a></span><span class="t"><span class="key">import</span> <span class="nam">argparse</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t6" href="#t6">6</a></span><span class="t"><span class="key">from</span> <span class="nam">pathlib</span> <span class="key">import</span> <span class="nam">Path</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t7" href="#t7">7</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t8" href="#t8">8</a></span><span class="t"><span class="key">import</span> <span class="nam">numpy</span> <span class="key">as</span> <span class="nam">np</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t7" href="#t7">7</a></span><span class="t"><span class="key">from</span> <span class="nam">typing</span> <span class="key">import</span> <span class="nam">Optional</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t8" href="#t8">8</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t9" href="#t9">9</a></span><span class="t"><span class="key">import</span> <span class="nam">matplotlib</span><span class="op">.</span><span class="nam">pyplot</span> <span class="key">as</span> <span class="nam">plt</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t10" href="#t10">10</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t11" href="#t11">11</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_common</span><span class="op">.</span><span class="nam">generic</span><span class="op">.</span><span class="nam">biobb_object</span> <span class="key">import</span> <span class="nam">BiobbObject</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t12" href="#t12">12</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_common</span><span class="op">.</span><span class="nam">configuration</span> <span class="key">import</span> <span class="nam">settings</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t10" href="#t10">10</a></span><span class="t"><span class="key">import</span> <span class="nam">numpy</span> <span class="key">as</span> <span class="nam">np</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t11" href="#t11">11</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_common</span><span class="op">.</span><span class="nam">configuration</span> <span class="key">import</span> <span class="nam">settings</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t12" href="#t12">12</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_common</span><span class="op">.</span><span class="nam">generic</span><span class="op">.</span><span class="nam">biobb_object</span> <span class="key">import</span> <span class="nam">BiobbObject</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t13" href="#t13">13</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_common</span><span class="op">.</span><span class="nam">tools</span><span class="op">.</span><span class="nam">file_utils</span> <span class="key">import</span> <span class="nam">launchlogger</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t14" href="#t14">14</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_dna</span><span class="op">.</span><span class="nam">utils</span><span class="op">.</span><span class="nam">loader</span> <span class="key">import</span> <span class="nam">read_series</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t14" href="#t14">14</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t15" href="#t15">15</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_dna</span><span class="op">.</span><span class="nam">utils</span> <span class="key">import</span> <span class="nam">constants</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t16" href="#t16">16</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t17" href="#t17">17</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t18" href="#t18">18</a></span><span class="t"><span class="key">class</span> <span class="nam">InterSequenceCorrelation</span><span class="op">(</span><span class="nam">BiobbObject</span><span class="op">)</span><span class="op">:</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">"""</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"><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"><span class="str">            * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory.</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.interseqcorr import interseqcorr</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t16" href="#t16">16</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_dna</span><span class="op">.</span><span class="nam">utils</span><span class="op">.</span><span class="nam">common</span> <span class="key">import</span> <span class="nam">_from_string_to_list</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t17" href="#t17">17</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_dna</span><span class="op">.</span><span class="nam">utils</span><span class="op">.</span><span class="nam">loader</span> <span class="key">import</span> <span class="nam">read_series</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">&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="run"><span class="n"><a id="t20" href="#t20">20</a></span><span class="t"><span class="key">class</span> <span class="nam">InterSequenceCorrelation</span><span class="op">(</span><span class="nam">BiobbObject</span><span class="op">)</span><span class="op">:</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">"""</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 InterSequenceCorrelation</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"><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="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_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="t28" href="#t28">28</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="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/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="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 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="t32" href="#t32">32</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="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"><span class="str">            * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory.</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">            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": "helpar",</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": "CGTAATCG"</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">            interseqcorr(</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/input/file.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/output/file.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/output/plot.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="t41" href="#t41">41</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="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">                "helpar_name": "helpar",</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": "CGTAATCG"</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">            interseqcorr(</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/input/file.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/output/file.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/output/plot.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="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>&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">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="t62" href="#t62">62</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="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>&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> <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">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="t83" href="#t83">83</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="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>&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">self</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_ser_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>&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>&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>&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="nam">kwargs</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="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><span class="str">"input_ser_path"</span><span class="op">:</span> <span class="nam">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="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_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="t81" href="#t81">81</a></span><span class="t">                <span class="str">"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="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="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">&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="com"># Check the properties</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_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="t87" href="#t87">87</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="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="op">@</span><span class="nam">launchlogger</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">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="t91" href="#t91">91</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="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"># Setup Biobb</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">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="t95" href="#t95">95</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="t96" href="#t96">96</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="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 sequence</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">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="t100" href="#t100">100</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="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"># get helical parameter from filename if not specified</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="run"><span class="n"><a id="t104" href="#t104">104</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="t105" href="#t105">105</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="t106" href="#t106">106</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="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="t107" href="#t107">107</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="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="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 can't be inferred from file, "</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">"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="t112" href="#t112">112</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="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">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="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 is invalid! "</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"Options: {constants.helical_parameters}"</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"># 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="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">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="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="str">"pearson"</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="key">else</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">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="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"># check seqpos</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">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="t126" href="#t126">126</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="t127" href="#t127">127</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="t128" href="#t128">128</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="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"># read input .ser file</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">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="t132" href="#t132">132</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="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="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="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="t135" href="#t135">135</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="t136" href="#t136">136</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="t137" href="#t137">137</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="t138" href="#t138">138</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="t139" href="#t139">139</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="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="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="t142" href="#t142">142</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="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"># make matrix</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_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="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">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">stage_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="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">corr_data</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">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="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="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"{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="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">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="t164" href="#t164">164</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="t165" href="#t165">165</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="t166" href="#t166">166</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="t167" href="#t167">167</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="t168" href="#t168">168</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="t169" href="#t169">169</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="t170" href="#t170">170</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="t171" href="#t171">171</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="t172" href="#t172">172</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="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="t173" href="#t173">173</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="t174" href="#t174">174</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="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"># Copy files to host</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">copy_to_host</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="str">""</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="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="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">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="t86" href="#t86">86</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="t87" href="#t87">87</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="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="nam">int</span><span class="op">(</span><span class="nam">elem</span><span class="op">)</span> <span class="key">for</span> <span class="nam">elem</span> <span class="key">in</span> <span class="nam">_from_string_to_list</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><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="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">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="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 the 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">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="t94" href="#t94">94</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="t95" href="#t95">95</a></span><span class="t">&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="op">@</span><span class="nam">launchlogger</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">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="t98" href="#t98">98</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="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"># Setup Biobb</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">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="t102" href="#t102">102</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="t103" href="#t103">103</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="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 sequence</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">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="t107" href="#t107">107</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="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="run"><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="run"><span class="n"><a id="t112" href="#t112">112</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="t113" href="#t113">113</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>&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">in</span> <span class="nam">Path</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">stage_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="pln"><span class="n"><a id="t115" href="#t115">115</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="t116" href="#t116">116</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="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">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>&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">"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="t120" href="#t120">120</a></span><span class="t">                    <span class="str">"so it must be specified!"</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="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="key">else</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">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="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 is invalid! "</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"Options: {constants.helical_parameters}"</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="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"># 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="t130" href="#t130">130</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="t131" href="#t131">131</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="t132" href="#t132">132</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="t133" href="#t133">133</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>  <span class="com"># type: ignore</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"># check seqpos</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="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">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="t138" href="#t138">138</a></span><span class="t">                <span class="key">raise</span> <span class="nam">ValueError</span><span class="op">(</span><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">        <span class="key">else</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">self</span><span class="op">.</span><span class="nam">seqpos</span> <span class="op">=</span> <span class="key">None</span>  <span class="com"># type: ignore</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"># read input .ser file</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">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="t144" href="#t144">144</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="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">usecols</span><span class="op">=</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</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="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="key">if</span> <span class="key">not</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="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="t148" href="#t148">148</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="t149" href="#t149">149</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="t150" href="#t150">150</a></span><span class="t">            <span class="nam">labels</span> <span class="op">=</span> <span class="op">[</span><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="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="run"><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">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="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"># make matrix</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_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="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 csv data</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_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">stage_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="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"># create heatmap</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">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="t163" href="#t163">163</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="t164" href="#t164">164</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="t165" href="#t165">165</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="t166" href="#t166">166</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="t167" href="#t167">167</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="t168" href="#t168">168</a></span><span class="t">                    <span class="nam">j</span> <span class="op">+</span> <span class="num">0.5</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">i</span> <span class="op">+</span> <span class="num">0.5</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"{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="t171" href="#t171">171</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="t172" href="#t172">172</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="t173" href="#t173">173</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="pln"><span class="n"><a id="t174" href="#t174">174</a></span><span class="t">                <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_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="t176" href="#t176">176</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="t177" href="#t177">177</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="t178" href="#t178">178</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="t179" href="#t179">179</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="t180" href="#t180">180</a></span><span class="t">            <span class="str">"Base Pair Correlation "</span> <span class="str">f"for Helical Parameter '{self.helpar_name}'"</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="run"><span class="n"><a id="t182" href="#t182">182</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="t183" href="#t183">183</a></span><span class="t">        <span class="nam">fig</span><span class="op">.</span><span class="nam">savefig</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">stage_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="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="t184" href="#t184">184</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="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"># Copy files to host</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">copy_to_host</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="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="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">Optional</span><span class="op">[</span><span class="nam">dict</span><span class="op">]</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="t189" href="#t189">189</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="t190" href="#t190">190</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><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="str">""</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="t191" href="#t191">191</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="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="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="t194" href="#t194">194</a></span><span class="t">&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="key">return</span> <span class="num">0</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="op">@</span><span class="nam">staticmethod</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">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="t199" href="#t199">199</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="t200" href="#t200">200</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="t201" href="#t201">201</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="t202" href="#t202">202</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="t203" href="#t203">203</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="t204" href="#t204">204</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="t205" href="#t205">205</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="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="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="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="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">interseqcorr</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">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_csv_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="t211" href="#t211">211</a></span><span class="t">    <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="t212" href="#t212">212</a></span><span class="t">    <span class="nam">properties</span><span class="op">:</span> <span class="nam">Optional</span><span class="op">[</span><span class="nam">dict</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="pln"><span class="n"><a id="t213" href="#t213">213</a></span><span class="t">    <span class="op">**</span><span class="nam">kwargs</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="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="t215" href="#t215">215</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="t216" href="#t216">216</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="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="nam">InterSequenceCorrelation</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">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="t220" href="#t220">220</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="t221" href="#t221">221</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="t222" href="#t222">222</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="t223" href="#t223">223</a></span><span class="t">        <span class="op">**</span><span class="nam">kwargs</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="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="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">&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">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="t228" href="#t228">228</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="t229" href="#t229">229</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>&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">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="t231" href="#t231">231</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="pln"><span class="n"><a id="t232" href="#t232">232</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="t233" href="#t233">233</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="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">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="t236" href="#t236">236</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>&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">"--input_ser_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">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="t239" href="#t239">239</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="pln"><span class="n"><a id="t240" href="#t240">240</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="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>&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">"--output_csv_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">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 file. Accepted formats: csv."</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="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">required_args</span><span class="op">.</span><span class="nam">add_argument</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">"--output_jpg_path"</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">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="t249" href="#t249">249</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="t250" href="#t250">250</a></span><span class="t">    <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">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="t253" href="#t253">253</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="t254" href="#t254">254</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="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">interseqcorr</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">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="t258" href="#t258">258</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="t259" href="#t259">259</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="t260" href="#t260">260</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="t261" href="#t261">261</a></span><span class="t">    <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="pln"><span class="n"><a id="t263" href="#t263">263</a></span><span class="t">&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">__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="t265" href="#t265">265</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">
@@ -328,8 +353,8 @@ <h2>
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-            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.4">coverage.py v7.6.4</a>,
-            created at 2024-11-04 11:05 +0000
+            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
+            created at 2024-11-15 12:07 +0000
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diff --git a/coverage/z_957b841f7413f0a1___init___py.html b/coverage/z_957b841f7413f0a1___init___py.html
index 62061dd..f8d426b 100644
--- a/coverage/z_957b841f7413f0a1___init___py.html
+++ b/coverage/z_957b841f7413f0a1___init___py.html
@@ -64,8 +64,8 @@ <h2>
             <a id="indexLink" class="nav" href="index.html">&Hat; index</a> &nbsp; &nbsp;
             <a id="nextFileLink" class="nav" href="z_020f76a90aa51c7b_test_bipopulations_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
-            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.4">coverage.py v7.6.4</a>,
-            created at 2024-11-04 11:05 +0000
+            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
+            created at 2024-11-15 12:07 +0000
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             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -88,8 +88,8 @@ <h2>
             <a class="nav" href="index.html">&Hat; index</a> &nbsp; &nbsp;
             <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/7.6.4">coverage.py v7.6.4</a>,
-            created at 2024-11-04 11:05 +0000
+            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
+            created at 2024-11-15 12:07 +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 b29b138..8225f6b 100644
--- a/coverage/z_97f47455ed834d2d_test_correlation_py.html
+++ b/coverage/z_97f47455ed834d2d_test_correlation_py.html
@@ -64,8 +64,8 @@ <h2>
             <a id="indexLink" class="nav" href="index.html">&Hat; index</a> &nbsp; &nbsp;
             <a id="nextFileLink" class="nav" href="z_8030ef0ea5bfd6aa_test_canal_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
-            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.4">coverage.py v7.6.4</a>,
-            created at 2024-11-04 11:05 +0000
+            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
+            created at 2024-11-15 12:07 +0000
         </p>
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             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -208,8 +208,8 @@ <h2>
             <a class="nav" href="index.html">&Hat; index</a> &nbsp; &nbsp;
             <a class="nav" href="z_8030ef0ea5bfd6aa_test_canal_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
-            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.4">coverage.py v7.6.4</a>,
-            created at 2024-11-04 11:05 +0000
+            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
+            created at 2024-11-15 12:07 +0000
         </p>
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 </footer>
diff --git a/coverage/z_9de9475b0a6fab52___init___py.html b/coverage/z_9de9475b0a6fab52___init___py.html
index a34df4e..58a9d59 100644
--- a/coverage/z_9de9475b0a6fab52___init___py.html
+++ b/coverage/z_9de9475b0a6fab52___init___py.html
@@ -64,8 +64,8 @@ <h2>
             <a id="indexLink" class="nav" href="index.html">&Hat; index</a> &nbsp; &nbsp;
             <a id="nextFileLink" class="nav" href="z_9de9475b0a6fab52_average_stiffness_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
-            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.4">coverage.py v7.6.4</a>,
-            created at 2024-11-04 11:05 +0000
+            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
+            created at 2024-11-15 12:07 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -92,8 +92,8 @@ <h2>
             <a class="nav" href="index.html">&Hat; index</a> &nbsp; &nbsp;
             <a class="nav" href="z_9de9475b0a6fab52_average_stiffness_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
-            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.4">coverage.py v7.6.4</a>,
-            created at 2024-11-04 11:05 +0000
+            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
+            created at 2024-11-15 12:07 +0000
         </p>
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 </footer>
diff --git a/coverage/z_9de9475b0a6fab52_average_stiffness_py.html b/coverage/z_9de9475b0a6fab52_average_stiffness_py.html
index 7330025..5e09ac8 100644
--- a/coverage/z_9de9475b0a6fab52_average_stiffness_py.html
+++ b/coverage/z_9de9475b0a6fab52_average_stiffness_py.html
@@ -2,7 +2,7 @@
 <html lang="en">
 <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8">
-    <title>Coverage for biobb_dna/stiffness/average_stiffness.py: 73%</title>
+    <title>Coverage for biobb_dna/stiffness/average_stiffness.py: 74%</title>
     <link rel="icon" sizes="32x32" href="favicon_32_cb_58284776.png">
     <link rel="stylesheet" href="style_cb_8e611ae1.css" type="text/css">
     <script src="coverage_html_cb_6fb7b396.js" defer></script>
@@ -12,7 +12,7 @@
     <div class="content">
         <h1>
             <span class="text">Coverage for </span><b>biobb_dna/stiffness/average_stiffness.py</b>:
-            <span class="pc_cov">73%</span>
+            <span class="pc_cov">74%</span>
         </h1>
         <aside id="help_panel_wrapper">
             <input id="help_panel_state" type="checkbox">
@@ -54,8 +54,8 @@ <h1>
             </div>
         </aside>
         <h2>
-            <span class="text">90 statements &nbsp;</span>
-            <button type="button" class="run button_toggle_run" value="run" data-shortcut="r" title="Toggle lines run">66<span class="text"> run</span></button>
+            <span class="text">92 statements &nbsp;</span>
+            <button type="button" class="run button_toggle_run" value="run" data-shortcut="r" title="Toggle lines run">68<span class="text"> run</span></button>
             <button type="button" class="mis show_mis button_toggle_mis" value="mis" data-shortcut="m" title="Toggle lines missing">24<span class="text"> missing</span></button>
             <button type="button" class="exc show_exc button_toggle_exc" value="exc" data-shortcut="x" title="Toggle lines excluded">0<span class="text"> excluded</span></button>
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@@ -64,8 +64,8 @@ <h2>
             <a id="indexLink" class="nav" href="index.html">&Hat; index</a> &nbsp; &nbsp;
             <a id="nextFileLink" class="nav" href="z_9de9475b0a6fab52_basepair_stiffness_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
-            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.4">coverage.py v7.6.4</a>,
-            created at 2024-11-04 11:05 +0000
+            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
+            created at 2024-11-15 12:07 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -84,240 +84,261 @@ <h2>
     <p class="pln"><span class="n"><a id="t2" href="#t2">2</a></span><span class="t"><span class="str">"""Module containing the AverageStiffness class and the command line interface."""</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t3" href="#t3">3</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t4" href="#t4">4</a></span><span class="t"><span class="key">import</span> <span class="nam">argparse</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t5" href="#t5">5</a></span><span class="t"><span class="key">from</span> <span class="nam">typing</span> <span class="key">import</span> <span class="nam">Optional</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t6" href="#t6">6</a></span><span class="t"><span class="key">from</span> <span class="nam">pathlib</span> <span class="key">import</span> <span class="nam">Path</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t5" href="#t5">5</a></span><span class="t"><span class="key">from</span> <span class="nam">pathlib</span> <span class="key">import</span> <span class="nam">Path</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t6" href="#t6">6</a></span><span class="t"><span class="key">from</span> <span class="nam">typing</span> <span class="key">import</span> <span class="nam">Optional</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t7" href="#t7">7</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t8" href="#t8">8</a></span><span class="t"><span class="key">import</span> <span class="nam">matplotlib</span><span class="op">.</span><span class="nam">pyplot</span> <span class="key">as</span> <span class="nam">plt</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t9" href="#t9">9</a></span><span class="t"><span class="key">import</span> <span class="nam">pandas</span> <span class="key">as</span> <span class="nam">pd</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t10" href="#t10">10</a></span><span class="t"><span class="key">import</span> <span class="nam">numpy</span> <span class="key">as</span> <span class="nam">np</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t11" href="#t11">11</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_dna</span><span class="op">.</span><span class="nam">utils</span> <span class="key">import</span> <span class="nam">constants</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t12" href="#t12">12</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_dna</span><span class="op">.</span><span class="nam">utils</span><span class="op">.</span><span class="nam">loader</span> <span class="key">import</span> <span class="nam">read_series</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t13" href="#t13">13</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_common</span><span class="op">.</span><span class="nam">generic</span><span class="op">.</span><span class="nam">biobb_object</span> <span class="key">import</span> <span class="nam">BiobbObject</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t14" href="#t14">14</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_common</span><span class="op">.</span><span class="nam">tools</span><span class="op">.</span><span class="nam">file_utils</span> <span class="key">import</span> <span class="nam">launchlogger</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t15" href="#t15">15</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_common</span><span class="op">.</span><span class="nam">configuration</span> <span class="key">import</span> <span class="nam">settings</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t16" href="#t16">16</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t17" href="#t17">17</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t18" href="#t18">18</a></span><span class="t"><span class="key">class</span> <span class="nam">AverageStiffness</span><span class="op">(</span><span class="nam">BiobbObject</span><span class="op">)</span><span class="op">:</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">"""</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 AverageStiffness</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 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="t22" href="#t22">22</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="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"><span class="str">            * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory.</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="run"><span class="n"><a id="t9" href="#t9">9</a></span><span class="t"><span class="key">import</span> <span class="nam">numpy</span> <span class="key">as</span> <span class="nam">np</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t10" href="#t10">10</a></span><span class="t"><span class="key">import</span> <span class="nam">pandas</span> <span class="key">as</span> <span class="nam">pd</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t11" href="#t11">11</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_common</span><span class="op">.</span><span class="nam">configuration</span> <span class="key">import</span> <span class="nam">settings</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t12" href="#t12">12</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_common</span><span class="op">.</span><span class="nam">generic</span><span class="op">.</span><span class="nam">biobb_object</span> <span class="key">import</span> <span class="nam">BiobbObject</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t13" href="#t13">13</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_common</span><span class="op">.</span><span class="nam">tools</span><span class="op">.</span><span class="nam">file_utils</span> <span class="key">import</span> <span class="nam">launchlogger</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t14" href="#t14">14</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t15" href="#t15">15</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_dna</span><span class="op">.</span><span class="nam">utils</span> <span class="key">import</span> <span class="nam">constants</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t16" href="#t16">16</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_dna</span><span class="op">.</span><span class="nam">utils</span><span class="op">.</span><span class="nam">common</span> <span class="key">import</span> <span class="nam">_from_string_to_list</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t17" href="#t17">17</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_dna</span><span class="op">.</span><span class="nam">utils</span><span class="op">.</span><span class="nam">loader</span> <span class="key">import</span> <span class="nam">read_series</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">&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="run"><span class="n"><a id="t20" href="#t20">20</a></span><span class="t"><span class="key">class</span> <span class="nam">AverageStiffness</span><span class="op">(</span><span class="nam">BiobbObject</span><span class="op">)</span><span class="op">:</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">"""</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 AverageStiffness</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 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="t24" href="#t24">24</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="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_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="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/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="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/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="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">            * **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="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 *usecols* 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">            * **helpar_name** (*str*) - (None) helical parameter name.</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">            * **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="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"><span class="str">            * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory.</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">            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="t42" href="#t42">42</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="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">                'helpar_name': 'twist',</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">                'sequence': 'GCAT',</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">            average_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_ser_path='/path/to/twist.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="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="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>&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">self</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_ser_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>&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>&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>&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="op">**</span><span class="nam">kwargs</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="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_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="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><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><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">KT</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">"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="t91" href="#t91">91</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="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="nam">int</span><span class="op">(</span><span class="nam">elem</span><span class="op">)</span> <span class="key">for</span> <span class="nam">elem</span> <span class="key">in</span> <span class="nam">_from_string_to_list</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><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="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="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="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="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:`AverageStiffness &lt;stiffness.average_stiffness.AverageStiffness>` 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"># 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">stage_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"># read input .ser file</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">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">stage_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="t140" href="#t140">140</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="t141" href="#t141">141</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="t142" href="#t142">142</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="t143" href="#t143">143</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="t144" href="#t144">144</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="t145" href="#t145">145</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="t146" href="#t146">146</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="t147" href="#t147">147</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="t148" href="#t148">148</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="t149" href="#t149">149</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="t150" href="#t150">150</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="t151" href="#t151">151</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="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">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"># calculate average stiffness</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">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="t156" href="#t156">156</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="t157" href="#t157">157</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="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"># save plot</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">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="t161" href="#t161">161</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="t162" href="#t162">162</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="t163" href="#t163">163</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="t164" href="#t164">164</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="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="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="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">xlabels</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_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="t168" href="#t168">168</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="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 Helical Parameter Stiffness: "</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"{self.helpar_name.capitalize()}"</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">savefig</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">stage_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="t174" href="#t174">174</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="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 table</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">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="t178" href="#t178">178</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="t179" href="#t179">179</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="t180" href="#t180">180</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="t181" href="#t181">181</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">stage_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="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="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="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"># Copy files to host</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">copy_to_host</span><span class="op">(</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="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"># get helical parameter from filename if not specified</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="run"><span class="n"><a id="t115" href="#t115">115</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="t116" href="#t116">116</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="t117" href="#t117">117</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>&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">in</span> <span class="nam">Path</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">stage_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="pln"><span class="n"><a id="t119" href="#t119">119</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="t120" href="#t120">120</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="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="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="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">"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="t124" href="#t124">124</a></span><span class="t">                    <span class="str">"so it must be specified!"</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="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="mis show_mis"><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>&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="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 base length and 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="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="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">"kcal/(mol*degree&#178;)"</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">scale</span> <span class="op">=</span> <span class="num">1.0</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="key">else</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">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="t139" href="#t139">139</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="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"># check seqpos</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="key">if</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="t143" href="#t143">143</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="t144" href="#t144">144</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="t145" href="#t145">145</a></span><span class="t">                    <span class="str">f"seqpos values must be between 1 and {len(self.sequence) - 2}"</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="op">)</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="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="t148" href="#t148">148</a></span><span class="t">                <span class="key">raise</span> <span class="nam">ValueError</span><span class="op">(</span><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="t149" href="#t149">149</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="t150" href="#t150">150</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="key">None</span>  <span class="com"># type: ignore</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"># read input .ser file</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">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="t154" href="#t154">154</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="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">usecols</span><span class="op">=</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</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="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="key">not</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="t157" href="#t157">157</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="t158" href="#t158">158</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="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><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="t160" href="#t160">160</a></span><span class="t">            <span class="nam">xlabels</span> <span class="op">=</span> <span class="op">[</span><span class="str">f"{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="t161" href="#t161">161</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="t162" href="#t162">162</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="t163" href="#t163">163</a></span><span class="t">            <span class="nam">xlabels</span> <span class="op">=</span> <span class="op">[</span><span class="str">f"{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="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"># calculate average stiffness</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">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="t167" href="#t167">167</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="t168" href="#t168">168</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="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"># save plot</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">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="t172" href="#t172">172</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">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> <span class="nam">avg_stiffness</span><span class="op">,</span> <span class="str">"-o"</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_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="t174" href="#t174">174</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="t175" href="#t175">175</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="t176" href="#t176">176</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="t177" href="#t177">177</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="t178" href="#t178">178</a></span><span class="t">            <span class="str">"Base Pair Helical Parameter Stiffness: "</span> <span class="str">f"{self.helpar_name.capitalize()}"</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>&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">fig</span><span class="op">.</span><span class="nam">savefig</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">stage_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="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> <span class="nam">index</span><span class="op">=</span><span class="nam">xlabels</span><span class="op">,</span> <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>&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>&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">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">stage_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"># Remove temporary file(s)</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">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="t190" href="#t190">190</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="str">""</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="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">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="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="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="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">return</span> <span class="num">0</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="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"># Copy files to host</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">copy_to_host</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><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="str">""</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">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">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="t200" href="#t200">200</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="t201" href="#t201">201</a></span><span class="t">        <span class="nam">properties</span><span class="op">:</span> <span class="nam">Optional</span><span class="op">[</span><span class="nam">dict</span><span class="op">]</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="t202" href="#t202">202</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="t203" href="#t203">203</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="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">AverageStiffness</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_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="t207" href="#t207">207</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="t208" href="#t208">208</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="t209" href="#t209">209</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="t210" href="#t210">210</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="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">average_stiffness</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_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="t204" href="#t204">204</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>&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_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">Optional</span><span class="op">[</span><span class="nam">dict</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="pln"><span class="n"><a id="t207" href="#t207">207</a></span><span class="t">    <span class="op">**</span><span class="nam">kwargs</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="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="t209" href="#t209">209</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="t210" href="#t210">210</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="t211" href="#t211">211</a></span><span class="t">&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="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="t213" href="#t213">213</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="t214" href="#t214">214</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="t215" href="#t215">215</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="t216" href="#t216">216</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="t217" href="#t217">217</a></span><span class="t">&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">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="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">'--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="t220" href="#t220">220</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="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_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="t222" href="#t222">222</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="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_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="t224" href="#t224">224</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="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">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="t227" href="#t227">227</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="t228" href="#t228">228</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="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">average_stiffness</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">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="t232" href="#t232">232</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="t233" href="#t233">233</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="t234" href="#t234">234</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="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">&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">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="t238" href="#t238">238</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="run"><span class="n"><a id="t212" href="#t212">212</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="t213" href="#t213">213</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="t214" href="#t214">214</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="t215" href="#t215">215</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="t216" href="#t216">216</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="t217" href="#t217">217</a></span><span class="t">        <span class="op">**</span><span class="nam">kwargs</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="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="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>&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">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="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="pln"><span class="n"><a id="t226" href="#t226">226</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="t227" href="#t227">227</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="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">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="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>&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="str">"--input_ser_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">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">"Helical parameter input ser file path. Accepted formats: ser."</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="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>&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">"--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">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="t238" href="#t238">238</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="pln"><span class="n"><a id="t239" href="#t239">239</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="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>&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">"--output_jpg_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">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 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="t244" href="#t244">244</a></span><span class="t">    <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="mis show_mis"><span class="n"><a id="t246" href="#t246">246</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="t247" href="#t247">247</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="t248" href="#t248">248</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="t249" href="#t249">249</a></span><span class="t">&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">average_stiffness</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_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="t252" href="#t252">252</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="t253" href="#t253">253</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="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>&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="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="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>
 </main>
 <footer>
     <div class="content">
@@ -326,8 +347,8 @@ <h2>
             <a class="nav" href="index.html">&Hat; index</a> &nbsp; &nbsp;
             <a class="nav" href="z_9de9475b0a6fab52_basepair_stiffness_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
-            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.4">coverage.py v7.6.4</a>,
-            created at 2024-11-04 11:05 +0000
+            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
+            created at 2024-11-15 12:07 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_9de9475b0a6fab52_basepair_stiffness_py.html b/coverage/z_9de9475b0a6fab52_basepair_stiffness_py.html
index 0822b46..a0bc361 100644
--- a/coverage/z_9de9475b0a6fab52_basepair_stiffness_py.html
+++ b/coverage/z_9de9475b0a6fab52_basepair_stiffness_py.html
@@ -54,8 +54,8 @@ <h1>
             </div>
         </aside>
         <h2>
-            <span class="text">81 statements &nbsp;</span>
-            <button type="button" class="run button_toggle_run" value="run" data-shortcut="r" title="Toggle lines run">64<span class="text"> run</span></button>
+            <span class="text">82 statements &nbsp;</span>
+            <button type="button" class="run button_toggle_run" value="run" data-shortcut="r" title="Toggle lines run">65<span class="text"> run</span></button>
             <button type="button" class="mis show_mis button_toggle_mis" value="mis" data-shortcut="m" title="Toggle lines missing">17<span class="text"> missing</span></button>
             <button type="button" class="exc show_exc button_toggle_exc" value="exc" data-shortcut="x" title="Toggle lines excluded">0<span class="text"> excluded</span></button>
         </h2>
@@ -64,8 +64,8 @@ <h2>
             <a id="indexLink" class="nav" href="index.html">&Hat; index</a> &nbsp; &nbsp;
             <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/7.6.4">coverage.py v7.6.4</a>,
-            created at 2024-11-04 11:05 +0000
+            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
+            created at 2024-11-15 12:07 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -83,257 +83,295 @@ <h2>
     <p class="pln"><span class="n"><a id="t1" href="#t1">1</a></span><span class="t"><span class="com">#!/usr/bin/env python3</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t2" href="#t2">2</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t3" href="#t3">3</a></span><span class="t"><span class="str">"""Module containing the HelParStiffness class and the command line interface."""</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t4" href="#t4">4</a></span><span class="t"><span class="key">import</span> <span class="nam">argparse</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t5" href="#t5">5</a></span><span class="t"><span class="key">from</span> <span class="nam">typing</span> <span class="key">import</span> <span class="nam">Optional</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t4" href="#t4">4</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t5" href="#t5">5</a></span><span class="t"><span class="key">import</span> <span class="nam">argparse</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t6" href="#t6">6</a></span><span class="t"><span class="key">from</span> <span class="nam">pathlib</span> <span class="key">import</span> <span class="nam">Path</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t7" href="#t7">7</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t8" href="#t8">8</a></span><span class="t"><span class="key">import</span> <span class="nam">pandas</span> <span class="key">as</span> <span class="nam">pd</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t9" href="#t9">9</a></span><span class="t"><span class="key">import</span> <span class="nam">numpy</span> <span class="key">as</span> <span class="nam">np</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t10" href="#t10">10</a></span><span class="t"><span class="key">import</span> <span class="nam">matplotlib</span><span class="op">.</span><span class="nam">pyplot</span> <span class="key">as</span> <span class="nam">plt</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t11" href="#t11">11</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t12" href="#t12">12</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_common</span><span class="op">.</span><span class="nam">generic</span><span class="op">.</span><span class="nam">biobb_object</span> <span class="key">import</span> <span class="nam">BiobbObject</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t13" href="#t13">13</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_common</span><span class="op">.</span><span class="nam">configuration</span> <span class="key">import</span> <span class="nam">settings</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t7" href="#t7">7</a></span><span class="t"><span class="key">from</span> <span class="nam">typing</span> <span class="key">import</span> <span class="nam">Optional</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t8" href="#t8">8</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t9" href="#t9">9</a></span><span class="t"><span class="key">import</span> <span class="nam">matplotlib</span><span class="op">.</span><span class="nam">pyplot</span> <span class="key">as</span> <span class="nam">plt</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t10" href="#t10">10</a></span><span class="t"><span class="key">import</span> <span class="nam">numpy</span> <span class="key">as</span> <span class="nam">np</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t11" href="#t11">11</a></span><span class="t"><span class="key">import</span> <span class="nam">pandas</span> <span class="key">as</span> <span class="nam">pd</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t12" href="#t12">12</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_common</span><span class="op">.</span><span class="nam">configuration</span> <span class="key">import</span> <span class="nam">settings</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t13" href="#t13">13</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_common</span><span class="op">.</span><span class="nam">generic</span><span class="op">.</span><span class="nam">biobb_object</span> <span class="key">import</span> <span class="nam">BiobbObject</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t14" href="#t14">14</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_common</span><span class="op">.</span><span class="nam">tools</span><span class="op">.</span><span class="nam">file_utils</span> <span class="key">import</span> <span class="nam">launchlogger</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t15" href="#t15">15</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_dna</span><span class="op">.</span><span class="nam">utils</span><span class="op">.</span><span class="nam">loader</span> <span class="key">import</span> <span class="nam">load_data</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t16" href="#t16">16</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t17" href="#t17">17</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t18" href="#t18">18</a></span><span class="t"><span class="key">class</span> <span class="nam">BPStiffness</span><span class="op">(</span><span class="nam">BiobbObject</span><span class="op">)</span><span class="op">:</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">"""</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"><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"><span class="str">            * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory.</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.stiffness.basepair_stiffness import basepair_stiffness</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t15" href="#t15">15</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t16" href="#t16">16</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_dna</span><span class="op">.</span><span class="nam">utils</span><span class="op">.</span><span class="nam">common</span> <span class="key">import</span> <span class="nam">_from_string_to_list</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t17" href="#t17">17</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_dna</span><span class="op">.</span><span class="nam">utils</span><span class="op">.</span><span class="nam">loader</span> <span class="key">import</span> <span class="nam">load_data</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">&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="run"><span class="n"><a id="t20" href="#t20">20</a></span><span class="t"><span class="key">class</span> <span class="nam">BPStiffness</span><span class="op">(</span><span class="nam">BiobbObject</span><span class="op">)</span><span class="op">:</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">"""</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 BPStiffness</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 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="t24" href="#t24">24</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="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 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="t28" href="#t28">28</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="t29" href="#t29">29</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="t30" href="#t30">30</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="t31" href="#t31">31</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="t32" href="#t32">32</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="t33" href="#t33">33</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="t34" href="#t34">34</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="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">            * **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="t37" href="#t37">37</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="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"><span class="str">            * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory.</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">            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">                'KT': 0.592186827,</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">                '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="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">            basepair_stiffness(</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_shift='path/to/basepair/shift.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_slide='path/to/basepair/slide.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_rise='path/to/basepair/rise.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_tilt='path/to/basepair/tilt.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_roll='path/to/basepair/roll.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">                input_filename_twist='path/to/basepair/twist.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_csv_path='path/to/output/file.csv',</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">                output_jpg_path='path/to/output/plot.jpg',</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">                properties=prop)</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">    Info:</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">        * wrapped_software:</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: In house</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">            * license: Apache-2.0</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">        * ontology:</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">            * name: EDAM</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">            * schema: http://edamontology.org/EDAM.owl</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="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">            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="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">                'KT': 0.592186827,</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">                '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="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">            basepair_stiffness(</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_shift='path/to/basepair/shift.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_slide='path/to/basepair/slide.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_rise='path/to/basepair/rise.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">                input_filename_tilt='path/to/basepair/tilt.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">                input_filename_roll='path/to/basepair/roll.csv',</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">                input_filename_twist='path/to/basepair/twist.csv',</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">                output_csv_path='path/to/output/file.csv',</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">                output_jpg_path='path/to/output/plot.jpg',</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">                properties=prop)</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">    Info:</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">        * wrapped_software:</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: In house</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">            * license: Apache-2.0</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">        * ontology:</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">            * name: EDAM</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">            * schema: http://edamontology.org/EDAM.owl</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="run"><span class="n"><a id="t69" href="#t69">69</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="t70" href="#t70">70</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="t71" href="#t71">71</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="t72" href="#t72">72</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="t73" href="#t73">73</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="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"># Call parent class constructor</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">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="t77" href="#t77">77</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="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"># Input/Output files</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">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="t81" href="#t81">81</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="t82" href="#t82">82</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="t83" href="#t83">83</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="t84" href="#t84">84</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="t85" href="#t85">85</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="t86" href="#t86">86</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="t87" href="#t87">87</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="t88" href="#t88">88</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="t89" href="#t89">89</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="t90" href="#t90">90</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="t91" href="#t91">91</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="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">        <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="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="t96" href="#t96">96</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="t97" href="#t97">97</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="t98" href="#t98">98</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="t99" href="#t99">99</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="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 the properties</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_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="t103" href="#t103">103</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="t104" href="#t104">104</a></span><span class="t">&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="op">@</span><span class="nam">launchlogger</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">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="t107" href="#t107">107</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="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"># Setup Biobb</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">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="t111" href="#t111">111</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="t112" href="#t112">112</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="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"># read input</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">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="t116" href="#t116">116</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="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="t117" href="#t117">117</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="t118" href="#t118">118</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="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="t119" href="#t119">119</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="t120" href="#t120">120</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="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="t121" href="#t121">121</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="t122" href="#t122">122</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="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="t123" href="#t123">123</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="t124" href="#t124">124</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="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="t125" href="#t125">125</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="t126" href="#t126">126</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="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="t69" href="#t69">69</a></span><span class="t"><span class="str">    """</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="run"><span class="n"><a id="t71" href="#t71">71</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="t72" href="#t72">72</a></span><span class="t">        <span class="nam">self</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="nam">input_filename_shift</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="nam">input_filename_slide</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="nam">input_filename_rise</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="nam">input_filename_tilt</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="nam">input_filename_roll</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="nam">input_filename_twist</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="nam">output_csv_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="nam">output_jpg_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="nam">properties</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">        <span class="op">**</span><span class="nam">kwargs</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="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="t84" href="#t84">84</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="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"># Call parent class constructor</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">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="t88" href="#t88">88</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="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"># Input/Output files</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">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="t92" href="#t92">92</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="t93" href="#t93">93</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="t94" href="#t94">94</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="t95" href="#t95">95</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="t96" href="#t96">96</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="t97" href="#t97">97</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="t98" href="#t98">98</a></span><span class="t">                <span class="str">"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="t99" href="#t99">99</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="t100" href="#t100">100</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="t101" href="#t101">101</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="t102" href="#t102">102</a></span><span class="t">                <span class="str">"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="t103" href="#t103">103</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="t104" href="#t104">104</a></span><span class="t">        <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="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">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="t107" href="#t107">107</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><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="t108" href="#t108">108</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="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="nam">int</span><span class="op">(</span><span class="nam">elem</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">for</span> <span class="nam">elem</span> <span class="key">in</span> <span class="nam">_from_string_to_list</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">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><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="t112" href="#t112">112</a></span><span class="t">            <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="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 the properties</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_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="t117" href="#t117">117</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="t118" href="#t118">118</a></span><span class="t">&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="op">@</span><span class="nam">launchlogger</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">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="t121" href="#t121">121</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="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"># Setup Biobb</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">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="t125" href="#t125">125</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="t126" href="#t126">126</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="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"># 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="t129" href="#t129">129</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="t130" href="#t130">130</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="t131" href="#t131">131</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="t132" href="#t132">132</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="t133" href="#t133">133</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="t134" href="#t134">134</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="t135" href="#t135">135</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="t136" href="#t136">136</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="t137" href="#t137">137</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="t138" href="#t138">138</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="t139" href="#t139">139</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="t140" href="#t140">140</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="t141" href="#t141">141</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="t142" href="#t142">142</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="t143" href="#t143">143</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="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">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">stage_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="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">stiff_df</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">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="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">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="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"{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="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">text</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="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="t163" href="#t163">163</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="t164" href="#t164">164</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="t165" href="#t165">165</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="t166" href="#t166">166</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="t167" href="#t167">167</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="t168" href="#t168">168</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="t169" href="#t169">169</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="t170" href="#t170">170</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="t171" href="#t171">171</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="t172" href="#t172">172</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="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">stage_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"># Copy files to host</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">copy_to_host</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="str">""</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="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="t128" href="#t128">128</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="t129" href="#t129">129</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">stage_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="t130" href="#t130">130</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">stage_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="t131" href="#t131">131</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">stage_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="t132" href="#t132">132</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">stage_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="t133" href="#t133">133</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">stage_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="t134" href="#t134">134</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">stage_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="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"># 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="t137" href="#t137">137</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="t138" href="#t138">138</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="t139" href="#t139">139</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><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="t140" href="#t140">140</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="t141" href="#t141">141</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="t142" href="#t142">142</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="t143" href="#t143">143</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="t144" href="#t144">144</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="t145" href="#t145">145</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="t146" href="#t146">146</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><span class="nam">stiff_diag</span><span class="op">,</span> <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> <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="t147" href="#t147">147</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="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">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">stage_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="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">stiff_df</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">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="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="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">0.5</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">0.5</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"{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="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="pln"><span class="n"><a id="t165" href="#t165">165</a></span><span class="t">                <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">text</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="num">0</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="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="t169" href="#t169">169</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="t170" href="#t170">170</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="t171" href="#t171">171</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="t172" href="#t172">172</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="pln"><span class="n"><a id="t173" href="#t173">173</a></span><span class="t">        <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_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="t175" href="#t175">175</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="t176" href="#t176">176</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="t177" href="#t177">177</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="t178" href="#t178">178</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">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="t179" href="#t179">179</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="t180" href="#t180">180</a></span><span class="t">        <span class="nam">fig</span><span class="op">.</span><span class="nam">savefig</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">stage_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="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="t181" href="#t181">181</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="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"># Copy files to host</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">copy_to_host</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="pln"><span class="n"><a id="t186" href="#t186">186</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="t187" href="#t187">187</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><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="str">""</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">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="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="run"><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">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="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">&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">Optional</span><span class="op">[</span><span class="nam">dict</span><span class="op">]</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="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="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="run"><span class="n"><a id="t192" href="#t192">192</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="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">&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="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="t196" href="#t196">196</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>&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_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="t198" href="#t198">198</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>&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">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="t200" href="#t200">200</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>&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_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="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>&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_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">Optional</span><span class="op">[</span><span class="nam">dict</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="pln"><span class="n"><a id="t205" href="#t205">205</a></span><span class="t">    <span class="op">**</span><span class="nam">kwargs</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="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:`BPStiffness &lt;stiffness.basepair_stiffness.BPStiffness>` 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.basepair_stiffness.BPStiffness.BPStiffness.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">BPStiffness</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_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="t212" href="#t212">212</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="t213" href="#t213">213</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="t214" href="#t214">214</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="t215" href="#t215">215</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="t216" href="#t216">216</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="t217" href="#t217">217</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="t218" href="#t218">218</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="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>&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="op">**</span><span class="nam">kwargs</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="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="t222" href="#t222">222</a></span><span class="t">&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">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="t225" href="#t225">225</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="t226" href="#t226">226</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>&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">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="t228" href="#t228">228</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="pln"><span class="n"><a id="t229" href="#t229">229</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="t230" href="#t230">230</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="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">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="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>&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">"--input_filename_shift"</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">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 csv file with shift inputs. 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">    <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">required_args</span><span class="op">.</span><span class="nam">add_argument</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="str">"--input_filename_slide"</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">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">"Path to csv file with slide inputs. Accepted formats: csv."</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="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>&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="str">"--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">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 csv file with rise inputs. Accepted formats: csv."</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="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">required_args</span><span class="op">.</span><span class="nam">add_argument</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">"--input_filename_tilt"</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">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="t251" href="#t251">251</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="pln"><span class="n"><a id="t252" href="#t252">252</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="t253" href="#t253">253</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>&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">"--input_filename_roll"</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">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">"Path to csv file with roll inputs. Accepted formats: csv."</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="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>&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">"--input_filename_twist"</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">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 csv file with twist inputs. Accepted formats: csv."</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="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">required_args</span><span class="op">.</span><span class="nam">add_argument</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="str">"--output_csv_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">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">"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="t267" href="#t267">267</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="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>&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">"--output_jpg_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">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 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="t272" href="#t272">272</a></span><span class="t">    <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">basepair_stiffness</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">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="t280" href="#t280">280</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="t281" href="#t281">281</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="t282" href="#t282">282</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="t283" href="#t283">283</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="t284" href="#t284">284</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="t285" href="#t285">285</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="t286" href="#t286">286</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="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>&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="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="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">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="t292" href="#t292">292</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">
@@ -342,8 +380,8 @@ <h2>
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-            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.4">coverage.py v7.6.4</a>,
-            created at 2024-11-04 11:05 +0000
+            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
+            created at 2024-11-15 12:07 +0000
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--- a/coverage/z_cda7f8e8576a7189_test_stiffness_py.html
+++ b/coverage/z_cda7f8e8576a7189_test_stiffness_py.html
@@ -64,8 +64,8 @@ <h2>
             <a id="indexLink" class="nav" href="index.html">&Hat; index</a> &nbsp; &nbsp;
             <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/7.6.4">coverage.py v7.6.4</a>,
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+            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
+            created at 2024-11-15 12:07 +0000
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@@ -129,8 +129,8 @@ <h2>
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             <a class="nav" href="z_833b0317e3c43dca___init___py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
-            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.4">coverage.py v7.6.4</a>,
-            created at 2024-11-04 11:05 +0000
+            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
+            created at 2024-11-15 12:07 +0000
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diff --git a/flake8/biobb_dna.interbp_correlations.interbpcorr.report.html b/flake8/biobb_dna.interbp_correlations.interbpcorr.report.html
new file mode 100644
index 0000000..88dec10
--- /dev/null
+++ b/flake8/biobb_dna.interbp_correlations.interbpcorr.report.html
@@ -0,0 +1,78 @@
+<!DOCTYPE html>
+<html>
+   <head>
+      <title>flake8 violations: biobb_dna/interbp_correlations/interbpcorr.py</title>
+      <meta http-equiv="Content-Type" value="text/html; charset=UTF-8">
+      <link rel="stylesheet" href="styles.css">
+<script>
+function bindHandler(link) {
+   var code = link.getAttribute('data-code');
+   var key = location.pathname + '#' + code;
+
+   var ul = link.parentNode.querySelector('.details');
+   if (sessionStorage[key] != 'open') {
+      ul.style.display = 'none';
+   }
+   link.addEventListener('click', function (event) {
+      if (!ul.style.display || ul.style.display == 'none') {
+         ul.style.display = 'block';
+         sessionStorage[key] = 'open';
+      } else {
+         ul.style.display = 'none';
+         sessionStorage[key] = 'closed';
+      }
+   });
+}
+
+window.addEventListener('DOMContentLoaded', function () {
+   var links = document.querySelectorAll('#index > li > a');
+   for (var i = 0; i < links.length; i++) {
+      bindHandler(links[i]);
+   }
+});
+</script>
+   </head>
+   <body>
+      <div id="masthead" class="sev-2"></div>
+      <div id="page">
+         <p id="srclink">
+            <a title="View full annotated source"
+               href="biobb_dna.interbp_correlations.interbpcorr.source.html">
+               <img src="file.svg" alt="&#x2261;">
+            </a></p>
+         <h1>
+            <a href="index.html">
+               <img src="back.svg" alt="&#x2B05;">
+               biobb_dna/interbp_correlations/interbpcorr.py
+            </a>
+         </h1>
+
+         <ul id="index">
+         
+         <li>
+            <a data-code="W503">
+               <span class="count sev-2">
+                  2
+               </span>
+               <strong>W503:</strong> line break before binary operator
+               
+            </a>
+            <ul class="details">
+            <li>
+               
+               <a href="biobb_dna.interbp_correlations.interbpcorr.source.html#l199">
+                  <tt><i>199</i>                 <span class="ow">and</span> <span class="n">ser2</span><span class="o">.</span><span class="n">name</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">constants</span><span class="o">.</span><span class="n">hp_angular</span></tt>
+               </a>
+            </li><li>
+               
+               <a href="biobb_dna.interbp_correlations.interbpcorr.source.html#l202">
+                  <tt><i>202</i>                 <span class="ow">and</span> <span class="n">ser1</span><span class="o">.</span><span class="n">name</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">constants</span><span class="o">.</span><span class="n">hp_angular</span></tt>
+               </a>
+            </li>
+            </ul>
+         </li>
+         
+         </ul>
+      </div>
+   </body>
+</html>
\ No newline at end of file
diff --git a/flake8/biobb_dna.interbp_correlations.interbpcorr.source.html b/flake8/biobb_dna.interbp_correlations.interbpcorr.source.html
new file mode 100644
index 0000000..49953cc
--- /dev/null
+++ b/flake8/biobb_dna.interbp_correlations.interbpcorr.source.html
@@ -0,0 +1,1178 @@
+<!DOCTYPE html>
+<html>
+   <head>
+      <title>biobb_dna/interbp_correlations/interbpcorr.py - flake8 annotated source</title>
+      <meta http-equiv="Content-Type" value="text/html; charset=UTF-8">
+      <link rel="stylesheet" href="styles.css">
+   </head>
+   <body>
+      <div id="masthead" class="sev-2"></div>
+      <div id="page">
+         <h1>
+            <a href="biobb_dna.interbp_correlations.interbpcorr.report.html">
+               <img src="back.svg" alt="&#x2B05;">
+               biobb_dna/interbp_correlations/interbpcorr.py source
+            </a>
+         </h1>
+
+         <div id="doc">
+            <div id="l1"
+               class="code sev- "><tt><i>1</i> <span class="ch">#!/usr/bin/env python3</span></tt>
+            </div>
+            <div id="l2"
+               class="code sev- "><tt><i>2</i> &nbsp;</tt>
+            </div>
+            <div id="l3"
+               class="code sev- "><tt><i>3</i> <span class="sd">&quot;&quot;&quot;Module containing the InterBasePairCorrelation class and the command line interface.&quot;&quot;&quot;</span></tt>
+            </div>
+            <div id="l4"
+               class="code sev- "><tt><i>4</i> &nbsp;</tt>
+            </div>
+            <div id="l5"
+               class="code sev- "><tt><i>5</i> <span class="kn">import</span> <span class="nn">argparse</span></tt>
+            </div>
+            <div id="l6"
+               class="code sev- "><tt><i>6</i> <span class="kn">from</span> <span class="nn">itertools</span> <span class="kn">import</span> <span class="n">product</span></tt>
+            </div>
+            <div id="l7"
+               class="code sev- "><tt><i>7</i> <span class="kn">from</span> <span class="nn">typing</span> <span class="kn">import</span> <span class="n">Optional</span></tt>
+            </div>
+            <div id="l8"
+               class="code sev- "><tt><i>8</i> &nbsp;</tt>
+            </div>
+            <div id="l9"
+               class="code sev- "><tt><i>9</i> <span class="kn">import</span> <span class="nn">matplotlib</span> <span class="k">as</span> <span class="nn">mpl</span></tt>
+            </div>
+            <div id="l10"
+               class="code sev- "><tt><i>10</i> <span class="kn">import</span> <span class="nn">matplotlib.pyplot</span> <span class="k">as</span> <span class="nn">plt</span></tt>
+            </div>
+            <div id="l11"
+               class="code sev- "><tt><i>11</i> <span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span></tt>
+            </div>
+            <div id="l12"
+               class="code sev- "><tt><i>12</i> <span class="kn">import</span> <span class="nn">pandas</span> <span class="k">as</span> <span class="nn">pd</span></tt>
+            </div>
+            <div id="l13"
+               class="code sev- "><tt><i>13</i> <span class="kn">from</span> <span class="nn">biobb_common.configuration</span> <span class="kn">import</span> <span class="n">settings</span></tt>
+            </div>
+            <div id="l14"
+               class="code sev- "><tt><i>14</i> <span class="kn">from</span> <span class="nn">biobb_common.generic.biobb_object</span> <span class="kn">import</span> <span class="n">BiobbObject</span></tt>
+            </div>
+            <div id="l15"
+               class="code sev- "><tt><i>15</i> <span class="kn">from</span> <span class="nn">biobb_common.tools.file_utils</span> <span class="kn">import</span> <span class="n">launchlogger</span></tt>
+            </div>
+            <div id="l16"
+               class="code sev- "><tt><i>16</i> &nbsp;</tt>
+            </div>
+            <div id="l17"
+               class="code sev- "><tt><i>17</i> <span class="kn">from</span> <span class="nn">biobb_dna.utils</span> <span class="kn">import</span> <span class="n">constants</span></tt>
+            </div>
+            <div id="l18"
+               class="code sev- "><tt><i>18</i> <span class="kn">from</span> <span class="nn">biobb_dna.utils.common</span> <span class="kn">import</span> <span class="n">_from_string_to_list</span></tt>
+            </div>
+            <div id="l19"
+               class="code sev- "><tt><i>19</i> <span class="kn">from</span> <span class="nn">biobb_dna.utils.loader</span> <span class="kn">import</span> <span class="n">read_series</span></tt>
+            </div>
+            <div id="l20"
+               class="code sev- "><tt><i>20</i> &nbsp;</tt>
+            </div>
+            <div id="l21"
+               class="code sev- "><tt><i>21</i> &nbsp;</tt>
+            </div>
+            <div id="l22"
+               class="code sev- "><tt><i>22</i> <span class="k">class</span> <span class="nc">InterBasePairCorrelation</span><span class="p">(</span><span class="n">BiobbObject</span><span class="p">):</span></tt>
+            </div>
+            <div id="l23"
+               class="code sev- "><tt><i>23</i> <span class="w">    </span><span class="sd">&quot;&quot;&quot;</span></tt>
+            </div>
+            <div id="l24"
+               class="code sev- "><tt><i>24</i> <span class="sd">    | biobb_dna InterBasePairCorrelation</span></tt>
+            </div>
+            <div id="l25"
+               class="code sev- "><tt><i>25</i> <span class="sd">    | Calculate correlation between all base pairs of a single sequence and for a single helical parameter.</span></tt>
+            </div>
+            <div id="l26"
+               class="code sev- "><tt><i>26</i> <span class="sd">    | Calculate correlation between neighboring base pairs and pairs of helical parameters.</span></tt>
+            </div>
+            <div id="l27"
+               class="code sev- "><tt><i>27</i> &nbsp;</tt>
+            </div>
+            <div id="l28"
+               class="code sev- "><tt><i>28</i> <span class="sd">    Args:</span></tt>
+            </div>
+            <div id="l29"
+               class="code sev- "><tt><i>29</i> <span class="sd">        input_filename_shift (str): Path to .ser file with data for helical parameter &#39;shift&#39;. File type: input. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/correlation/canal_output_shift.ser&gt;`_. Accepted formats: ser (edam:format_2330).</span></tt>
+            </div>
+            <div id="l30"
+               class="code sev- "><tt><i>30</i> <span class="sd">        input_filename_slide (str): Path to .ser file with data for helical parameter &#39;slide&#39;. File type: input. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/correlation/canal_output_slide.ser&gt;`_. Accepted formats: ser (edam:format_2330).</span></tt>
+            </div>
+            <div id="l31"
+               class="code sev- "><tt><i>31</i> <span class="sd">        input_filename_rise (str): Path to .ser file with data for helical parameter &#39;rise&#39;. File type: input. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/correlation/canal_output_rise.ser&gt;`_. Accepted formats: ser (edam:format_2330).</span></tt>
+            </div>
+            <div id="l32"
+               class="code sev- "><tt><i>32</i> <span class="sd">        input_filename_tilt (str): Path to .ser file with data for helical parameter &#39;tilt&#39;. File type: input. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/correlation/canal_output_tilt.ser&gt;`_. Accepted formats: ser (edam:format_2330).</span></tt>
+            </div>
+            <div id="l33"
+               class="code sev- "><tt><i>33</i> <span class="sd">        input_filename_roll (str): Path to .ser file with data for helical parameter &#39;roll&#39;. File type: input. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/correlation/canal_output_roll.ser&gt;`_. Accepted formats: ser (edam:format_2330).</span></tt>
+            </div>
+            <div id="l34"
+               class="code sev- "><tt><i>34</i> <span class="sd">        input_filename_twist (str): Path to .ser file with data for helical parameter &#39;twist&#39;. File type: input. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/correlation/canal_output_twist.ser&gt;`_. Accepted formats: ser (edam:format_2330).</span></tt>
+            </div>
+            <div id="l35"
+               class="code sev- "><tt><i>35</i> <span class="sd">        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&gt;`_. Accepted formats: csv (edam:format_3752).</span></tt>
+            </div>
+            <div id="l36"
+               class="code sev- "><tt><i>36</i> <span class="sd">        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&gt;`_. Accepted formats: jpg (edam:format_3579).</span></tt>
+            </div>
+            <div id="l37"
+               class="code sev- "><tt><i>37</i> <span class="sd">        properties (dict):</span></tt>
+            </div>
+            <div id="l38"
+               class="code sev- "><tt><i>38</i> <span class="sd">            * **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></tt>
+            </div>
+            <div id="l39"
+               class="code sev- "><tt><i>39</i> <span class="sd">            * **seqpos** (*list*) - (None) list of sequence positions (columns indices starting by 0) to analyze.  If not specified it will analyse the complete sequence.</span></tt>
+            </div>
+            <div id="l40"
+               class="code sev- "><tt><i>40</i> <span class="sd">            * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.</span></tt>
+            </div>
+            <div id="l41"
+               class="code sev- "><tt><i>41</i> <span class="sd">            * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.</span></tt>
+            </div>
+            <div id="l42"
+               class="code sev- "><tt><i>42</i> <span class="sd">            * **sandbox_path** (*str*) - (&quot;./&quot;) [WF property] Parent path to the sandbox directory.</span></tt>
+            </div>
+            <div id="l43"
+               class="code sev- "><tt><i>43</i> &nbsp;</tt>
+            </div>
+            <div id="l44"
+               class="code sev- "><tt><i>44</i> <span class="sd">    Examples:</span></tt>
+            </div>
+            <div id="l45"
+               class="code sev- "><tt><i>45</i> <span class="sd">        This is a use example of how to use the building block from Python::</span></tt>
+            </div>
+            <div id="l46"
+               class="code sev- "><tt><i>46</i> &nbsp;</tt>
+            </div>
+            <div id="l47"
+               class="code sev- "><tt><i>47</i> <span class="sd">            from biobb_dna.interbp_correlations.interbpcorr import interbpcorr</span></tt>
+            </div>
+            <div id="l48"
+               class="code sev- "><tt><i>48</i> &nbsp;</tt>
+            </div>
+            <div id="l49"
+               class="code sev- "><tt><i>49</i> <span class="sd">            interbpcorr(</span></tt>
+            </div>
+            <div id="l50"
+               class="code sev- "><tt><i>50</i> <span class="sd">                input_filename_shift=&#39;path/to/input/shift.ser&#39;,</span></tt>
+            </div>
+            <div id="l51"
+               class="code sev- "><tt><i>51</i> <span class="sd">                input_filename_slide=&#39;path/to/input/slide.ser&#39;,</span></tt>
+            </div>
+            <div id="l52"
+               class="code sev- "><tt><i>52</i> <span class="sd">                input_filename_rise=&#39;path/to/input/slide.ser&#39;,</span></tt>
+            </div>
+            <div id="l53"
+               class="code sev- "><tt><i>53</i> <span class="sd">                input_filename_tilt=&#39;path/to/input/tilt.ser&#39;,</span></tt>
+            </div>
+            <div id="l54"
+               class="code sev- "><tt><i>54</i> <span class="sd">                input_filename_roll=&#39;path/to/input/roll.ser&#39;,</span></tt>
+            </div>
+            <div id="l55"
+               class="code sev- "><tt><i>55</i> <span class="sd">                input_filename_twist=&#39;path/to/input/twist.ser&#39;,</span></tt>
+            </div>
+            <div id="l56"
+               class="code sev- "><tt><i>56</i> <span class="sd">                output_csv_path=&#39;path/to/output/file.csv&#39;,</span></tt>
+            </div>
+            <div id="l57"
+               class="code sev- "><tt><i>57</i> <span class="sd">                output_jpg_path=&#39;path/to/output/plot.jpg&#39;,</span></tt>
+            </div>
+            <div id="l58"
+               class="code sev- "><tt><i>58</i> <span class="sd">                properties=prop)</span></tt>
+            </div>
+            <div id="l59"
+               class="code sev- "><tt><i>59</i> <span class="sd">    Info:</span></tt>
+            </div>
+            <div id="l60"
+               class="code sev- "><tt><i>60</i> <span class="sd">        * wrapped_software:</span></tt>
+            </div>
+            <div id="l61"
+               class="code sev- "><tt><i>61</i> <span class="sd">            * name: In house</span></tt>
+            </div>
+            <div id="l62"
+               class="code sev- "><tt><i>62</i> <span class="sd">            * license: Apache-2.0</span></tt>
+            </div>
+            <div id="l63"
+               class="code sev- "><tt><i>63</i> <span class="sd">        * ontology:</span></tt>
+            </div>
+            <div id="l64"
+               class="code sev- "><tt><i>64</i> <span class="sd">            * name: EDAM</span></tt>
+            </div>
+            <div id="l65"
+               class="code sev- "><tt><i>65</i> <span class="sd">            * schema: http://edamontology.org/EDAM.owl</span></tt>
+            </div>
+            <div id="l66"
+               class="code sev- "><tt><i>66</i> &nbsp;</tt>
+            </div>
+            <div id="l67"
+               class="code sev- "><tt><i>67</i> <span class="sd">    &quot;&quot;&quot;</span></tt>
+            </div>
+            <div id="l68"
+               class="code sev- "><tt><i>68</i> &nbsp;</tt>
+            </div>
+            <div id="l69"
+               class="code sev- "><tt><i>69</i>     <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span></tt>
+            </div>
+            <div id="l70"
+               class="code sev- "><tt><i>70</i>         <span class="bp">self</span><span class="p">,</span></tt>
+            </div>
+            <div id="l71"
+               class="code sev- "><tt><i>71</i>         <span class="n">input_filename_shift</span><span class="p">,</span></tt>
+            </div>
+            <div id="l72"
+               class="code sev- "><tt><i>72</i>         <span class="n">input_filename_slide</span><span class="p">,</span></tt>
+            </div>
+            <div id="l73"
+               class="code sev- "><tt><i>73</i>         <span class="n">input_filename_rise</span><span class="p">,</span></tt>
+            </div>
+            <div id="l74"
+               class="code sev- "><tt><i>74</i>         <span class="n">input_filename_tilt</span><span class="p">,</span></tt>
+            </div>
+            <div id="l75"
+               class="code sev- "><tt><i>75</i>         <span class="n">input_filename_roll</span><span class="p">,</span></tt>
+            </div>
+            <div id="l76"
+               class="code sev- "><tt><i>76</i>         <span class="n">input_filename_twist</span><span class="p">,</span></tt>
+            </div>
+            <div id="l77"
+               class="code sev- "><tt><i>77</i>         <span class="n">output_csv_path</span><span class="p">,</span></tt>
+            </div>
+            <div id="l78"
+               class="code sev- "><tt><i>78</i>         <span class="n">output_jpg_path</span><span class="p">,</span></tt>
+            </div>
+            <div id="l79"
+               class="code sev- "><tt><i>79</i>         <span class="n">properties</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span></tt>
+            </div>
+            <div id="l80"
+               class="code sev- "><tt><i>80</i>         <span class="o">**</span><span class="n">kwargs</span><span class="p">,</span></tt>
+            </div>
+            <div id="l81"
+               class="code sev- "><tt><i>81</i>     <span class="p">)</span> <span class="o">-&gt;</span> <span class="kc">None</span><span class="p">:</span></tt>
+            </div>
+            <div id="l82"
+               class="code sev- "><tt><i>82</i>         <span class="n">properties</span> <span class="o">=</span> <span class="n">properties</span> <span class="ow">or</span> <span class="p">{}</span></tt>
+            </div>
+            <div id="l83"
+               class="code sev- "><tt><i>83</i> &nbsp;</tt>
+            </div>
+            <div id="l84"
+               class="code sev- "><tt><i>84</i>         <span class="c1"># Call parent class constructor</span></tt>
+            </div>
+            <div id="l85"
+               class="code sev- "><tt><i>85</i>         <span class="nb">super</span><span class="p">()</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="n">properties</span><span class="p">)</span></tt>
+            </div>
+            <div id="l86"
+               class="code sev- "><tt><i>86</i>         <span class="bp">self</span><span class="o">.</span><span class="n">locals_var_dict</span> <span class="o">=</span> <span class="nb">locals</span><span class="p">()</span><span class="o">.</span><span class="n">copy</span><span class="p">()</span></tt>
+            </div>
+            <div id="l87"
+               class="code sev- "><tt><i>87</i> &nbsp;</tt>
+            </div>
+            <div id="l88"
+               class="code sev- "><tt><i>88</i>         <span class="c1"># Input/Output files</span></tt>
+            </div>
+            <div id="l89"
+               class="code sev- "><tt><i>89</i>         <span class="bp">self</span><span class="o">.</span><span class="n">io_dict</span> <span class="o">=</span> <span class="p">{</span></tt>
+            </div>
+            <div id="l90"
+               class="code sev- "><tt><i>90</i>             <span class="s2">&quot;in&quot;</span><span class="p">:</span> <span class="p">{</span></tt>
+            </div>
+            <div id="l91"
+               class="code sev- "><tt><i>91</i>                 <span class="s2">&quot;input_filename_shift&quot;</span><span class="p">:</span> <span class="n">input_filename_shift</span><span class="p">,</span></tt>
+            </div>
+            <div id="l92"
+               class="code sev- "><tt><i>92</i>                 <span class="s2">&quot;input_filename_slide&quot;</span><span class="p">:</span> <span class="n">input_filename_slide</span><span class="p">,</span></tt>
+            </div>
+            <div id="l93"
+               class="code sev- "><tt><i>93</i>                 <span class="s2">&quot;input_filename_rise&quot;</span><span class="p">:</span> <span class="n">input_filename_rise</span><span class="p">,</span></tt>
+            </div>
+            <div id="l94"
+               class="code sev- "><tt><i>94</i>                 <span class="s2">&quot;input_filename_tilt&quot;</span><span class="p">:</span> <span class="n">input_filename_tilt</span><span class="p">,</span></tt>
+            </div>
+            <div id="l95"
+               class="code sev- "><tt><i>95</i>                 <span class="s2">&quot;input_filename_roll&quot;</span><span class="p">:</span> <span class="n">input_filename_roll</span><span class="p">,</span></tt>
+            </div>
+            <div id="l96"
+               class="code sev- "><tt><i>96</i>                 <span class="s2">&quot;input_filename_twist&quot;</span><span class="p">:</span> <span class="n">input_filename_twist</span><span class="p">,</span></tt>
+            </div>
+            <div id="l97"
+               class="code sev- "><tt><i>97</i>             <span class="p">},</span></tt>
+            </div>
+            <div id="l98"
+               class="code sev- "><tt><i>98</i>             <span class="s2">&quot;out&quot;</span><span class="p">:</span> <span class="p">{</span></tt>
+            </div>
+            <div id="l99"
+               class="code sev- "><tt><i>99</i>                 <span class="s2">&quot;output_csv_path&quot;</span><span class="p">:</span> <span class="n">output_csv_path</span><span class="p">,</span></tt>
+            </div>
+            <div id="l100"
+               class="code sev- "><tt><i>100</i>                 <span class="s2">&quot;output_jpg_path&quot;</span><span class="p">:</span> <span class="n">output_jpg_path</span><span class="p">,</span></tt>
+            </div>
+            <div id="l101"
+               class="code sev- "><tt><i>101</i>             <span class="p">},</span></tt>
+            </div>
+            <div id="l102"
+               class="code sev- "><tt><i>102</i>         <span class="p">}</span></tt>
+            </div>
+            <div id="l103"
+               class="code sev- "><tt><i>103</i> &nbsp;</tt>
+            </div>
+            <div id="l104"
+               class="code sev- "><tt><i>104</i>         <span class="bp">self</span><span class="o">.</span><span class="n">properties</span> <span class="o">=</span> <span class="n">properties</span></tt>
+            </div>
+            <div id="l105"
+               class="code sev- "><tt><i>105</i>         <span class="bp">self</span><span class="o">.</span><span class="n">sequence</span> <span class="o">=</span> <span class="n">properties</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">&quot;sequence&quot;</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span></tt>
+            </div>
+            <div id="l106"
+               class="code sev- "><tt><i>106</i>         <span class="bp">self</span><span class="o">.</span><span class="n">seqpos</span> <span class="o">=</span> <span class="p">[</span></tt>
+            </div>
+            <div id="l107"
+               class="code sev- "><tt><i>107</i>             <span class="nb">int</span><span class="p">(</span><span class="n">elem</span><span class="p">)</span> <span class="k">for</span> <span class="n">elem</span> <span class="ow">in</span> <span class="n">_from_string_to_list</span><span class="p">(</span><span class="n">properties</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">&quot;seqpos&quot;</span><span class="p">,</span> <span class="kc">None</span><span class="p">))</span></tt>
+            </div>
+            <div id="l108"
+               class="code sev- "><tt><i>108</i>         <span class="p">]</span></tt>
+            </div>
+            <div id="l109"
+               class="code sev- "><tt><i>109</i> &nbsp;</tt>
+            </div>
+            <div id="l110"
+               class="code sev- "><tt><i>110</i>         <span class="c1"># Check the properties</span></tt>
+            </div>
+            <div id="l111"
+               class="code sev- "><tt><i>111</i>         <span class="bp">self</span><span class="o">.</span><span class="n">check_properties</span><span class="p">(</span><span class="n">properties</span><span class="p">)</span></tt>
+            </div>
+            <div id="l112"
+               class="code sev- "><tt><i>112</i>         <span class="bp">self</span><span class="o">.</span><span class="n">check_arguments</span><span class="p">()</span></tt>
+            </div>
+            <div id="l113"
+               class="code sev- "><tt><i>113</i> &nbsp;</tt>
+            </div>
+            <div id="l114"
+               class="code sev- "><tt><i>114</i>     <span class="nd">@launchlogger</span></tt>
+            </div>
+            <div id="l115"
+               class="code sev- "><tt><i>115</i>     <span class="k">def</span> <span class="nf">launch</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">int</span><span class="p">:</span></tt>
+            </div>
+            <div id="l116"
+               class="code sev- "><tt><i>116</i> <span class="w">        </span><span class="sd">&quot;&quot;&quot;Execute the :class:`HelParCorrelation &lt;correlations.interbpcorr.InterBasePairCorrelation&gt;` object.&quot;&quot;&quot;</span></tt>
+            </div>
+            <div id="l117"
+               class="code sev- "><tt><i>117</i> &nbsp;</tt>
+            </div>
+            <div id="l118"
+               class="code sev- "><tt><i>118</i>         <span class="c1"># Setup Biobb</span></tt>
+            </div>
+            <div id="l119"
+               class="code sev- "><tt><i>119</i>         <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">check_restart</span><span class="p">():</span></tt>
+            </div>
+            <div id="l120"
+               class="code sev- "><tt><i>120</i>             <span class="k">return</span> <span class="mi">0</span></tt>
+            </div>
+            <div id="l121"
+               class="code sev- "><tt><i>121</i>         <span class="bp">self</span><span class="o">.</span><span class="n">stage_files</span><span class="p">()</span></tt>
+            </div>
+            <div id="l122"
+               class="code sev- "><tt><i>122</i> &nbsp;</tt>
+            </div>
+            <div id="l123"
+               class="code sev- "><tt><i>123</i>         <span class="c1"># check sequence</span></tt>
+            </div>
+            <div id="l124"
+               class="code sev- "><tt><i>124</i>         <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">sequence</span> <span class="ow">is</span> <span class="kc">None</span> <span class="ow">or</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">sequence</span><span class="p">)</span> <span class="o">&lt;</span> <span class="mi">2</span><span class="p">:</span></tt>
+            </div>
+            <div id="l125"
+               class="code sev- "><tt><i>125</i>             <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s2">&quot;sequence is null or too short!&quot;</span><span class="p">)</span></tt>
+            </div>
+            <div id="l126"
+               class="code sev- "><tt><i>126</i> &nbsp;</tt>
+            </div>
+            <div id="l127"
+               class="code sev- "><tt><i>127</i>         <span class="c1"># check seqpos</span></tt>
+            </div>
+            <div id="l128"
+               class="code sev- "><tt><i>128</i>         <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">seqpos</span><span class="p">:</span></tt>
+            </div>
+            <div id="l129"
+               class="code sev- "><tt><i>129</i>             <span class="k">if</span> <span class="ow">not</span> <span class="p">(</span><span class="nb">isinstance</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">seqpos</span><span class="p">,</span> <span class="nb">list</span><span class="p">)</span> <span class="ow">and</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">seqpos</span><span class="p">)</span> <span class="o">&gt;</span> <span class="mi">1</span><span class="p">):</span></tt>
+            </div>
+            <div id="l130"
+               class="code sev- "><tt><i>130</i>                 <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s2">&quot;seqpos must be a list of at least two integers&quot;</span><span class="p">)</span></tt>
+            </div>
+            <div id="l131"
+               class="code sev- "><tt><i>131</i>         <span class="k">else</span><span class="p">:</span></tt>
+            </div>
+            <div id="l132"
+               class="code sev- "><tt><i>132</i>             <span class="bp">self</span><span class="o">.</span><span class="n">seqpos</span> <span class="o">=</span> <span class="kc">None</span>  <span class="c1"># type: ignore</span></tt>
+            </div>
+            <div id="l133"
+               class="code sev- "><tt><i>133</i> &nbsp;</tt>
+            </div>
+            <div id="l134"
+               class="code sev- "><tt><i>134</i>         <span class="c1"># read input</span></tt>
+            </div>
+            <div id="l135"
+               class="code sev- "><tt><i>135</i>         <span class="n">shift</span> <span class="o">=</span> <span class="n">read_series</span><span class="p">(</span></tt>
+            </div>
+            <div id="l136"
+               class="code sev- "><tt><i>136</i>             <span class="bp">self</span><span class="o">.</span><span class="n">stage_io_dict</span><span class="p">[</span><span class="s2">&quot;in&quot;</span><span class="p">][</span><span class="s2">&quot;input_filename_shift&quot;</span><span class="p">],</span> <span class="n">usecols</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">seqpos</span></tt>
+            </div>
+            <div id="l137"
+               class="code sev- "><tt><i>137</i>         <span class="p">)</span></tt>
+            </div>
+            <div id="l138"
+               class="code sev- "><tt><i>138</i>         <span class="n">slide</span> <span class="o">=</span> <span class="n">read_series</span><span class="p">(</span></tt>
+            </div>
+            <div id="l139"
+               class="code sev- "><tt><i>139</i>             <span class="bp">self</span><span class="o">.</span><span class="n">stage_io_dict</span><span class="p">[</span><span class="s2">&quot;in&quot;</span><span class="p">][</span><span class="s2">&quot;input_filename_slide&quot;</span><span class="p">],</span> <span class="n">usecols</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">seqpos</span></tt>
+            </div>
+            <div id="l140"
+               class="code sev- "><tt><i>140</i>         <span class="p">)</span></tt>
+            </div>
+            <div id="l141"
+               class="code sev- "><tt><i>141</i>         <span class="n">rise</span> <span class="o">=</span> <span class="n">read_series</span><span class="p">(</span></tt>
+            </div>
+            <div id="l142"
+               class="code sev- "><tt><i>142</i>             <span class="bp">self</span><span class="o">.</span><span class="n">stage_io_dict</span><span class="p">[</span><span class="s2">&quot;in&quot;</span><span class="p">][</span><span class="s2">&quot;input_filename_rise&quot;</span><span class="p">],</span> <span class="n">usecols</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">seqpos</span></tt>
+            </div>
+            <div id="l143"
+               class="code sev- "><tt><i>143</i>         <span class="p">)</span></tt>
+            </div>
+            <div id="l144"
+               class="code sev- "><tt><i>144</i>         <span class="n">tilt</span> <span class="o">=</span> <span class="n">read_series</span><span class="p">(</span></tt>
+            </div>
+            <div id="l145"
+               class="code sev- "><tt><i>145</i>             <span class="bp">self</span><span class="o">.</span><span class="n">stage_io_dict</span><span class="p">[</span><span class="s2">&quot;in&quot;</span><span class="p">][</span><span class="s2">&quot;input_filename_tilt&quot;</span><span class="p">],</span> <span class="n">usecols</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">seqpos</span></tt>
+            </div>
+            <div id="l146"
+               class="code sev- "><tt><i>146</i>         <span class="p">)</span></tt>
+            </div>
+            <div id="l147"
+               class="code sev- "><tt><i>147</i>         <span class="n">roll</span> <span class="o">=</span> <span class="n">read_series</span><span class="p">(</span></tt>
+            </div>
+            <div id="l148"
+               class="code sev- "><tt><i>148</i>             <span class="bp">self</span><span class="o">.</span><span class="n">stage_io_dict</span><span class="p">[</span><span class="s2">&quot;in&quot;</span><span class="p">][</span><span class="s2">&quot;input_filename_roll&quot;</span><span class="p">],</span> <span class="n">usecols</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">seqpos</span></tt>
+            </div>
+            <div id="l149"
+               class="code sev- "><tt><i>149</i>         <span class="p">)</span></tt>
+            </div>
+            <div id="l150"
+               class="code sev- "><tt><i>150</i>         <span class="n">twist</span> <span class="o">=</span> <span class="n">read_series</span><span class="p">(</span></tt>
+            </div>
+            <div id="l151"
+               class="code sev- "><tt><i>151</i>             <span class="bp">self</span><span class="o">.</span><span class="n">stage_io_dict</span><span class="p">[</span><span class="s2">&quot;in&quot;</span><span class="p">][</span><span class="s2">&quot;input_filename_twist&quot;</span><span class="p">],</span> <span class="n">usecols</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">seqpos</span></tt>
+            </div>
+            <div id="l152"
+               class="code sev- "><tt><i>152</i>         <span class="p">)</span></tt>
+            </div>
+            <div id="l153"
+               class="code sev- "><tt><i>153</i> &nbsp;</tt>
+            </div>
+            <div id="l154"
+               class="code sev- "><tt><i>154</i>         <span class="k">if</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">seqpos</span><span class="p">:</span></tt>
+            </div>
+            <div id="l155"
+               class="code sev- "><tt><i>155</i>             <span class="c1"># drop first and last columns</span></tt>
+            </div>
+            <div id="l156"
+               class="code sev- "><tt><i>156</i>             <span class="n">shift</span> <span class="o">=</span> <span class="n">shift</span><span class="p">[</span><span class="n">shift</span><span class="o">.</span><span class="n">columns</span><span class="p">[</span><span class="mi">1</span><span class="p">:</span><span class="o">-</span><span class="mi">2</span><span class="p">]]</span></tt>
+            </div>
+            <div id="l157"
+               class="code sev- "><tt><i>157</i>             <span class="n">slide</span> <span class="o">=</span> <span class="n">slide</span><span class="p">[</span><span class="n">slide</span><span class="o">.</span><span class="n">columns</span><span class="p">[</span><span class="mi">1</span><span class="p">:</span><span class="o">-</span><span class="mi">2</span><span class="p">]]</span></tt>
+            </div>
+            <div id="l158"
+               class="code sev- "><tt><i>158</i>             <span class="n">rise</span> <span class="o">=</span> <span class="n">rise</span><span class="p">[</span><span class="n">rise</span><span class="o">.</span><span class="n">columns</span><span class="p">[</span><span class="mi">1</span><span class="p">:</span><span class="o">-</span><span class="mi">2</span><span class="p">]]</span></tt>
+            </div>
+            <div id="l159"
+               class="code sev- "><tt><i>159</i>             <span class="n">tilt</span> <span class="o">=</span> <span class="n">tilt</span><span class="p">[</span><span class="n">tilt</span><span class="o">.</span><span class="n">columns</span><span class="p">[</span><span class="mi">1</span><span class="p">:</span><span class="o">-</span><span class="mi">2</span><span class="p">]]</span></tt>
+            </div>
+            <div id="l160"
+               class="code sev- "><tt><i>160</i>             <span class="n">roll</span> <span class="o">=</span> <span class="n">roll</span><span class="p">[</span><span class="n">roll</span><span class="o">.</span><span class="n">columns</span><span class="p">[</span><span class="mi">1</span><span class="p">:</span><span class="o">-</span><span class="mi">2</span><span class="p">]]</span></tt>
+            </div>
+            <div id="l161"
+               class="code sev- "><tt><i>161</i>             <span class="n">twist</span> <span class="o">=</span> <span class="n">twist</span><span class="p">[</span><span class="n">twist</span><span class="o">.</span><span class="n">columns</span><span class="p">[</span><span class="mi">1</span><span class="p">:</span><span class="o">-</span><span class="mi">2</span><span class="p">]]</span></tt>
+            </div>
+            <div id="l162"
+               class="code sev- "><tt><i>162</i>             <span class="n">labels</span> <span class="o">=</span> <span class="p">[</span></tt>
+            </div>
+            <div id="l163"
+               class="code sev- "><tt><i>163</i>                 <span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">i</span><span class="o">+</span><span class="mi">1</span><span class="si">}</span><span class="s2">_</span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">sequence</span><span class="p">[</span><span class="n">i</span><span class="p">:</span><span class="n">i</span><span class="o">+</span><span class="mi">2</span><span class="p">]</span><span class="si">}</span><span class="s2">&quot;</span></tt>
+            </div>
+            <div id="l164"
+               class="code sev- "><tt><i>164</i>                 <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="nb">len</span><span class="p">(</span><span class="n">shift</span><span class="o">.</span><span class="n">columns</span><span class="p">)</span> <span class="o">+</span> <span class="mi">1</span><span class="p">)</span></tt>
+            </div>
+            <div id="l165"
+               class="code sev- "><tt><i>165</i>             <span class="p">]</span></tt>
+            </div>
+            <div id="l166"
+               class="code sev- "><tt><i>166</i>             <span class="n">corr_index</span> <span class="o">=</span> <span class="p">[</span></tt>
+            </div>
+            <div id="l167"
+               class="code sev- "><tt><i>167</i>                 <span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">sequence</span><span class="p">[</span><span class="n">i</span><span class="p">:</span><span class="n">i</span><span class="o">+</span><span class="mi">3</span><span class="p">]</span><span class="si">}</span><span class="s2">&quot;</span> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="nb">len</span><span class="p">(</span><span class="n">shift</span><span class="o">.</span><span class="n">columns</span><span class="p">)</span> <span class="o">+</span> <span class="mi">1</span><span class="p">)</span></tt>
+            </div>
+            <div id="l168"
+               class="code sev- "><tt><i>168</i>             <span class="p">]</span></tt>
+            </div>
+            <div id="l169"
+               class="code sev- "><tt><i>169</i>         <span class="k">else</span><span class="p">:</span></tt>
+            </div>
+            <div id="l170"
+               class="code sev- "><tt><i>170</i>             <span class="n">labels</span> <span class="o">=</span> <span class="p">[</span><span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">i</span><span class="o">+</span><span class="mi">1</span><span class="si">}</span><span class="s2">_</span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">sequence</span><span class="p">[</span><span class="n">i</span><span class="p">:</span><span class="n">i</span><span class="o">+</span><span class="mi">2</span><span class="p">]</span><span class="si">}</span><span class="s2">&quot;</span> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">seqpos</span><span class="p">]</span></tt>
+            </div>
+            <div id="l171"
+               class="code sev- "><tt><i>171</i>             <span class="n">corr_index</span> <span class="o">=</span> <span class="p">[</span><span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">sequence</span><span class="p">[</span><span class="n">i</span><span class="p">:</span><span class="n">i</span><span class="o">+</span><span class="mi">3</span><span class="p">]</span><span class="si">}</span><span class="s2">&quot;</span> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">seqpos</span><span class="p">]</span></tt>
+            </div>
+            <div id="l172"
+               class="code sev- "><tt><i>172</i> &nbsp;</tt>
+            </div>
+            <div id="l173"
+               class="code sev- "><tt><i>173</i>         <span class="c1"># rename duplicated subunits</span></tt>
+            </div>
+            <div id="l174"
+               class="code sev- "><tt><i>174</i>         <span class="n">shift</span><span class="o">.</span><span class="n">columns</span> <span class="o">=</span> <span class="n">labels</span></tt>
+            </div>
+            <div id="l175"
+               class="code sev- "><tt><i>175</i>         <span class="n">slide</span><span class="o">.</span><span class="n">columns</span> <span class="o">=</span> <span class="n">labels</span></tt>
+            </div>
+            <div id="l176"
+               class="code sev- "><tt><i>176</i>         <span class="n">rise</span><span class="o">.</span><span class="n">columns</span> <span class="o">=</span> <span class="n">labels</span></tt>
+            </div>
+            <div id="l177"
+               class="code sev- "><tt><i>177</i>         <span class="n">tilt</span><span class="o">.</span><span class="n">columns</span> <span class="o">=</span> <span class="n">labels</span></tt>
+            </div>
+            <div id="l178"
+               class="code sev- "><tt><i>178</i>         <span class="n">roll</span><span class="o">.</span><span class="n">columns</span> <span class="o">=</span> <span class="n">labels</span></tt>
+            </div>
+            <div id="l179"
+               class="code sev- "><tt><i>179</i>         <span class="n">twist</span><span class="o">.</span><span class="n">columns</span> <span class="o">=</span> <span class="n">labels</span></tt>
+            </div>
+            <div id="l180"
+               class="code sev- "><tt><i>180</i> &nbsp;</tt>
+            </div>
+            <div id="l181"
+               class="code sev- "><tt><i>181</i>         <span class="c1"># set names to each dataset</span></tt>
+            </div>
+            <div id="l182"
+               class="code sev- "><tt><i>182</i>         <span class="n">shift</span><span class="o">.</span><span class="n">name</span> <span class="o">=</span> <span class="s2">&quot;shift&quot;</span></tt>
+            </div>
+            <div id="l183"
+               class="code sev- "><tt><i>183</i>         <span class="n">slide</span><span class="o">.</span><span class="n">name</span> <span class="o">=</span> <span class="s2">&quot;slide&quot;</span></tt>
+            </div>
+            <div id="l184"
+               class="code sev- "><tt><i>184</i>         <span class="n">rise</span><span class="o">.</span><span class="n">name</span> <span class="o">=</span> <span class="s2">&quot;rise&quot;</span></tt>
+            </div>
+            <div id="l185"
+               class="code sev- "><tt><i>185</i>         <span class="n">tilt</span><span class="o">.</span><span class="n">name</span> <span class="o">=</span> <span class="s2">&quot;tilt&quot;</span></tt>
+            </div>
+            <div id="l186"
+               class="code sev- "><tt><i>186</i>         <span class="n">roll</span><span class="o">.</span><span class="n">name</span> <span class="o">=</span> <span class="s2">&quot;roll&quot;</span></tt>
+            </div>
+            <div id="l187"
+               class="code sev- "><tt><i>187</i>         <span class="n">twist</span><span class="o">.</span><span class="n">name</span> <span class="o">=</span> <span class="s2">&quot;twist&quot;</span></tt>
+            </div>
+            <div id="l188"
+               class="code sev- "><tt><i>188</i> &nbsp;</tt>
+            </div>
+            <div id="l189"
+               class="code sev- "><tt><i>189</i>         <span class="c1"># get correlation between neighboring basepairs among all helical parameters</span></tt>
+            </div>
+            <div id="l190"
+               class="code sev- "><tt><i>190</i>         <span class="n">results</span> <span class="o">=</span> <span class="p">{}</span></tt>
+            </div>
+            <div id="l191"
+               class="code sev- "><tt><i>191</i>         <span class="n">datasets</span> <span class="o">=</span> <span class="p">[</span><span class="n">shift</span><span class="p">,</span> <span class="n">slide</span><span class="p">,</span> <span class="n">rise</span><span class="p">,</span> <span class="n">tilt</span><span class="p">,</span> <span class="n">roll</span><span class="p">,</span> <span class="n">twist</span><span class="p">]</span></tt>
+            </div>
+            <div id="l192"
+               class="code sev- "><tt><i>192</i>         <span class="k">for</span> <span class="n">ser1</span><span class="p">,</span> <span class="n">ser2</span> <span class="ow">in</span> <span class="n">product</span><span class="p">(</span><span class="n">datasets</span><span class="p">,</span> <span class="n">datasets</span><span class="p">):</span></tt>
+            </div>
+            <div id="l193"
+               class="code sev- "><tt><i>193</i>             <span class="n">ser2_shifted</span> <span class="o">=</span> <span class="n">ser2</span><span class="o">.</span><span class="n">shift</span><span class="p">(</span><span class="n">axis</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span></tt>
+            </div>
+            <div id="l194"
+               class="code sev- "><tt><i>194</i>             <span class="n">ser2_shifted</span><span class="p">[</span><span class="n">labels</span><span class="p">[</span><span class="mi">0</span><span class="p">]]</span> <span class="o">=</span> <span class="n">ser2</span><span class="p">[</span><span class="n">labels</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">]]</span></tt>
+            </div>
+            <div id="l195"
+               class="code sev- "><tt><i>195</i>             <span class="k">if</span> <span class="n">ser1</span><span class="o">.</span><span class="n">name</span> <span class="ow">in</span> <span class="n">constants</span><span class="o">.</span><span class="n">hp_angular</span> <span class="ow">and</span> <span class="n">ser2</span><span class="o">.</span><span class="n">name</span> <span class="ow">in</span> <span class="n">constants</span><span class="o">.</span><span class="n">hp_angular</span><span class="p">:</span></tt>
+            </div>
+            <div id="l196"
+               class="code sev- "><tt><i>196</i>                 <span class="n">method</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">circular</span></tt>
+            </div>
+            <div id="l197"
+               class="code sev- "><tt><i>197</i>             <span class="k">elif</span> <span class="p">(</span></tt>
+            </div>
+            <div id="l198"
+               class="code sev- "><tt><i>198</i>                 <span class="n">ser1</span><span class="o">.</span><span class="n">name</span> <span class="ow">in</span> <span class="n">constants</span><span class="o">.</span><span class="n">hp_angular</span></tt>
+            </div>
+            <div id="l199"
+               class="code sev-2  le">
+               <ul class="violations">
+               
+                  <li>
+                     <span class="count sev-2">
+                        W503
+                     </span>
+                     Line break before binary operator</li>
+               
+               </ul><tt><i>199</i>                 <span class="ow">and</span> <span class="n">ser2</span><span class="o">.</span><span class="n">name</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">constants</span><span class="o">.</span><span class="n">hp_angular</span></tt>
+            </div>
+            <div id="l200"
+               class="code sev- "><tt><i>200</i>             <span class="p">)</span> <span class="ow">or</span> <span class="p">(</span></tt>
+            </div>
+            <div id="l201"
+               class="code sev- "><tt><i>201</i>                 <span class="n">ser2</span><span class="o">.</span><span class="n">name</span> <span class="ow">in</span> <span class="n">constants</span><span class="o">.</span><span class="n">hp_angular</span></tt>
+            </div>
+            <div id="l202"
+               class="code sev-2  le">
+               <ul class="violations">
+               
+                  <li>
+                     <span class="count sev-2">
+                        W503
+                     </span>
+                     Line break before binary operator</li>
+               
+               </ul><tt><i>202</i>                 <span class="ow">and</span> <span class="n">ser1</span><span class="o">.</span><span class="n">name</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">constants</span><span class="o">.</span><span class="n">hp_angular</span></tt>
+            </div>
+            <div id="l203"
+               class="code sev- "><tt><i>203</i>             <span class="p">):</span></tt>
+            </div>
+            <div id="l204"
+               class="code sev- "><tt><i>204</i>                 <span class="n">method</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">circlineal</span></tt>
+            </div>
+            <div id="l205"
+               class="code sev- "><tt><i>205</i>             <span class="k">else</span><span class="p">:</span></tt>
+            </div>
+            <div id="l206"
+               class="code sev- "><tt><i>206</i>                 <span class="n">method</span> <span class="o">=</span> <span class="s2">&quot;pearson&quot;</span>  <span class="c1"># type: ignore</span></tt>
+            </div>
+            <div id="l207"
+               class="code sev- "><tt><i>207</i>             <span class="n">corr_data</span> <span class="o">=</span> <span class="n">ser1</span><span class="o">.</span><span class="n">corrwith</span><span class="p">(</span><span class="n">ser2_shifted</span><span class="p">,</span> <span class="n">method</span><span class="o">=</span><span class="n">method</span><span class="p">)</span></tt>
+            </div>
+            <div id="l208"
+               class="code sev- "><tt><i>208</i>             <span class="n">corr_data</span><span class="o">.</span><span class="n">index</span> <span class="o">=</span> <span class="n">corr_index</span></tt>
+            </div>
+            <div id="l209"
+               class="code sev- "><tt><i>209</i>             <span class="n">results</span><span class="p">[</span><span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">ser1</span><span class="o">.</span><span class="n">name</span><span class="si">}</span><span class="s2">/</span><span class="si">{</span><span class="n">ser2</span><span class="o">.</span><span class="n">name</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">]</span> <span class="o">=</span> <span class="n">corr_data</span></tt>
+            </div>
+            <div id="l210"
+               class="code sev- "><tt><i>210</i>         <span class="n">result_df</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="o">.</span><span class="n">from_dict</span><span class="p">(</span><span class="n">results</span><span class="p">)</span></tt>
+            </div>
+            <div id="l211"
+               class="code sev- "><tt><i>211</i>         <span class="n">result_df</span><span class="o">.</span><span class="n">index</span> <span class="o">=</span> <span class="n">corr_index</span>  <span class="c1"># type: ignore</span></tt>
+            </div>
+            <div id="l212"
+               class="code sev- "><tt><i>212</i> &nbsp;</tt>
+            </div>
+            <div id="l213"
+               class="code sev- "><tt><i>213</i>         <span class="c1"># save csv data</span></tt>
+            </div>
+            <div id="l214"
+               class="code sev- "><tt><i>214</i>         <span class="n">result_df</span><span class="o">.</span><span class="n">to_csv</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">stage_io_dict</span><span class="p">[</span><span class="s2">&quot;out&quot;</span><span class="p">][</span><span class="s2">&quot;output_csv_path&quot;</span><span class="p">])</span></tt>
+            </div>
+            <div id="l215"
+               class="code sev- "><tt><i>215</i> &nbsp;</tt>
+            </div>
+            <div id="l216"
+               class="code sev- "><tt><i>216</i>         <span class="c1"># create heatmap</span></tt>
+            </div>
+            <div id="l217"
+               class="code sev- "><tt><i>217</i>         <span class="n">cmap</span> <span class="o">=</span> <span class="n">plt</span><span class="o">.</span><span class="n">get_cmap</span><span class="p">(</span><span class="s2">&quot;bwr&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">copy</span><span class="p">()</span></tt>
+            </div>
+            <div id="l218"
+               class="code sev- "><tt><i>218</i>         <span class="n">bounds</span> <span class="o">=</span> <span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">,</span> <span class="o">-</span><span class="mf">0.8</span><span class="p">,</span> <span class="o">-</span><span class="mf">0.6</span><span class="p">,</span> <span class="o">-</span><span class="mf">0.4</span><span class="p">,</span> <span class="o">-</span><span class="mf">0.2</span><span class="p">,</span> <span class="mf">0.2</span><span class="p">,</span> <span class="mf">0.4</span><span class="p">,</span> <span class="mf">0.6</span><span class="p">,</span> <span class="mf">0.8</span><span class="p">,</span> <span class="mi">1</span><span class="p">]</span></tt>
+            </div>
+            <div id="l219"
+               class="code sev- "><tt><i>219</i>         <span class="n">num</span> <span class="o">=</span> <span class="n">cmap</span><span class="o">.</span><span class="n">N</span></tt>
+            </div>
+            <div id="l220"
+               class="code sev- "><tt><i>220</i>         <span class="n">norm</span> <span class="o">=</span> <span class="n">mpl</span><span class="o">.</span><span class="n">colors</span><span class="o">.</span><span class="n">BoundaryNorm</span><span class="p">(</span><span class="n">bounds</span><span class="p">,</span> <span class="n">num</span><span class="p">)</span>  <span class="c1"># type: ignore</span></tt>
+            </div>
+            <div id="l221"
+               class="code sev- "><tt><i>221</i>         <span class="n">cmap</span><span class="o">.</span><span class="n">set_bad</span><span class="p">(</span><span class="n">color</span><span class="o">=</span><span class="s2">&quot;gainsboro&quot;</span><span class="p">)</span></tt>
+            </div>
+            <div id="l222"
+               class="code sev- "><tt><i>222</i>         <span class="n">fig</span><span class="p">,</span> <span class="n">ax</span> <span class="o">=</span> <span class="n">plt</span><span class="o">.</span><span class="n">subplots</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="n">dpi</span><span class="o">=</span><span class="mi">300</span><span class="p">,</span> <span class="n">figsize</span><span class="o">=</span><span class="p">(</span><span class="mf">7.5</span><span class="p">,</span> <span class="mi">5</span><span class="p">),</span> <span class="n">tight_layout</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span></tt>
+            </div>
+            <div id="l223"
+               class="code sev- "><tt><i>223</i>         <span class="n">im</span> <span class="o">=</span> <span class="n">ax</span><span class="o">.</span><span class="n">imshow</span><span class="p">(</span><span class="n">result_df</span><span class="p">,</span> <span class="n">cmap</span><span class="o">=</span><span class="n">cmap</span><span class="p">,</span> <span class="n">norm</span><span class="o">=</span><span class="n">norm</span><span class="p">,</span> <span class="n">aspect</span><span class="o">=</span><span class="s2">&quot;auto&quot;</span><span class="p">)</span></tt>
+            </div>
+            <div id="l224"
+               class="code sev- "><tt><i>224</i>         <span class="n">plt</span><span class="o">.</span><span class="n">colorbar</span><span class="p">(</span><span class="n">im</span><span class="p">,</span> <span class="n">ticks</span><span class="o">=</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">,</span> <span class="o">-</span><span class="mf">0.8</span><span class="p">,</span> <span class="o">-</span><span class="mf">0.6</span><span class="p">,</span> <span class="o">-</span><span class="mf">0.4</span><span class="p">,</span> <span class="o">-</span><span class="mf">0.2</span><span class="p">,</span> <span class="mf">0.2</span><span class="p">,</span> <span class="mf">0.4</span><span class="p">,</span> <span class="mf">0.6</span><span class="p">,</span> <span class="mf">0.8</span><span class="p">,</span> <span class="mi">1</span><span class="p">])</span></tt>
+            </div>
+            <div id="l225"
+               class="code sev- "><tt><i>225</i> &nbsp;</tt>
+            </div>
+            <div id="l226"
+               class="code sev- "><tt><i>226</i>         <span class="c1"># axes</span></tt>
+            </div>
+            <div id="l227"
+               class="code sev- "><tt><i>227</i>         <span class="n">xlocs</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">arange</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">result_df</span><span class="o">.</span><span class="n">columns</span><span class="p">))</span></tt>
+            </div>
+            <div id="l228"
+               class="code sev- "><tt><i>228</i>         <span class="n">_</span> <span class="o">=</span> <span class="n">ax</span><span class="o">.</span><span class="n">set_xticks</span><span class="p">(</span><span class="n">xlocs</span><span class="p">)</span></tt>
+            </div>
+            <div id="l229"
+               class="code sev- "><tt><i>229</i>         <span class="n">_</span> <span class="o">=</span> <span class="n">ax</span><span class="o">.</span><span class="n">set_xticklabels</span><span class="p">(</span><span class="n">result_df</span><span class="o">.</span><span class="n">columns</span><span class="o">.</span><span class="n">to_list</span><span class="p">(),</span> <span class="n">rotation</span><span class="o">=</span><span class="mi">90</span><span class="p">)</span></tt>
+            </div>
+            <div id="l230"
+               class="code sev- "><tt><i>230</i> &nbsp;</tt>
+            </div>
+            <div id="l231"
+               class="code sev- "><tt><i>231</i>         <span class="n">ylocs</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">arange</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">result_df</span><span class="o">.</span><span class="n">index</span><span class="p">))</span></tt>
+            </div>
+            <div id="l232"
+               class="code sev- "><tt><i>232</i>         <span class="n">_</span> <span class="o">=</span> <span class="n">ax</span><span class="o">.</span><span class="n">set_yticks</span><span class="p">(</span><span class="n">ylocs</span><span class="p">)</span></tt>
+            </div>
+            <div id="l233"
+               class="code sev- "><tt><i>233</i>         <span class="n">_</span> <span class="o">=</span> <span class="n">ax</span><span class="o">.</span><span class="n">set_yticklabels</span><span class="p">(</span><span class="n">result_df</span><span class="o">.</span><span class="n">index</span><span class="o">.</span><span class="n">to_list</span><span class="p">())</span>  <span class="c1"># type: ignore</span></tt>
+            </div>
+            <div id="l234"
+               class="code sev- "><tt><i>234</i> &nbsp;</tt>
+            </div>
+            <div id="l235"
+               class="code sev- "><tt><i>235</i>         <span class="n">ax</span><span class="o">.</span><span class="n">set_title</span><span class="p">(</span></tt>
+            </div>
+            <div id="l236"
+               class="code sev- "><tt><i>236</i>             <span class="s2">&quot;Correlation for neighboring basepairs &quot;</span> <span class="s2">&quot;and pairs of helical parameters&quot;</span></tt>
+            </div>
+            <div id="l237"
+               class="code sev- "><tt><i>237</i>         <span class="p">)</span></tt>
+            </div>
+            <div id="l238"
+               class="code sev- "><tt><i>238</i> &nbsp;</tt>
+            </div>
+            <div id="l239"
+               class="code sev- "><tt><i>239</i>         <span class="n">fig</span><span class="o">.</span><span class="n">tight_layout</span><span class="p">()</span></tt>
+            </div>
+            <div id="l240"
+               class="code sev- "><tt><i>240</i>         <span class="n">fig</span><span class="o">.</span><span class="n">savefig</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">stage_io_dict</span><span class="p">[</span><span class="s2">&quot;out&quot;</span><span class="p">][</span><span class="s2">&quot;output_jpg_path&quot;</span><span class="p">],</span> <span class="nb">format</span><span class="o">=</span><span class="s2">&quot;jpg&quot;</span><span class="p">)</span></tt>
+            </div>
+            <div id="l241"
+               class="code sev- "><tt><i>241</i>         <span class="n">plt</span><span class="o">.</span><span class="n">close</span><span class="p">()</span></tt>
+            </div>
+            <div id="l242"
+               class="code sev- "><tt><i>242</i> &nbsp;</tt>
+            </div>
+            <div id="l243"
+               class="code sev- "><tt><i>243</i>         <span class="c1"># Copy files to host</span></tt>
+            </div>
+            <div id="l244"
+               class="code sev- "><tt><i>244</i>         <span class="bp">self</span><span class="o">.</span><span class="n">copy_to_host</span><span class="p">()</span></tt>
+            </div>
+            <div id="l245"
+               class="code sev- "><tt><i>245</i> &nbsp;</tt>
+            </div>
+            <div id="l246"
+               class="code sev- "><tt><i>246</i>         <span class="c1"># Remove temporary file(s)</span></tt>
+            </div>
+            <div id="l247"
+               class="code sev- "><tt><i>247</i>         <span class="bp">self</span><span class="o">.</span><span class="n">tmp_files</span><span class="o">.</span><span class="n">extend</span><span class="p">(</span></tt>
+            </div>
+            <div id="l248"
+               class="code sev- "><tt><i>248</i>             <span class="p">[</span></tt>
+            </div>
+            <div id="l249"
+               class="code sev- "><tt><i>249</i>                 <span class="bp">self</span><span class="o">.</span><span class="n">stage_io_dict</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">&quot;unique_dir&quot;</span><span class="p">,</span> <span class="s2">&quot;&quot;</span><span class="p">),</span></tt>
+            </div>
+            <div id="l250"
+               class="code sev- "><tt><i>250</i>             <span class="p">]</span></tt>
+            </div>
+            <div id="l251"
+               class="code sev- "><tt><i>251</i>         <span class="p">)</span></tt>
+            </div>
+            <div id="l252"
+               class="code sev- "><tt><i>252</i>         <span class="bp">self</span><span class="o">.</span><span class="n">remove_tmp_files</span><span class="p">()</span></tt>
+            </div>
+            <div id="l253"
+               class="code sev- "><tt><i>253</i> &nbsp;</tt>
+            </div>
+            <div id="l254"
+               class="code sev- "><tt><i>254</i>         <span class="bp">self</span><span class="o">.</span><span class="n">check_arguments</span><span class="p">(</span><span class="n">output_files_created</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">raise_exception</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span></tt>
+            </div>
+            <div id="l255"
+               class="code sev- "><tt><i>255</i> &nbsp;</tt>
+            </div>
+            <div id="l256"
+               class="code sev- "><tt><i>256</i>         <span class="k">return</span> <span class="mi">0</span></tt>
+            </div>
+            <div id="l257"
+               class="code sev- "><tt><i>257</i> &nbsp;</tt>
+            </div>
+            <div id="l258"
+               class="code sev- "><tt><i>258</i>     <span class="nd">@staticmethod</span></tt>
+            </div>
+            <div id="l259"
+               class="code sev- "><tt><i>259</i>     <span class="k">def</span> <span class="nf">circular</span><span class="p">(</span><span class="n">x1</span><span class="p">,</span> <span class="n">x2</span><span class="p">):</span></tt>
+            </div>
+            <div id="l260"
+               class="code sev- "><tt><i>260</i>         <span class="n">x1</span> <span class="o">=</span> <span class="n">x1</span> <span class="o">*</span> <span class="n">np</span><span class="o">.</span><span class="n">pi</span> <span class="o">/</span> <span class="mi">180</span></tt>
+            </div>
+            <div id="l261"
+               class="code sev- "><tt><i>261</i>         <span class="n">x2</span> <span class="o">=</span> <span class="n">x2</span> <span class="o">*</span> <span class="n">np</span><span class="o">.</span><span class="n">pi</span> <span class="o">/</span> <span class="mi">180</span></tt>
+            </div>
+            <div id="l262"
+               class="code sev- "><tt><i>262</i>         <span class="n">diff_1</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">sin</span><span class="p">(</span><span class="n">x1</span> <span class="o">-</span> <span class="n">x1</span><span class="o">.</span><span class="n">mean</span><span class="p">())</span></tt>
+            </div>
+            <div id="l263"
+               class="code sev- "><tt><i>263</i>         <span class="n">diff_2</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">sin</span><span class="p">(</span><span class="n">x2</span> <span class="o">-</span> <span class="n">x2</span><span class="o">.</span><span class="n">mean</span><span class="p">())</span></tt>
+            </div>
+            <div id="l264"
+               class="code sev- "><tt><i>264</i>         <span class="n">num</span> <span class="o">=</span> <span class="p">(</span><span class="n">diff_1</span> <span class="o">*</span> <span class="n">diff_2</span><span class="p">)</span><span class="o">.</span><span class="n">sum</span><span class="p">()</span></tt>
+            </div>
+            <div id="l265"
+               class="code sev- "><tt><i>265</i>         <span class="n">den</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">sqrt</span><span class="p">((</span><span class="n">diff_1</span><span class="o">**</span><span class="mi">2</span><span class="p">)</span><span class="o">.</span><span class="n">sum</span><span class="p">()</span> <span class="o">*</span> <span class="p">(</span><span class="n">diff_2</span><span class="o">**</span><span class="mi">2</span><span class="p">)</span><span class="o">.</span><span class="n">sum</span><span class="p">())</span></tt>
+            </div>
+            <div id="l266"
+               class="code sev- "><tt><i>266</i>         <span class="k">return</span> <span class="n">num</span> <span class="o">/</span> <span class="n">den</span></tt>
+            </div>
+            <div id="l267"
+               class="code sev- "><tt><i>267</i> &nbsp;</tt>
+            </div>
+            <div id="l268"
+               class="code sev- "><tt><i>268</i>     <span class="nd">@staticmethod</span></tt>
+            </div>
+            <div id="l269"
+               class="code sev- "><tt><i>269</i>     <span class="k">def</span> <span class="nf">circlineal</span><span class="p">(</span><span class="n">x1</span><span class="p">,</span> <span class="n">x2</span><span class="p">):</span></tt>
+            </div>
+            <div id="l270"
+               class="code sev- "><tt><i>270</i>         <span class="n">x2</span> <span class="o">=</span> <span class="n">x2</span> <span class="o">*</span> <span class="n">np</span><span class="o">.</span><span class="n">pi</span> <span class="o">/</span> <span class="mi">180</span></tt>
+            </div>
+            <div id="l271"
+               class="code sev- "><tt><i>271</i>         <span class="n">rc</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">corrcoef</span><span class="p">(</span><span class="n">x1</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">cos</span><span class="p">(</span><span class="n">x2</span><span class="p">))[</span><span class="mi">1</span><span class="p">,</span> <span class="mi">0</span><span class="p">]</span></tt>
+            </div>
+            <div id="l272"
+               class="code sev- "><tt><i>272</i>         <span class="n">rs</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">corrcoef</span><span class="p">(</span><span class="n">x1</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">sin</span><span class="p">(</span><span class="n">x2</span><span class="p">))[</span><span class="mi">1</span><span class="p">,</span> <span class="mi">0</span><span class="p">]</span></tt>
+            </div>
+            <div id="l273"
+               class="code sev- "><tt><i>273</i>         <span class="n">rcs</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">corrcoef</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">sin</span><span class="p">(</span><span class="n">x2</span><span class="p">),</span> <span class="n">np</span><span class="o">.</span><span class="n">cos</span><span class="p">(</span><span class="n">x2</span><span class="p">))[</span><span class="mi">1</span><span class="p">,</span> <span class="mi">0</span><span class="p">]</span></tt>
+            </div>
+            <div id="l274"
+               class="code sev- "><tt><i>274</i>         <span class="n">num</span> <span class="o">=</span> <span class="p">(</span><span class="n">rc</span><span class="o">**</span><span class="mi">2</span><span class="p">)</span> <span class="o">+</span> <span class="p">(</span><span class="n">rs</span><span class="o">**</span><span class="mi">2</span><span class="p">)</span> <span class="o">-</span> <span class="mi">2</span> <span class="o">*</span> <span class="n">rc</span> <span class="o">*</span> <span class="n">rs</span> <span class="o">*</span> <span class="n">rcs</span></tt>
+            </div>
+            <div id="l275"
+               class="code sev- "><tt><i>275</i>         <span class="n">den</span> <span class="o">=</span> <span class="mi">1</span> <span class="o">-</span> <span class="p">(</span><span class="n">rcs</span><span class="o">**</span><span class="mi">2</span><span class="p">)</span></tt>
+            </div>
+            <div id="l276"
+               class="code sev- "><tt><i>276</i>         <span class="n">correlation</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">sqrt</span><span class="p">(</span><span class="n">num</span> <span class="o">/</span> <span class="n">den</span><span class="p">)</span></tt>
+            </div>
+            <div id="l277"
+               class="code sev- "><tt><i>277</i>         <span class="k">if</span> <span class="n">np</span><span class="o">.</span><span class="n">corrcoef</span><span class="p">(</span><span class="n">x1</span><span class="p">,</span> <span class="n">x2</span><span class="p">)[</span><span class="mi">1</span><span class="p">,</span> <span class="mi">0</span><span class="p">]</span> <span class="o">&lt;</span> <span class="mi">0</span><span class="p">:</span></tt>
+            </div>
+            <div id="l278"
+               class="code sev- "><tt><i>278</i>             <span class="n">correlation</span> <span class="o">*=</span> <span class="o">-</span><span class="mi">1</span></tt>
+            </div>
+            <div id="l279"
+               class="code sev- "><tt><i>279</i>         <span class="k">return</span> <span class="n">correlation</span></tt>
+            </div>
+            <div id="l280"
+               class="code sev- "><tt><i>280</i> &nbsp;</tt>
+            </div>
+            <div id="l281"
+               class="code sev- "><tt><i>281</i> &nbsp;</tt>
+            </div>
+            <div id="l282"
+               class="code sev- "><tt><i>282</i> <span class="k">def</span> <span class="nf">interbpcorr</span><span class="p">(</span></tt>
+            </div>
+            <div id="l283"
+               class="code sev- "><tt><i>283</i>     <span class="n">input_filename_shift</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span></tt>
+            </div>
+            <div id="l284"
+               class="code sev- "><tt><i>284</i>     <span class="n">input_filename_slide</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span></tt>
+            </div>
+            <div id="l285"
+               class="code sev- "><tt><i>285</i>     <span class="n">input_filename_rise</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span></tt>
+            </div>
+            <div id="l286"
+               class="code sev- "><tt><i>286</i>     <span class="n">input_filename_tilt</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span></tt>
+            </div>
+            <div id="l287"
+               class="code sev- "><tt><i>287</i>     <span class="n">input_filename_roll</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span></tt>
+            </div>
+            <div id="l288"
+               class="code sev- "><tt><i>288</i>     <span class="n">input_filename_twist</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span></tt>
+            </div>
+            <div id="l289"
+               class="code sev- "><tt><i>289</i>     <span class="n">output_csv_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span></tt>
+            </div>
+            <div id="l290"
+               class="code sev- "><tt><i>290</i>     <span class="n">output_jpg_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span></tt>
+            </div>
+            <div id="l291"
+               class="code sev- "><tt><i>291</i>     <span class="n">properties</span><span class="p">:</span> <span class="n">Optional</span><span class="p">[</span><span class="nb">dict</span><span class="p">]</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span></tt>
+            </div>
+            <div id="l292"
+               class="code sev- "><tt><i>292</i>     <span class="o">**</span><span class="n">kwargs</span><span class="p">,</span></tt>
+            </div>
+            <div id="l293"
+               class="code sev- "><tt><i>293</i> <span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">int</span><span class="p">:</span></tt>
+            </div>
+            <div id="l294"
+               class="code sev- "><tt><i>294</i> <span class="w">    </span><span class="sd">&quot;&quot;&quot;Create :class:`HelParCorrelation &lt;correlations.interbpcorr.InterBasePairCorrelation&gt;` class and</span></tt>
+            </div>
+            <div id="l295"
+               class="code sev- "><tt><i>295</i> <span class="sd">    execute the :meth:`launch() &lt;correlations.interbpcorr.InterBasePairCorrelation.launch&gt;` method.&quot;&quot;&quot;</span></tt>
+            </div>
+            <div id="l296"
+               class="code sev- "><tt><i>296</i> &nbsp;</tt>
+            </div>
+            <div id="l297"
+               class="code sev- "><tt><i>297</i>     <span class="k">return</span> <span class="n">InterBasePairCorrelation</span><span class="p">(</span></tt>
+            </div>
+            <div id="l298"
+               class="code sev- "><tt><i>298</i>         <span class="n">input_filename_shift</span><span class="o">=</span><span class="n">input_filename_shift</span><span class="p">,</span></tt>
+            </div>
+            <div id="l299"
+               class="code sev- "><tt><i>299</i>         <span class="n">input_filename_slide</span><span class="o">=</span><span class="n">input_filename_slide</span><span class="p">,</span></tt>
+            </div>
+            <div id="l300"
+               class="code sev- "><tt><i>300</i>         <span class="n">input_filename_rise</span><span class="o">=</span><span class="n">input_filename_rise</span><span class="p">,</span></tt>
+            </div>
+            <div id="l301"
+               class="code sev- "><tt><i>301</i>         <span class="n">input_filename_tilt</span><span class="o">=</span><span class="n">input_filename_tilt</span><span class="p">,</span></tt>
+            </div>
+            <div id="l302"
+               class="code sev- "><tt><i>302</i>         <span class="n">input_filename_roll</span><span class="o">=</span><span class="n">input_filename_roll</span><span class="p">,</span></tt>
+            </div>
+            <div id="l303"
+               class="code sev- "><tt><i>303</i>         <span class="n">input_filename_twist</span><span class="o">=</span><span class="n">input_filename_twist</span><span class="p">,</span></tt>
+            </div>
+            <div id="l304"
+               class="code sev- "><tt><i>304</i>         <span class="n">output_csv_path</span><span class="o">=</span><span class="n">output_csv_path</span><span class="p">,</span></tt>
+            </div>
+            <div id="l305"
+               class="code sev- "><tt><i>305</i>         <span class="n">output_jpg_path</span><span class="o">=</span><span class="n">output_jpg_path</span><span class="p">,</span></tt>
+            </div>
+            <div id="l306"
+               class="code sev- "><tt><i>306</i>         <span class="n">properties</span><span class="o">=</span><span class="n">properties</span><span class="p">,</span></tt>
+            </div>
+            <div id="l307"
+               class="code sev- "><tt><i>307</i>         <span class="o">**</span><span class="n">kwargs</span><span class="p">,</span></tt>
+            </div>
+            <div id="l308"
+               class="code sev- "><tt><i>308</i>     <span class="p">)</span><span class="o">.</span><span class="n">launch</span><span class="p">()</span></tt>
+            </div>
+            <div id="l309"
+               class="code sev- "><tt><i>309</i> &nbsp;</tt>
+            </div>
+            <div id="l310"
+               class="code sev- "><tt><i>310</i> &nbsp;</tt>
+            </div>
+            <div id="l311"
+               class="code sev- "><tt><i>311</i> <span class="k">def</span> <span class="nf">main</span><span class="p">():</span></tt>
+            </div>
+            <div id="l312"
+               class="code sev- "><tt><i>312</i> <span class="w">    </span><span class="sd">&quot;&quot;&quot;Command line execution of this building block. Please check the command line documentation.&quot;&quot;&quot;</span></tt>
+            </div>
+            <div id="l313"
+               class="code sev- "><tt><i>313</i>     <span class="n">parser</span> <span class="o">=</span> <span class="n">argparse</span><span class="o">.</span><span class="n">ArgumentParser</span><span class="p">(</span></tt>
+            </div>
+            <div id="l314"
+               class="code sev- "><tt><i>314</i>         <span class="n">description</span><span class="o">=</span><span class="s2">&quot;Load .ser file from Canal output and calculate correlation between base pairs of the corresponding sequence.&quot;</span><span class="p">,</span></tt>
+            </div>
+            <div id="l315"
+               class="code sev- "><tt><i>315</i>         <span class="n">formatter_class</span><span class="o">=</span><span class="k">lambda</span> <span class="n">prog</span><span class="p">:</span> <span class="n">argparse</span><span class="o">.</span><span class="n">RawTextHelpFormatter</span><span class="p">(</span><span class="n">prog</span><span class="p">,</span> <span class="n">width</span><span class="o">=</span><span class="mi">99999</span><span class="p">),</span></tt>
+            </div>
+            <div id="l316"
+               class="code sev- "><tt><i>316</i>     <span class="p">)</span></tt>
+            </div>
+            <div id="l317"
+               class="code sev- "><tt><i>317</i>     <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s2">&quot;--config&quot;</span><span class="p">,</span> <span class="n">required</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s2">&quot;Configuration file&quot;</span><span class="p">)</span></tt>
+            </div>
+            <div id="l318"
+               class="code sev- "><tt><i>318</i> &nbsp;</tt>
+            </div>
+            <div id="l319"
+               class="code sev- "><tt><i>319</i>     <span class="n">required_args</span> <span class="o">=</span> <span class="n">parser</span><span class="o">.</span><span class="n">add_argument_group</span><span class="p">(</span><span class="s2">&quot;required arguments&quot;</span><span class="p">)</span></tt>
+            </div>
+            <div id="l320"
+               class="code sev- "><tt><i>320</i>     <span class="n">required_args</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span></tt>
+            </div>
+            <div id="l321"
+               class="code sev- "><tt><i>321</i>         <span class="s2">&quot;--input_filename_shift&quot;</span><span class="p">,</span></tt>
+            </div>
+            <div id="l322"
+               class="code sev- "><tt><i>322</i>         <span class="n">required</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span></tt>
+            </div>
+            <div id="l323"
+               class="code sev- "><tt><i>323</i>         <span class="n">help</span><span class="o">=</span><span class="s2">&quot;Path to ser file for helical parameter shift. Accepted formats: ser.&quot;</span><span class="p">,</span></tt>
+            </div>
+            <div id="l324"
+               class="code sev- "><tt><i>324</i>     <span class="p">)</span></tt>
+            </div>
+            <div id="l325"
+               class="code sev- "><tt><i>325</i>     <span class="n">required_args</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span></tt>
+            </div>
+            <div id="l326"
+               class="code sev- "><tt><i>326</i>         <span class="s2">&quot;--input_filename_slide&quot;</span><span class="p">,</span></tt>
+            </div>
+            <div id="l327"
+               class="code sev- "><tt><i>327</i>         <span class="n">required</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span></tt>
+            </div>
+            <div id="l328"
+               class="code sev- "><tt><i>328</i>         <span class="n">help</span><span class="o">=</span><span class="s2">&quot;Path to ser file for helical parameter slide. Accepted formats: ser.&quot;</span><span class="p">,</span></tt>
+            </div>
+            <div id="l329"
+               class="code sev- "><tt><i>329</i>     <span class="p">)</span></tt>
+            </div>
+            <div id="l330"
+               class="code sev- "><tt><i>330</i>     <span class="n">required_args</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span></tt>
+            </div>
+            <div id="l331"
+               class="code sev- "><tt><i>331</i>         <span class="s2">&quot;--input_filename_rise&quot;</span><span class="p">,</span></tt>
+            </div>
+            <div id="l332"
+               class="code sev- "><tt><i>332</i>         <span class="n">required</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span></tt>
+            </div>
+            <div id="l333"
+               class="code sev- "><tt><i>333</i>         <span class="n">help</span><span class="o">=</span><span class="s2">&quot;Path to ser file for helical parameter rise. Accepted formats: ser.&quot;</span><span class="p">,</span></tt>
+            </div>
+            <div id="l334"
+               class="code sev- "><tt><i>334</i>     <span class="p">)</span></tt>
+            </div>
+            <div id="l335"
+               class="code sev- "><tt><i>335</i>     <span class="n">required_args</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span></tt>
+            </div>
+            <div id="l336"
+               class="code sev- "><tt><i>336</i>         <span class="s2">&quot;--input_filename_tilt&quot;</span><span class="p">,</span></tt>
+            </div>
+            <div id="l337"
+               class="code sev- "><tt><i>337</i>         <span class="n">required</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span></tt>
+            </div>
+            <div id="l338"
+               class="code sev- "><tt><i>338</i>         <span class="n">help</span><span class="o">=</span><span class="s2">&quot;Path to ser file for helical parameter tilt. Accepted formats: ser.&quot;</span><span class="p">,</span></tt>
+            </div>
+            <div id="l339"
+               class="code sev- "><tt><i>339</i>     <span class="p">)</span></tt>
+            </div>
+            <div id="l340"
+               class="code sev- "><tt><i>340</i>     <span class="n">required_args</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span></tt>
+            </div>
+            <div id="l341"
+               class="code sev- "><tt><i>341</i>         <span class="s2">&quot;--input_filename_roll&quot;</span><span class="p">,</span></tt>
+            </div>
+            <div id="l342"
+               class="code sev- "><tt><i>342</i>         <span class="n">required</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span></tt>
+            </div>
+            <div id="l343"
+               class="code sev- "><tt><i>343</i>         <span class="n">help</span><span class="o">=</span><span class="s2">&quot;Path to ser file for helical parameter roll. Accepted formats: ser.&quot;</span><span class="p">,</span></tt>
+            </div>
+            <div id="l344"
+               class="code sev- "><tt><i>344</i>     <span class="p">)</span></tt>
+            </div>
+            <div id="l345"
+               class="code sev- "><tt><i>345</i>     <span class="n">required_args</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span></tt>
+            </div>
+            <div id="l346"
+               class="code sev- "><tt><i>346</i>         <span class="s2">&quot;--input_filename_twist&quot;</span><span class="p">,</span></tt>
+            </div>
+            <div id="l347"
+               class="code sev- "><tt><i>347</i>         <span class="n">required</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span></tt>
+            </div>
+            <div id="l348"
+               class="code sev- "><tt><i>348</i>         <span class="n">help</span><span class="o">=</span><span class="s2">&quot;Path to ser file for helical parameter twist. Accepted formats: ser.&quot;</span><span class="p">,</span></tt>
+            </div>
+            <div id="l349"
+               class="code sev- "><tt><i>349</i>     <span class="p">)</span></tt>
+            </div>
+            <div id="l350"
+               class="code sev- "><tt><i>350</i>     <span class="n">required_args</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span></tt>
+            </div>
+            <div id="l351"
+               class="code sev- "><tt><i>351</i>         <span class="s2">&quot;--output_csv_path&quot;</span><span class="p">,</span></tt>
+            </div>
+            <div id="l352"
+               class="code sev- "><tt><i>352</i>         <span class="n">required</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span></tt>
+            </div>
+            <div id="l353"
+               class="code sev- "><tt><i>353</i>         <span class="n">help</span><span class="o">=</span><span class="s2">&quot;Path to output file. Accepted formats: csv.&quot;</span><span class="p">,</span></tt>
+            </div>
+            <div id="l354"
+               class="code sev- "><tt><i>354</i>     <span class="p">)</span></tt>
+            </div>
+            <div id="l355"
+               class="code sev- "><tt><i>355</i>     <span class="n">required_args</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span></tt>
+            </div>
+            <div id="l356"
+               class="code sev- "><tt><i>356</i>         <span class="s2">&quot;--output_jpg_path&quot;</span><span class="p">,</span></tt>
+            </div>
+            <div id="l357"
+               class="code sev- "><tt><i>357</i>         <span class="n">required</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span></tt>
+            </div>
+            <div id="l358"
+               class="code sev- "><tt><i>358</i>         <span class="n">help</span><span class="o">=</span><span class="s2">&quot;Path to output plot. Accepted formats: jpg.&quot;</span><span class="p">,</span></tt>
+            </div>
+            <div id="l359"
+               class="code sev- "><tt><i>359</i>     <span class="p">)</span></tt>
+            </div>
+            <div id="l360"
+               class="code sev- "><tt><i>360</i> &nbsp;</tt>
+            </div>
+            <div id="l361"
+               class="code sev- "><tt><i>361</i>     <span class="n">args</span> <span class="o">=</span> <span class="n">parser</span><span class="o">.</span><span class="n">parse_args</span><span class="p">()</span></tt>
+            </div>
+            <div id="l362"
+               class="code sev- "><tt><i>362</i>     <span class="n">args</span><span class="o">.</span><span class="n">config</span> <span class="o">=</span> <span class="n">args</span><span class="o">.</span><span class="n">config</span> <span class="ow">or</span> <span class="s2">&quot;</span><span class="si">{}</span><span class="s2">&quot;</span></tt>
+            </div>
+            <div id="l363"
+               class="code sev- "><tt><i>363</i>     <span class="n">properties</span> <span class="o">=</span> <span class="n">settings</span><span class="o">.</span><span class="n">ConfReader</span><span class="p">(</span><span class="n">config</span><span class="o">=</span><span class="n">args</span><span class="o">.</span><span class="n">config</span><span class="p">)</span><span class="o">.</span><span class="n">get_prop_dic</span><span class="p">()</span></tt>
+            </div>
+            <div id="l364"
+               class="code sev- "><tt><i>364</i> &nbsp;</tt>
+            </div>
+            <div id="l365"
+               class="code sev- "><tt><i>365</i>     <span class="n">interbpcorr</span><span class="p">(</span></tt>
+            </div>
+            <div id="l366"
+               class="code sev- "><tt><i>366</i>         <span class="n">input_filename_shift</span><span class="o">=</span><span class="n">args</span><span class="o">.</span><span class="n">input_filename_shift</span><span class="p">,</span></tt>
+            </div>
+            <div id="l367"
+               class="code sev- "><tt><i>367</i>         <span class="n">input_filename_slide</span><span class="o">=</span><span class="n">args</span><span class="o">.</span><span class="n">input_filename_slide</span><span class="p">,</span></tt>
+            </div>
+            <div id="l368"
+               class="code sev- "><tt><i>368</i>         <span class="n">input_filename_rise</span><span class="o">=</span><span class="n">args</span><span class="o">.</span><span class="n">input_filename_rise</span><span class="p">,</span></tt>
+            </div>
+            <div id="l369"
+               class="code sev- "><tt><i>369</i>         <span class="n">input_filename_tilt</span><span class="o">=</span><span class="n">args</span><span class="o">.</span><span class="n">input_filename_tilt</span><span class="p">,</span></tt>
+            </div>
+            <div id="l370"
+               class="code sev- "><tt><i>370</i>         <span class="n">input_filename_roll</span><span class="o">=</span><span class="n">args</span><span class="o">.</span><span class="n">input_filename_roll</span><span class="p">,</span></tt>
+            </div>
+            <div id="l371"
+               class="code sev- "><tt><i>371</i>         <span class="n">input_filename_twist</span><span class="o">=</span><span class="n">args</span><span class="o">.</span><span class="n">input_filename_twist</span><span class="p">,</span></tt>
+            </div>
+            <div id="l372"
+               class="code sev- "><tt><i>372</i>         <span class="n">output_csv_path</span><span class="o">=</span><span class="n">args</span><span class="o">.</span><span class="n">output_csv_path</span><span class="p">,</span></tt>
+            </div>
+            <div id="l373"
+               class="code sev- "><tt><i>373</i>         <span class="n">output_jpg_path</span><span class="o">=</span><span class="n">args</span><span class="o">.</span><span class="n">output_jpg_path</span><span class="p">,</span></tt>
+            </div>
+            <div id="l374"
+               class="code sev- "><tt><i>374</i>         <span class="n">properties</span><span class="o">=</span><span class="n">properties</span><span class="p">,</span></tt>
+            </div>
+            <div id="l375"
+               class="code sev- "><tt><i>375</i>     <span class="p">)</span></tt>
+            </div>
+            <div id="l376"
+               class="code sev- "><tt><i>376</i> &nbsp;</tt>
+            </div>
+            <div id="l377"
+               class="code sev- "><tt><i>377</i> &nbsp;</tt>
+            </div>
+            <div id="l378"
+               class="code sev- "><tt><i>378</i> <span class="k">if</span> <span class="vm">__name__</span> <span class="o">==</span> <span class="s2">&quot;__main__&quot;</span><span class="p">:</span></tt>
+            </div>
+            <div id="l379"
+               class="code sev- "><tt><i>379</i>     <span class="n">main</span><span class="p">()</span></tt>
+            </div>
+            
+         </div>
+      </div>
+   </body>
+</html>
\ No newline at end of file
diff --git a/flake8/biobb_dna.intrabp_correlations.intrabpcorr.report.html b/flake8/biobb_dna.intrabp_correlations.intrabpcorr.report.html
new file mode 100644
index 0000000..1f8bd4f
--- /dev/null
+++ b/flake8/biobb_dna.intrabp_correlations.intrabpcorr.report.html
@@ -0,0 +1,78 @@
+<!DOCTYPE html>
+<html>
+   <head>
+      <title>flake8 violations: biobb_dna/intrabp_correlations/intrabpcorr.py</title>
+      <meta http-equiv="Content-Type" value="text/html; charset=UTF-8">
+      <link rel="stylesheet" href="styles.css">
+<script>
+function bindHandler(link) {
+   var code = link.getAttribute('data-code');
+   var key = location.pathname + '#' + code;
+
+   var ul = link.parentNode.querySelector('.details');
+   if (sessionStorage[key] != 'open') {
+      ul.style.display = 'none';
+   }
+   link.addEventListener('click', function (event) {
+      if (!ul.style.display || ul.style.display == 'none') {
+         ul.style.display = 'block';
+         sessionStorage[key] = 'open';
+      } else {
+         ul.style.display = 'none';
+         sessionStorage[key] = 'closed';
+      }
+   });
+}
+
+window.addEventListener('DOMContentLoaded', function () {
+   var links = document.querySelectorAll('#index > li > a');
+   for (var i = 0; i < links.length; i++) {
+      bindHandler(links[i]);
+   }
+});
+</script>
+   </head>
+   <body>
+      <div id="masthead" class="sev-2"></div>
+      <div id="page">
+         <p id="srclink">
+            <a title="View full annotated source"
+               href="biobb_dna.intrabp_correlations.intrabpcorr.source.html">
+               <img src="file.svg" alt="&#x2261;">
+            </a></p>
+         <h1>
+            <a href="index.html">
+               <img src="back.svg" alt="&#x2B05;">
+               biobb_dna/intrabp_correlations/intrabpcorr.py
+            </a>
+         </h1>
+
+         <ul id="index">
+         
+         <li>
+            <a data-code="W503">
+               <span class="count sev-2">
+                  2
+               </span>
+               <strong>W503:</strong> line break before binary operator
+               
+            </a>
+            <ul class="details">
+            <li>
+               
+               <a href="biobb_dna.intrabp_correlations.intrabpcorr.source.html#l199">
+                  <tt><i>199</i>                 <span class="ow">and</span> <span class="n">ser2</span><span class="o">.</span><span class="n">name</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">constants</span><span class="o">.</span><span class="n">hp_angular</span></tt>
+               </a>
+            </li><li>
+               
+               <a href="biobb_dna.intrabp_correlations.intrabpcorr.source.html#l202">
+                  <tt><i>202</i>                 <span class="ow">and</span> <span class="n">ser1</span><span class="o">.</span><span class="n">name</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">constants</span><span class="o">.</span><span class="n">hp_angular</span></tt>
+               </a>
+            </li>
+            </ul>
+         </li>
+         
+         </ul>
+      </div>
+   </body>
+</html>
\ No newline at end of file
diff --git a/flake8/biobb_dna.intrabp_correlations.intrabpcorr.source.html b/flake8/biobb_dna.intrabp_correlations.intrabpcorr.source.html
new file mode 100644
index 0000000..7596875
--- /dev/null
+++ b/flake8/biobb_dna.intrabp_correlations.intrabpcorr.source.html
@@ -0,0 +1,1166 @@
+<!DOCTYPE html>
+<html>
+   <head>
+      <title>biobb_dna/intrabp_correlations/intrabpcorr.py - flake8 annotated source</title>
+      <meta http-equiv="Content-Type" value="text/html; charset=UTF-8">
+      <link rel="stylesheet" href="styles.css">
+   </head>
+   <body>
+      <div id="masthead" class="sev-2"></div>
+      <div id="page">
+         <h1>
+            <a href="biobb_dna.intrabp_correlations.intrabpcorr.report.html">
+               <img src="back.svg" alt="&#x2B05;">
+               biobb_dna/intrabp_correlations/intrabpcorr.py source
+            </a>
+         </h1>
+
+         <div id="doc">
+            <div id="l1"
+               class="code sev- "><tt><i>1</i> <span class="ch">#!/usr/bin/env python3</span></tt>
+            </div>
+            <div id="l2"
+               class="code sev- "><tt><i>2</i> &nbsp;</tt>
+            </div>
+            <div id="l3"
+               class="code sev- "><tt><i>3</i> <span class="sd">&quot;&quot;&quot;Module containing the IntraBasePairCorrelation class and the command line interface.&quot;&quot;&quot;</span></tt>
+            </div>
+            <div id="l4"
+               class="code sev- "><tt><i>4</i> &nbsp;</tt>
+            </div>
+            <div id="l5"
+               class="code sev- "><tt><i>5</i> <span class="kn">import</span> <span class="nn">argparse</span></tt>
+            </div>
+            <div id="l6"
+               class="code sev- "><tt><i>6</i> <span class="kn">from</span> <span class="nn">itertools</span> <span class="kn">import</span> <span class="n">product</span></tt>
+            </div>
+            <div id="l7"
+               class="code sev- "><tt><i>7</i> <span class="kn">from</span> <span class="nn">typing</span> <span class="kn">import</span> <span class="n">Optional</span></tt>
+            </div>
+            <div id="l8"
+               class="code sev- "><tt><i>8</i> &nbsp;</tt>
+            </div>
+            <div id="l9"
+               class="code sev- "><tt><i>9</i> <span class="kn">import</span> <span class="nn">matplotlib</span> <span class="k">as</span> <span class="nn">mpl</span></tt>
+            </div>
+            <div id="l10"
+               class="code sev- "><tt><i>10</i> <span class="kn">import</span> <span class="nn">matplotlib.pyplot</span> <span class="k">as</span> <span class="nn">plt</span></tt>
+            </div>
+            <div id="l11"
+               class="code sev- "><tt><i>11</i> <span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span></tt>
+            </div>
+            <div id="l12"
+               class="code sev- "><tt><i>12</i> <span class="kn">import</span> <span class="nn">pandas</span> <span class="k">as</span> <span class="nn">pd</span></tt>
+            </div>
+            <div id="l13"
+               class="code sev- "><tt><i>13</i> <span class="kn">from</span> <span class="nn">biobb_common.configuration</span> <span class="kn">import</span> <span class="n">settings</span></tt>
+            </div>
+            <div id="l14"
+               class="code sev- "><tt><i>14</i> <span class="kn">from</span> <span class="nn">biobb_common.generic.biobb_object</span> <span class="kn">import</span> <span class="n">BiobbObject</span></tt>
+            </div>
+            <div id="l15"
+               class="code sev- "><tt><i>15</i> <span class="kn">from</span> <span class="nn">biobb_common.tools.file_utils</span> <span class="kn">import</span> <span class="n">launchlogger</span></tt>
+            </div>
+            <div id="l16"
+               class="code sev- "><tt><i>16</i> &nbsp;</tt>
+            </div>
+            <div id="l17"
+               class="code sev- "><tt><i>17</i> <span class="kn">from</span> <span class="nn">biobb_dna.utils</span> <span class="kn">import</span> <span class="n">constants</span></tt>
+            </div>
+            <div id="l18"
+               class="code sev- "><tt><i>18</i> <span class="kn">from</span> <span class="nn">biobb_dna.utils.common</span> <span class="kn">import</span> <span class="n">_from_string_to_list</span></tt>
+            </div>
+            <div id="l19"
+               class="code sev- "><tt><i>19</i> <span class="kn">from</span> <span class="nn">biobb_dna.utils.loader</span> <span class="kn">import</span> <span class="n">read_series</span></tt>
+            </div>
+            <div id="l20"
+               class="code sev- "><tt><i>20</i> &nbsp;</tt>
+            </div>
+            <div id="l21"
+               class="code sev- "><tt><i>21</i> &nbsp;</tt>
+            </div>
+            <div id="l22"
+               class="code sev- "><tt><i>22</i> <span class="k">class</span> <span class="nc">IntraBasePairCorrelation</span><span class="p">(</span><span class="n">BiobbObject</span><span class="p">):</span></tt>
+            </div>
+            <div id="l23"
+               class="code sev- "><tt><i>23</i> <span class="w">    </span><span class="sd">&quot;&quot;&quot;</span></tt>
+            </div>
+            <div id="l24"
+               class="code sev- "><tt><i>24</i> <span class="sd">    | biobb_dna IntraBasePairCorrelation</span></tt>
+            </div>
+            <div id="l25"
+               class="code sev- "><tt><i>25</i> <span class="sd">    | Calculate correlation between all intra-base pairs of a single sequence and for a single helical parameter.</span></tt>
+            </div>
+            <div id="l26"
+               class="code sev- "><tt><i>26</i> <span class="sd">    | Calculate correlation between neighboring base pairs and pairs of helical parameters.</span></tt>
+            </div>
+            <div id="l27"
+               class="code sev- "><tt><i>27</i> &nbsp;</tt>
+            </div>
+            <div id="l28"
+               class="code sev- "><tt><i>28</i> <span class="sd">    Args:</span></tt>
+            </div>
+            <div id="l29"
+               class="code sev- "><tt><i>29</i> <span class="sd">        input_filename_shear (str): Path to .ser file with data for helical parameter &#39;shear&#39;. File type: input. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/correlation/canal_output_shear.ser&gt;`_. Accepted formats: ser (edam:format_2330).</span></tt>
+            </div>
+            <div id="l30"
+               class="code sev- "><tt><i>30</i> <span class="sd">        input_filename_stretch (str): Path to .ser file with data for helical parameter &#39;stretch&#39;. File type: input. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/correlation/canal_output_stretch.ser&gt;`_. Accepted formats: ser (edam:format_2330).</span></tt>
+            </div>
+            <div id="l31"
+               class="code sev- "><tt><i>31</i> <span class="sd">        input_filename_stagger (str): Path to .ser file with data for helical parameter &#39;stagger&#39;. File type: input. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/correlation/canal_output_stagger.ser&gt;`_. Accepted formats: ser (edam:format_2330).</span></tt>
+            </div>
+            <div id="l32"
+               class="code sev- "><tt><i>32</i> <span class="sd">        input_filename_buckle (str): Path to .ser file with data for helical parameter &#39;buckle&#39;. File type: input. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/correlation/canal_output_buckle.ser&gt;`_. Accepted formats: ser (edam:format_2330).</span></tt>
+            </div>
+            <div id="l33"
+               class="code sev- "><tt><i>33</i> <span class="sd">        input_filename_propel (str): Path to .ser file with data for helical parameter &#39;propel&#39;. File type: input. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/correlation/canal_output_propel.ser&gt;`_. Accepted formats: ser (edam:format_2330).</span></tt>
+            </div>
+            <div id="l34"
+               class="code sev- "><tt><i>34</i> <span class="sd">        input_filename_opening (str): Path to .ser file with data for helical parameter &#39;opening&#39;. File type: input. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/correlation/canal_output_opening.ser&gt;`_. Accepted formats: ser (edam:format_2330).</span></tt>
+            </div>
+            <div id="l35"
+               class="code sev- "><tt><i>35</i> <span class="sd">        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&gt;`_. Accepted formats: csv (edam:format_3752).</span></tt>
+            </div>
+            <div id="l36"
+               class="code sev- "><tt><i>36</i> <span class="sd">        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&gt;`_. Accepted formats: jpg (edam:format_3579).</span></tt>
+            </div>
+            <div id="l37"
+               class="code sev- "><tt><i>37</i> <span class="sd">        properties (dict):</span></tt>
+            </div>
+            <div id="l38"
+               class="code sev- "><tt><i>38</i> <span class="sd">            * **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></tt>
+            </div>
+            <div id="l39"
+               class="code sev- "><tt><i>39</i> <span class="sd">            * **seqpos** (*list*) - (None) list of sequence positions (columns indices starting by 0) to analyze.  If not specified it will analyse the complete sequence.</span></tt>
+            </div>
+            <div id="l40"
+               class="code sev- "><tt><i>40</i> <span class="sd">            * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.</span></tt>
+            </div>
+            <div id="l41"
+               class="code sev- "><tt><i>41</i> <span class="sd">            * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.</span></tt>
+            </div>
+            <div id="l42"
+               class="code sev- "><tt><i>42</i> <span class="sd">            * **sandbox_path** (*str*) - (&quot;./&quot;) [WF property] Parent path to the sandbox directory.</span></tt>
+            </div>
+            <div id="l43"
+               class="code sev- "><tt><i>43</i> &nbsp;</tt>
+            </div>
+            <div id="l44"
+               class="code sev- "><tt><i>44</i> <span class="sd">    Examples:</span></tt>
+            </div>
+            <div id="l45"
+               class="code sev- "><tt><i>45</i> <span class="sd">        This is a use example of how to use the building block from Python::</span></tt>
+            </div>
+            <div id="l46"
+               class="code sev- "><tt><i>46</i> &nbsp;</tt>
+            </div>
+            <div id="l47"
+               class="code sev- "><tt><i>47</i> <span class="sd">            from biobb_dna.intrabp_correlations.intrabpcorr import intrabpcorr</span></tt>
+            </div>
+            <div id="l48"
+               class="code sev- "><tt><i>48</i> &nbsp;</tt>
+            </div>
+            <div id="l49"
+               class="code sev- "><tt><i>49</i> <span class="sd">            intrabpcorr(</span></tt>
+            </div>
+            <div id="l50"
+               class="code sev- "><tt><i>50</i> <span class="sd">                input_filename_shear=&#39;path/to/input/shear.ser&#39;,</span></tt>
+            </div>
+            <div id="l51"
+               class="code sev- "><tt><i>51</i> <span class="sd">                input_filename_stretch=&#39;path/to/input/stretch.ser&#39;,</span></tt>
+            </div>
+            <div id="l52"
+               class="code sev- "><tt><i>52</i> <span class="sd">                input_filename_stagger=&#39;path/to/input/stagger.ser&#39;,</span></tt>
+            </div>
+            <div id="l53"
+               class="code sev- "><tt><i>53</i> <span class="sd">                input_filename_buckle=&#39;path/to/input/buckle.ser&#39;,</span></tt>
+            </div>
+            <div id="l54"
+               class="code sev- "><tt><i>54</i> <span class="sd">                input_filename_propel=&#39;path/to/input/propel.ser&#39;,</span></tt>
+            </div>
+            <div id="l55"
+               class="code sev- "><tt><i>55</i> <span class="sd">                input_filename_opening=&#39;path/to/input/opening.ser&#39;,</span></tt>
+            </div>
+            <div id="l56"
+               class="code sev- "><tt><i>56</i> <span class="sd">                output_csv_path=&#39;path/to/output/file.csv&#39;,</span></tt>
+            </div>
+            <div id="l57"
+               class="code sev- "><tt><i>57</i> <span class="sd">                output_jpg_path=&#39;path/to/output/plot.jpg&#39;,</span></tt>
+            </div>
+            <div id="l58"
+               class="code sev- "><tt><i>58</i> <span class="sd">                properties=prop)</span></tt>
+            </div>
+            <div id="l59"
+               class="code sev- "><tt><i>59</i> <span class="sd">    Info:</span></tt>
+            </div>
+            <div id="l60"
+               class="code sev- "><tt><i>60</i> <span class="sd">        * wrapped_software:</span></tt>
+            </div>
+            <div id="l61"
+               class="code sev- "><tt><i>61</i> <span class="sd">            * name: In house</span></tt>
+            </div>
+            <div id="l62"
+               class="code sev- "><tt><i>62</i> <span class="sd">            * license: Apache-2.0</span></tt>
+            </div>
+            <div id="l63"
+               class="code sev- "><tt><i>63</i> <span class="sd">        * ontology:</span></tt>
+            </div>
+            <div id="l64"
+               class="code sev- "><tt><i>64</i> <span class="sd">            * name: EDAM</span></tt>
+            </div>
+            <div id="l65"
+               class="code sev- "><tt><i>65</i> <span class="sd">            * schema: http://edamontology.org/EDAM.owl</span></tt>
+            </div>
+            <div id="l66"
+               class="code sev- "><tt><i>66</i> &nbsp;</tt>
+            </div>
+            <div id="l67"
+               class="code sev- "><tt><i>67</i> <span class="sd">    &quot;&quot;&quot;</span></tt>
+            </div>
+            <div id="l68"
+               class="code sev- "><tt><i>68</i> &nbsp;</tt>
+            </div>
+            <div id="l69"
+               class="code sev- "><tt><i>69</i>     <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span></tt>
+            </div>
+            <div id="l70"
+               class="code sev- "><tt><i>70</i>         <span class="bp">self</span><span class="p">,</span></tt>
+            </div>
+            <div id="l71"
+               class="code sev- "><tt><i>71</i>         <span class="n">input_filename_shear</span><span class="p">,</span></tt>
+            </div>
+            <div id="l72"
+               class="code sev- "><tt><i>72</i>         <span class="n">input_filename_stretch</span><span class="p">,</span></tt>
+            </div>
+            <div id="l73"
+               class="code sev- "><tt><i>73</i>         <span class="n">input_filename_stagger</span><span class="p">,</span></tt>
+            </div>
+            <div id="l74"
+               class="code sev- "><tt><i>74</i>         <span class="n">input_filename_buckle</span><span class="p">,</span></tt>
+            </div>
+            <div id="l75"
+               class="code sev- "><tt><i>75</i>         <span class="n">input_filename_propel</span><span class="p">,</span></tt>
+            </div>
+            <div id="l76"
+               class="code sev- "><tt><i>76</i>         <span class="n">input_filename_opening</span><span class="p">,</span></tt>
+            </div>
+            <div id="l77"
+               class="code sev- "><tt><i>77</i>         <span class="n">output_csv_path</span><span class="p">,</span></tt>
+            </div>
+            <div id="l78"
+               class="code sev- "><tt><i>78</i>         <span class="n">output_jpg_path</span><span class="p">,</span></tt>
+            </div>
+            <div id="l79"
+               class="code sev- "><tt><i>79</i>         <span class="n">properties</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span></tt>
+            </div>
+            <div id="l80"
+               class="code sev- "><tt><i>80</i>         <span class="o">**</span><span class="n">kwargs</span><span class="p">,</span></tt>
+            </div>
+            <div id="l81"
+               class="code sev- "><tt><i>81</i>     <span class="p">)</span> <span class="o">-&gt;</span> <span class="kc">None</span><span class="p">:</span></tt>
+            </div>
+            <div id="l82"
+               class="code sev- "><tt><i>82</i>         <span class="n">properties</span> <span class="o">=</span> <span class="n">properties</span> <span class="ow">or</span> <span class="p">{}</span></tt>
+            </div>
+            <div id="l83"
+               class="code sev- "><tt><i>83</i> &nbsp;</tt>
+            </div>
+            <div id="l84"
+               class="code sev- "><tt><i>84</i>         <span class="c1"># Call parent class constructor</span></tt>
+            </div>
+            <div id="l85"
+               class="code sev- "><tt><i>85</i>         <span class="nb">super</span><span class="p">()</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="n">properties</span><span class="p">)</span></tt>
+            </div>
+            <div id="l86"
+               class="code sev- "><tt><i>86</i>         <span class="bp">self</span><span class="o">.</span><span class="n">locals_var_dict</span> <span class="o">=</span> <span class="nb">locals</span><span class="p">()</span><span class="o">.</span><span class="n">copy</span><span class="p">()</span></tt>
+            </div>
+            <div id="l87"
+               class="code sev- "><tt><i>87</i> &nbsp;</tt>
+            </div>
+            <div id="l88"
+               class="code sev- "><tt><i>88</i>         <span class="c1"># Input/Output files</span></tt>
+            </div>
+            <div id="l89"
+               class="code sev- "><tt><i>89</i>         <span class="bp">self</span><span class="o">.</span><span class="n">io_dict</span> <span class="o">=</span> <span class="p">{</span></tt>
+            </div>
+            <div id="l90"
+               class="code sev- "><tt><i>90</i>             <span class="s2">&quot;in&quot;</span><span class="p">:</span> <span class="p">{</span></tt>
+            </div>
+            <div id="l91"
+               class="code sev- "><tt><i>91</i>                 <span class="s2">&quot;input_filename_shear&quot;</span><span class="p">:</span> <span class="n">input_filename_shear</span><span class="p">,</span></tt>
+            </div>
+            <div id="l92"
+               class="code sev- "><tt><i>92</i>                 <span class="s2">&quot;input_filename_stretch&quot;</span><span class="p">:</span> <span class="n">input_filename_stretch</span><span class="p">,</span></tt>
+            </div>
+            <div id="l93"
+               class="code sev- "><tt><i>93</i>                 <span class="s2">&quot;input_filename_stagger&quot;</span><span class="p">:</span> <span class="n">input_filename_stagger</span><span class="p">,</span></tt>
+            </div>
+            <div id="l94"
+               class="code sev- "><tt><i>94</i>                 <span class="s2">&quot;input_filename_buckle&quot;</span><span class="p">:</span> <span class="n">input_filename_buckle</span><span class="p">,</span></tt>
+            </div>
+            <div id="l95"
+               class="code sev- "><tt><i>95</i>                 <span class="s2">&quot;input_filename_propel&quot;</span><span class="p">:</span> <span class="n">input_filename_propel</span><span class="p">,</span></tt>
+            </div>
+            <div id="l96"
+               class="code sev- "><tt><i>96</i>                 <span class="s2">&quot;input_filename_opening&quot;</span><span class="p">:</span> <span class="n">input_filename_opening</span><span class="p">,</span></tt>
+            </div>
+            <div id="l97"
+               class="code sev- "><tt><i>97</i>             <span class="p">},</span></tt>
+            </div>
+            <div id="l98"
+               class="code sev- "><tt><i>98</i>             <span class="s2">&quot;out&quot;</span><span class="p">:</span> <span class="p">{</span></tt>
+            </div>
+            <div id="l99"
+               class="code sev- "><tt><i>99</i>                 <span class="s2">&quot;output_csv_path&quot;</span><span class="p">:</span> <span class="n">output_csv_path</span><span class="p">,</span></tt>
+            </div>
+            <div id="l100"
+               class="code sev- "><tt><i>100</i>                 <span class="s2">&quot;output_jpg_path&quot;</span><span class="p">:</span> <span class="n">output_jpg_path</span><span class="p">,</span></tt>
+            </div>
+            <div id="l101"
+               class="code sev- "><tt><i>101</i>             <span class="p">},</span></tt>
+            </div>
+            <div id="l102"
+               class="code sev- "><tt><i>102</i>         <span class="p">}</span></tt>
+            </div>
+            <div id="l103"
+               class="code sev- "><tt><i>103</i> &nbsp;</tt>
+            </div>
+            <div id="l104"
+               class="code sev- "><tt><i>104</i>         <span class="bp">self</span><span class="o">.</span><span class="n">properties</span> <span class="o">=</span> <span class="n">properties</span></tt>
+            </div>
+            <div id="l105"
+               class="code sev- "><tt><i>105</i>         <span class="bp">self</span><span class="o">.</span><span class="n">sequence</span> <span class="o">=</span> <span class="n">properties</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">&quot;sequence&quot;</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span></tt>
+            </div>
+            <div id="l106"
+               class="code sev- "><tt><i>106</i>         <span class="bp">self</span><span class="o">.</span><span class="n">seqpos</span> <span class="o">=</span> <span class="p">[</span></tt>
+            </div>
+            <div id="l107"
+               class="code sev- "><tt><i>107</i>             <span class="nb">int</span><span class="p">(</span><span class="n">elem</span><span class="p">)</span> <span class="k">for</span> <span class="n">elem</span> <span class="ow">in</span> <span class="n">_from_string_to_list</span><span class="p">(</span><span class="n">properties</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">&quot;seqpos&quot;</span><span class="p">,</span> <span class="kc">None</span><span class="p">))</span></tt>
+            </div>
+            <div id="l108"
+               class="code sev- "><tt><i>108</i>         <span class="p">]</span></tt>
+            </div>
+            <div id="l109"
+               class="code sev- "><tt><i>109</i> &nbsp;</tt>
+            </div>
+            <div id="l110"
+               class="code sev- "><tt><i>110</i>         <span class="c1"># Check the properties</span></tt>
+            </div>
+            <div id="l111"
+               class="code sev- "><tt><i>111</i>         <span class="bp">self</span><span class="o">.</span><span class="n">check_properties</span><span class="p">(</span><span class="n">properties</span><span class="p">)</span></tt>
+            </div>
+            <div id="l112"
+               class="code sev- "><tt><i>112</i>         <span class="bp">self</span><span class="o">.</span><span class="n">check_arguments</span><span class="p">()</span></tt>
+            </div>
+            <div id="l113"
+               class="code sev- "><tt><i>113</i> &nbsp;</tt>
+            </div>
+            <div id="l114"
+               class="code sev- "><tt><i>114</i>     <span class="nd">@launchlogger</span></tt>
+            </div>
+            <div id="l115"
+               class="code sev- "><tt><i>115</i>     <span class="k">def</span> <span class="nf">launch</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">int</span><span class="p">:</span></tt>
+            </div>
+            <div id="l116"
+               class="code sev- "><tt><i>116</i> <span class="w">        </span><span class="sd">&quot;&quot;&quot;Execute the :class:`HelParCorrelation &lt;intrabp_correlations.intrabpcorr.IntraBasePairCorrelation&gt;` object.&quot;&quot;&quot;</span></tt>
+            </div>
+            <div id="l117"
+               class="code sev- "><tt><i>117</i> &nbsp;</tt>
+            </div>
+            <div id="l118"
+               class="code sev- "><tt><i>118</i>         <span class="c1"># Setup Biobb</span></tt>
+            </div>
+            <div id="l119"
+               class="code sev- "><tt><i>119</i>         <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">check_restart</span><span class="p">():</span></tt>
+            </div>
+            <div id="l120"
+               class="code sev- "><tt><i>120</i>             <span class="k">return</span> <span class="mi">0</span></tt>
+            </div>
+            <div id="l121"
+               class="code sev- "><tt><i>121</i>         <span class="bp">self</span><span class="o">.</span><span class="n">stage_files</span><span class="p">()</span></tt>
+            </div>
+            <div id="l122"
+               class="code sev- "><tt><i>122</i> &nbsp;</tt>
+            </div>
+            <div id="l123"
+               class="code sev- "><tt><i>123</i>         <span class="c1"># check sequence</span></tt>
+            </div>
+            <div id="l124"
+               class="code sev- "><tt><i>124</i>         <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">sequence</span> <span class="ow">is</span> <span class="kc">None</span> <span class="ow">or</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">sequence</span><span class="p">)</span> <span class="o">&lt;</span> <span class="mi">2</span><span class="p">:</span></tt>
+            </div>
+            <div id="l125"
+               class="code sev- "><tt><i>125</i>             <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s2">&quot;sequence is null or too short!&quot;</span><span class="p">)</span></tt>
+            </div>
+            <div id="l126"
+               class="code sev- "><tt><i>126</i> &nbsp;</tt>
+            </div>
+            <div id="l127"
+               class="code sev- "><tt><i>127</i>         <span class="c1"># check seqpos</span></tt>
+            </div>
+            <div id="l128"
+               class="code sev- "><tt><i>128</i>         <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">seqpos</span><span class="p">:</span></tt>
+            </div>
+            <div id="l129"
+               class="code sev- "><tt><i>129</i>             <span class="k">if</span> <span class="ow">not</span> <span class="p">(</span><span class="nb">isinstance</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">seqpos</span><span class="p">,</span> <span class="nb">list</span><span class="p">)</span> <span class="ow">and</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">seqpos</span><span class="p">)</span> <span class="o">&gt;</span> <span class="mi">1</span><span class="p">):</span></tt>
+            </div>
+            <div id="l130"
+               class="code sev- "><tt><i>130</i>                 <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s2">&quot;seqpos must be a list of at least two integers&quot;</span><span class="p">)</span></tt>
+            </div>
+            <div id="l131"
+               class="code sev- "><tt><i>131</i>         <span class="k">else</span><span class="p">:</span></tt>
+            </div>
+            <div id="l132"
+               class="code sev- "><tt><i>132</i>             <span class="bp">self</span><span class="o">.</span><span class="n">seqpos</span> <span class="o">=</span> <span class="kc">None</span>  <span class="c1"># type: ignore</span></tt>
+            </div>
+            <div id="l133"
+               class="code sev- "><tt><i>133</i> &nbsp;</tt>
+            </div>
+            <div id="l134"
+               class="code sev- "><tt><i>134</i>         <span class="c1"># read input</span></tt>
+            </div>
+            <div id="l135"
+               class="code sev- "><tt><i>135</i>         <span class="n">shear</span> <span class="o">=</span> <span class="n">read_series</span><span class="p">(</span></tt>
+            </div>
+            <div id="l136"
+               class="code sev- "><tt><i>136</i>             <span class="bp">self</span><span class="o">.</span><span class="n">stage_io_dict</span><span class="p">[</span><span class="s2">&quot;in&quot;</span><span class="p">][</span><span class="s2">&quot;input_filename_shear&quot;</span><span class="p">],</span> <span class="n">usecols</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">seqpos</span></tt>
+            </div>
+            <div id="l137"
+               class="code sev- "><tt><i>137</i>         <span class="p">)</span></tt>
+            </div>
+            <div id="l138"
+               class="code sev- "><tt><i>138</i>         <span class="n">stretch</span> <span class="o">=</span> <span class="n">read_series</span><span class="p">(</span></tt>
+            </div>
+            <div id="l139"
+               class="code sev- "><tt><i>139</i>             <span class="bp">self</span><span class="o">.</span><span class="n">stage_io_dict</span><span class="p">[</span><span class="s2">&quot;in&quot;</span><span class="p">][</span><span class="s2">&quot;input_filename_stretch&quot;</span><span class="p">],</span> <span class="n">usecols</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">seqpos</span></tt>
+            </div>
+            <div id="l140"
+               class="code sev- "><tt><i>140</i>         <span class="p">)</span></tt>
+            </div>
+            <div id="l141"
+               class="code sev- "><tt><i>141</i>         <span class="n">stagger</span> <span class="o">=</span> <span class="n">read_series</span><span class="p">(</span></tt>
+            </div>
+            <div id="l142"
+               class="code sev- "><tt><i>142</i>             <span class="bp">self</span><span class="o">.</span><span class="n">stage_io_dict</span><span class="p">[</span><span class="s2">&quot;in&quot;</span><span class="p">][</span><span class="s2">&quot;input_filename_stagger&quot;</span><span class="p">],</span> <span class="n">usecols</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">seqpos</span></tt>
+            </div>
+            <div id="l143"
+               class="code sev- "><tt><i>143</i>         <span class="p">)</span></tt>
+            </div>
+            <div id="l144"
+               class="code sev- "><tt><i>144</i>         <span class="n">buckle</span> <span class="o">=</span> <span class="n">read_series</span><span class="p">(</span></tt>
+            </div>
+            <div id="l145"
+               class="code sev- "><tt><i>145</i>             <span class="bp">self</span><span class="o">.</span><span class="n">stage_io_dict</span><span class="p">[</span><span class="s2">&quot;in&quot;</span><span class="p">][</span><span class="s2">&quot;input_filename_buckle&quot;</span><span class="p">],</span> <span class="n">usecols</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">seqpos</span></tt>
+            </div>
+            <div id="l146"
+               class="code sev- "><tt><i>146</i>         <span class="p">)</span></tt>
+            </div>
+            <div id="l147"
+               class="code sev- "><tt><i>147</i>         <span class="n">propel</span> <span class="o">=</span> <span class="n">read_series</span><span class="p">(</span></tt>
+            </div>
+            <div id="l148"
+               class="code sev- "><tt><i>148</i>             <span class="bp">self</span><span class="o">.</span><span class="n">stage_io_dict</span><span class="p">[</span><span class="s2">&quot;in&quot;</span><span class="p">][</span><span class="s2">&quot;input_filename_propel&quot;</span><span class="p">],</span> <span class="n">usecols</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">seqpos</span></tt>
+            </div>
+            <div id="l149"
+               class="code sev- "><tt><i>149</i>         <span class="p">)</span></tt>
+            </div>
+            <div id="l150"
+               class="code sev- "><tt><i>150</i>         <span class="n">opening</span> <span class="o">=</span> <span class="n">read_series</span><span class="p">(</span></tt>
+            </div>
+            <div id="l151"
+               class="code sev- "><tt><i>151</i>             <span class="bp">self</span><span class="o">.</span><span class="n">stage_io_dict</span><span class="p">[</span><span class="s2">&quot;in&quot;</span><span class="p">][</span><span class="s2">&quot;input_filename_opening&quot;</span><span class="p">],</span> <span class="n">usecols</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">seqpos</span></tt>
+            </div>
+            <div id="l152"
+               class="code sev- "><tt><i>152</i>         <span class="p">)</span></tt>
+            </div>
+            <div id="l153"
+               class="code sev- "><tt><i>153</i> &nbsp;</tt>
+            </div>
+            <div id="l154"
+               class="code sev- "><tt><i>154</i>         <span class="k">if</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">seqpos</span><span class="p">:</span></tt>
+            </div>
+            <div id="l155"
+               class="code sev- "><tt><i>155</i>             <span class="c1"># drop first and last columns</span></tt>
+            </div>
+            <div id="l156"
+               class="code sev- "><tt><i>156</i>             <span class="n">shear</span> <span class="o">=</span> <span class="n">shear</span><span class="p">[</span><span class="n">shear</span><span class="o">.</span><span class="n">columns</span><span class="p">[</span><span class="mi">1</span><span class="p">:</span><span class="o">-</span><span class="mi">1</span><span class="p">]]</span></tt>
+            </div>
+            <div id="l157"
+               class="code sev- "><tt><i>157</i>             <span class="n">stretch</span> <span class="o">=</span> <span class="n">stretch</span><span class="p">[</span><span class="n">stretch</span><span class="o">.</span><span class="n">columns</span><span class="p">[</span><span class="mi">1</span><span class="p">:</span><span class="o">-</span><span class="mi">1</span><span class="p">]]</span></tt>
+            </div>
+            <div id="l158"
+               class="code sev- "><tt><i>158</i>             <span class="n">stagger</span> <span class="o">=</span> <span class="n">stagger</span><span class="p">[</span><span class="n">stagger</span><span class="o">.</span><span class="n">columns</span><span class="p">[</span><span class="mi">1</span><span class="p">:</span><span class="o">-</span><span class="mi">1</span><span class="p">]]</span></tt>
+            </div>
+            <div id="l159"
+               class="code sev- "><tt><i>159</i>             <span class="n">buckle</span> <span class="o">=</span> <span class="n">buckle</span><span class="p">[</span><span class="n">buckle</span><span class="o">.</span><span class="n">columns</span><span class="p">[</span><span class="mi">1</span><span class="p">:</span><span class="o">-</span><span class="mi">1</span><span class="p">]]</span></tt>
+            </div>
+            <div id="l160"
+               class="code sev- "><tt><i>160</i>             <span class="n">propel</span> <span class="o">=</span> <span class="n">propel</span><span class="p">[</span><span class="n">propel</span><span class="o">.</span><span class="n">columns</span><span class="p">[</span><span class="mi">1</span><span class="p">:</span><span class="o">-</span><span class="mi">1</span><span class="p">]]</span></tt>
+            </div>
+            <div id="l161"
+               class="code sev- "><tt><i>161</i>             <span class="n">opening</span> <span class="o">=</span> <span class="n">opening</span><span class="p">[</span><span class="n">opening</span><span class="o">.</span><span class="n">columns</span><span class="p">[</span><span class="mi">1</span><span class="p">:</span><span class="o">-</span><span class="mi">1</span><span class="p">]]</span></tt>
+            </div>
+            <div id="l162"
+               class="code sev- "><tt><i>162</i>             <span class="n">labels</span> <span class="o">=</span> <span class="p">[</span></tt>
+            </div>
+            <div id="l163"
+               class="code sev- "><tt><i>163</i>                 <span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">i</span><span class="o">+</span><span class="mi">1</span><span class="si">}</span><span class="s2">_</span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">sequence</span><span class="p">[</span><span class="n">i</span><span class="p">:</span><span class="n">i</span><span class="o">+</span><span class="mi">1</span><span class="p">]</span><span class="si">}</span><span class="s2">&quot;</span></tt>
+            </div>
+            <div id="l164"
+               class="code sev- "><tt><i>164</i>                 <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="nb">len</span><span class="p">(</span><span class="n">shear</span><span class="o">.</span><span class="n">columns</span><span class="p">)</span> <span class="o">+</span> <span class="mi">1</span><span class="p">)</span></tt>
+            </div>
+            <div id="l165"
+               class="code sev- "><tt><i>165</i>             <span class="p">]</span></tt>
+            </div>
+            <div id="l166"
+               class="code sev- "><tt><i>166</i>             <span class="n">corr_index</span> <span class="o">=</span> <span class="p">[</span></tt>
+            </div>
+            <div id="l167"
+               class="code sev- "><tt><i>167</i>                 <span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">sequence</span><span class="p">[</span><span class="n">i</span><span class="p">:</span><span class="n">i</span><span class="o">+</span><span class="mi">2</span><span class="p">]</span><span class="si">}</span><span class="s2">&quot;</span> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="nb">len</span><span class="p">(</span><span class="n">shear</span><span class="o">.</span><span class="n">columns</span><span class="p">)</span> <span class="o">+</span> <span class="mi">1</span><span class="p">)</span></tt>
+            </div>
+            <div id="l168"
+               class="code sev- "><tt><i>168</i>             <span class="p">]</span></tt>
+            </div>
+            <div id="l169"
+               class="code sev- "><tt><i>169</i>         <span class="k">else</span><span class="p">:</span></tt>
+            </div>
+            <div id="l170"
+               class="code sev- "><tt><i>170</i>             <span class="n">labels</span> <span class="o">=</span> <span class="p">[</span><span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">i</span><span class="o">+</span><span class="mi">1</span><span class="si">}</span><span class="s2">_</span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">sequence</span><span class="p">[</span><span class="n">i</span><span class="p">:</span><span class="n">i</span><span class="o">+</span><span class="mi">1</span><span class="p">]</span><span class="si">}</span><span class="s2">&quot;</span> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">seqpos</span><span class="p">]</span></tt>
+            </div>
+            <div id="l171"
+               class="code sev- "><tt><i>171</i>             <span class="n">corr_index</span> <span class="o">=</span> <span class="p">[</span><span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">sequence</span><span class="p">[</span><span class="n">i</span><span class="p">:</span><span class="n">i</span><span class="o">+</span><span class="mi">2</span><span class="p">]</span><span class="si">}</span><span class="s2">&quot;</span> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">seqpos</span><span class="p">]</span></tt>
+            </div>
+            <div id="l172"
+               class="code sev- "><tt><i>172</i> &nbsp;</tt>
+            </div>
+            <div id="l173"
+               class="code sev- "><tt><i>173</i>         <span class="c1"># rename duplicated subunits</span></tt>
+            </div>
+            <div id="l174"
+               class="code sev- "><tt><i>174</i>         <span class="n">shear</span><span class="o">.</span><span class="n">columns</span> <span class="o">=</span> <span class="n">labels</span></tt>
+            </div>
+            <div id="l175"
+               class="code sev- "><tt><i>175</i>         <span class="n">stretch</span><span class="o">.</span><span class="n">columns</span> <span class="o">=</span> <span class="n">labels</span></tt>
+            </div>
+            <div id="l176"
+               class="code sev- "><tt><i>176</i>         <span class="n">stagger</span><span class="o">.</span><span class="n">columns</span> <span class="o">=</span> <span class="n">labels</span></tt>
+            </div>
+            <div id="l177"
+               class="code sev- "><tt><i>177</i>         <span class="n">buckle</span><span class="o">.</span><span class="n">columns</span> <span class="o">=</span> <span class="n">labels</span></tt>
+            </div>
+            <div id="l178"
+               class="code sev- "><tt><i>178</i>         <span class="n">propel</span><span class="o">.</span><span class="n">columns</span> <span class="o">=</span> <span class="n">labels</span></tt>
+            </div>
+            <div id="l179"
+               class="code sev- "><tt><i>179</i>         <span class="n">opening</span><span class="o">.</span><span class="n">columns</span> <span class="o">=</span> <span class="n">labels</span></tt>
+            </div>
+            <div id="l180"
+               class="code sev- "><tt><i>180</i> &nbsp;</tt>
+            </div>
+            <div id="l181"
+               class="code sev- "><tt><i>181</i>         <span class="c1"># set names to each dataset</span></tt>
+            </div>
+            <div id="l182"
+               class="code sev- "><tt><i>182</i>         <span class="n">shear</span><span class="o">.</span><span class="n">name</span> <span class="o">=</span> <span class="s2">&quot;shear&quot;</span></tt>
+            </div>
+            <div id="l183"
+               class="code sev- "><tt><i>183</i>         <span class="n">stretch</span><span class="o">.</span><span class="n">name</span> <span class="o">=</span> <span class="s2">&quot;stretch&quot;</span></tt>
+            </div>
+            <div id="l184"
+               class="code sev- "><tt><i>184</i>         <span class="n">stagger</span><span class="o">.</span><span class="n">name</span> <span class="o">=</span> <span class="s2">&quot;stagger&quot;</span></tt>
+            </div>
+            <div id="l185"
+               class="code sev- "><tt><i>185</i>         <span class="n">buckle</span><span class="o">.</span><span class="n">name</span> <span class="o">=</span> <span class="s2">&quot;buckle&quot;</span></tt>
+            </div>
+            <div id="l186"
+               class="code sev- "><tt><i>186</i>         <span class="n">propel</span><span class="o">.</span><span class="n">name</span> <span class="o">=</span> <span class="s2">&quot;propel&quot;</span></tt>
+            </div>
+            <div id="l187"
+               class="code sev- "><tt><i>187</i>         <span class="n">opening</span><span class="o">.</span><span class="n">name</span> <span class="o">=</span> <span class="s2">&quot;opening&quot;</span></tt>
+            </div>
+            <div id="l188"
+               class="code sev- "><tt><i>188</i> &nbsp;</tt>
+            </div>
+            <div id="l189"
+               class="code sev- "><tt><i>189</i>         <span class="c1"># get correlation between neighboring basepairs among all helical parameters</span></tt>
+            </div>
+            <div id="l190"
+               class="code sev- "><tt><i>190</i>         <span class="n">results</span> <span class="o">=</span> <span class="p">{}</span></tt>
+            </div>
+            <div id="l191"
+               class="code sev- "><tt><i>191</i>         <span class="n">datasets</span> <span class="o">=</span> <span class="p">[</span><span class="n">shear</span><span class="p">,</span> <span class="n">stretch</span><span class="p">,</span> <span class="n">stagger</span><span class="p">,</span> <span class="n">buckle</span><span class="p">,</span> <span class="n">propel</span><span class="p">,</span> <span class="n">opening</span><span class="p">]</span></tt>
+            </div>
+            <div id="l192"
+               class="code sev- "><tt><i>192</i>         <span class="k">for</span> <span class="n">ser1</span><span class="p">,</span> <span class="n">ser2</span> <span class="ow">in</span> <span class="n">product</span><span class="p">(</span><span class="n">datasets</span><span class="p">,</span> <span class="n">datasets</span><span class="p">):</span></tt>
+            </div>
+            <div id="l193"
+               class="code sev- "><tt><i>193</i>             <span class="n">ser2_shifted</span> <span class="o">=</span> <span class="n">ser2</span><span class="o">.</span><span class="n">shift</span><span class="p">(</span><span class="n">axis</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span></tt>
+            </div>
+            <div id="l194"
+               class="code sev- "><tt><i>194</i>             <span class="n">ser2_shifted</span><span class="p">[</span><span class="n">labels</span><span class="p">[</span><span class="mi">0</span><span class="p">]]</span> <span class="o">=</span> <span class="n">ser2</span><span class="p">[</span><span class="n">labels</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">]]</span></tt>
+            </div>
+            <div id="l195"
+               class="code sev- "><tt><i>195</i>             <span class="k">if</span> <span class="n">ser1</span><span class="o">.</span><span class="n">name</span> <span class="ow">in</span> <span class="n">constants</span><span class="o">.</span><span class="n">hp_angular</span> <span class="ow">and</span> <span class="n">ser2</span><span class="o">.</span><span class="n">name</span> <span class="ow">in</span> <span class="n">constants</span><span class="o">.</span><span class="n">hp_angular</span><span class="p">:</span></tt>
+            </div>
+            <div id="l196"
+               class="code sev- "><tt><i>196</i>                 <span class="n">method</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">circular</span></tt>
+            </div>
+            <div id="l197"
+               class="code sev- "><tt><i>197</i>             <span class="k">elif</span> <span class="p">(</span></tt>
+            </div>
+            <div id="l198"
+               class="code sev- "><tt><i>198</i>                 <span class="n">ser1</span><span class="o">.</span><span class="n">name</span> <span class="ow">in</span> <span class="n">constants</span><span class="o">.</span><span class="n">hp_angular</span></tt>
+            </div>
+            <div id="l199"
+               class="code sev-2  le">
+               <ul class="violations">
+               
+                  <li>
+                     <span class="count sev-2">
+                        W503
+                     </span>
+                     Line break before binary operator</li>
+               
+               </ul><tt><i>199</i>                 <span class="ow">and</span> <span class="n">ser2</span><span class="o">.</span><span class="n">name</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">constants</span><span class="o">.</span><span class="n">hp_angular</span></tt>
+            </div>
+            <div id="l200"
+               class="code sev- "><tt><i>200</i>             <span class="p">)</span> <span class="ow">or</span> <span class="p">(</span></tt>
+            </div>
+            <div id="l201"
+               class="code sev- "><tt><i>201</i>                 <span class="n">ser2</span><span class="o">.</span><span class="n">name</span> <span class="ow">in</span> <span class="n">constants</span><span class="o">.</span><span class="n">hp_angular</span></tt>
+            </div>
+            <div id="l202"
+               class="code sev-2  le">
+               <ul class="violations">
+               
+                  <li>
+                     <span class="count sev-2">
+                        W503
+                     </span>
+                     Line break before binary operator</li>
+               
+               </ul><tt><i>202</i>                 <span class="ow">and</span> <span class="n">ser1</span><span class="o">.</span><span class="n">name</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">constants</span><span class="o">.</span><span class="n">hp_angular</span></tt>
+            </div>
+            <div id="l203"
+               class="code sev- "><tt><i>203</i>             <span class="p">):</span></tt>
+            </div>
+            <div id="l204"
+               class="code sev- "><tt><i>204</i>                 <span class="n">method</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">circlineal</span></tt>
+            </div>
+            <div id="l205"
+               class="code sev- "><tt><i>205</i>             <span class="k">else</span><span class="p">:</span></tt>
+            </div>
+            <div id="l206"
+               class="code sev- "><tt><i>206</i>                 <span class="n">method</span> <span class="o">=</span> <span class="s2">&quot;pearson&quot;</span>  <span class="c1"># type: ignore</span></tt>
+            </div>
+            <div id="l207"
+               class="code sev- "><tt><i>207</i>             <span class="n">corr_data</span> <span class="o">=</span> <span class="n">ser1</span><span class="o">.</span><span class="n">corrwith</span><span class="p">(</span><span class="n">ser2_shifted</span><span class="p">,</span> <span class="n">method</span><span class="o">=</span><span class="n">method</span><span class="p">)</span></tt>
+            </div>
+            <div id="l208"
+               class="code sev- "><tt><i>208</i>             <span class="n">corr_data</span><span class="o">.</span><span class="n">index</span> <span class="o">=</span> <span class="n">corr_index</span></tt>
+            </div>
+            <div id="l209"
+               class="code sev- "><tt><i>209</i>             <span class="n">results</span><span class="p">[</span><span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">ser1</span><span class="o">.</span><span class="n">name</span><span class="si">}</span><span class="s2">/</span><span class="si">{</span><span class="n">ser2</span><span class="o">.</span><span class="n">name</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">]</span> <span class="o">=</span> <span class="n">corr_data</span></tt>
+            </div>
+            <div id="l210"
+               class="code sev- "><tt><i>210</i>         <span class="n">result_df</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="o">.</span><span class="n">from_dict</span><span class="p">(</span><span class="n">results</span><span class="p">)</span></tt>
+            </div>
+            <div id="l211"
+               class="code sev- "><tt><i>211</i>         <span class="n">result_df</span><span class="o">.</span><span class="n">index</span> <span class="o">=</span> <span class="n">corr_index</span>  <span class="c1"># type: ignore</span></tt>
+            </div>
+            <div id="l212"
+               class="code sev- "><tt><i>212</i> &nbsp;</tt>
+            </div>
+            <div id="l213"
+               class="code sev- "><tt><i>213</i>         <span class="c1"># save csv data</span></tt>
+            </div>
+            <div id="l214"
+               class="code sev- "><tt><i>214</i>         <span class="n">result_df</span><span class="o">.</span><span class="n">to_csv</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">stage_io_dict</span><span class="p">[</span><span class="s2">&quot;out&quot;</span><span class="p">][</span><span class="s2">&quot;output_csv_path&quot;</span><span class="p">])</span></tt>
+            </div>
+            <div id="l215"
+               class="code sev- "><tt><i>215</i> &nbsp;</tt>
+            </div>
+            <div id="l216"
+               class="code sev- "><tt><i>216</i>         <span class="c1"># create heatmap</span></tt>
+            </div>
+            <div id="l217"
+               class="code sev- "><tt><i>217</i>         <span class="n">cmap</span> <span class="o">=</span> <span class="n">plt</span><span class="o">.</span><span class="n">get_cmap</span><span class="p">(</span><span class="s2">&quot;bwr&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">copy</span><span class="p">()</span></tt>
+            </div>
+            <div id="l218"
+               class="code sev- "><tt><i>218</i>         <span class="n">bounds</span> <span class="o">=</span> <span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">,</span> <span class="o">-</span><span class="mf">0.8</span><span class="p">,</span> <span class="o">-</span><span class="mf">0.6</span><span class="p">,</span> <span class="o">-</span><span class="mf">0.4</span><span class="p">,</span> <span class="o">-</span><span class="mf">0.2</span><span class="p">,</span> <span class="mf">0.2</span><span class="p">,</span> <span class="mf">0.4</span><span class="p">,</span> <span class="mf">0.6</span><span class="p">,</span> <span class="mf">0.8</span><span class="p">,</span> <span class="mi">1</span><span class="p">]</span></tt>
+            </div>
+            <div id="l219"
+               class="code sev- "><tt><i>219</i>         <span class="n">num</span> <span class="o">=</span> <span class="n">cmap</span><span class="o">.</span><span class="n">N</span></tt>
+            </div>
+            <div id="l220"
+               class="code sev- "><tt><i>220</i>         <span class="n">norm</span> <span class="o">=</span> <span class="n">mpl</span><span class="o">.</span><span class="n">colors</span><span class="o">.</span><span class="n">BoundaryNorm</span><span class="p">(</span><span class="n">bounds</span><span class="p">,</span> <span class="n">num</span><span class="p">)</span>  <span class="c1"># type: ignore</span></tt>
+            </div>
+            <div id="l221"
+               class="code sev- "><tt><i>221</i>         <span class="n">cmap</span><span class="o">.</span><span class="n">set_bad</span><span class="p">(</span><span class="n">color</span><span class="o">=</span><span class="s2">&quot;gainsboro&quot;</span><span class="p">)</span></tt>
+            </div>
+            <div id="l222"
+               class="code sev- "><tt><i>222</i>         <span class="n">fig</span><span class="p">,</span> <span class="n">ax</span> <span class="o">=</span> <span class="n">plt</span><span class="o">.</span><span class="n">subplots</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="n">dpi</span><span class="o">=</span><span class="mi">300</span><span class="p">,</span> <span class="n">figsize</span><span class="o">=</span><span class="p">(</span><span class="mf">7.5</span><span class="p">,</span> <span class="mi">5</span><span class="p">),</span> <span class="n">tight_layout</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span></tt>
+            </div>
+            <div id="l223"
+               class="code sev- "><tt><i>223</i>         <span class="n">im</span> <span class="o">=</span> <span class="n">ax</span><span class="o">.</span><span class="n">imshow</span><span class="p">(</span><span class="n">result_df</span><span class="p">,</span> <span class="n">cmap</span><span class="o">=</span><span class="n">cmap</span><span class="p">,</span> <span class="n">norm</span><span class="o">=</span><span class="n">norm</span><span class="p">,</span> <span class="n">aspect</span><span class="o">=</span><span class="s2">&quot;auto&quot;</span><span class="p">)</span></tt>
+            </div>
+            <div id="l224"
+               class="code sev- "><tt><i>224</i>         <span class="n">plt</span><span class="o">.</span><span class="n">colorbar</span><span class="p">(</span><span class="n">im</span><span class="p">,</span> <span class="n">ticks</span><span class="o">=</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">,</span> <span class="o">-</span><span class="mf">0.8</span><span class="p">,</span> <span class="o">-</span><span class="mf">0.6</span><span class="p">,</span> <span class="o">-</span><span class="mf">0.4</span><span class="p">,</span> <span class="o">-</span><span class="mf">0.2</span><span class="p">,</span> <span class="mf">0.2</span><span class="p">,</span> <span class="mf">0.4</span><span class="p">,</span> <span class="mf">0.6</span><span class="p">,</span> <span class="mf">0.8</span><span class="p">,</span> <span class="mi">1</span><span class="p">])</span></tt>
+            </div>
+            <div id="l225"
+               class="code sev- "><tt><i>225</i> &nbsp;</tt>
+            </div>
+            <div id="l226"
+               class="code sev- "><tt><i>226</i>         <span class="c1"># axes</span></tt>
+            </div>
+            <div id="l227"
+               class="code sev- "><tt><i>227</i>         <span class="n">xlocs</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">arange</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">result_df</span><span class="o">.</span><span class="n">columns</span><span class="p">))</span></tt>
+            </div>
+            <div id="l228"
+               class="code sev- "><tt><i>228</i>         <span class="n">_</span> <span class="o">=</span> <span class="n">ax</span><span class="o">.</span><span class="n">set_xticks</span><span class="p">(</span><span class="n">xlocs</span><span class="p">)</span></tt>
+            </div>
+            <div id="l229"
+               class="code sev- "><tt><i>229</i>         <span class="n">_</span> <span class="o">=</span> <span class="n">ax</span><span class="o">.</span><span class="n">set_xticklabels</span><span class="p">(</span><span class="n">result_df</span><span class="o">.</span><span class="n">columns</span><span class="o">.</span><span class="n">to_list</span><span class="p">(),</span> <span class="n">rotation</span><span class="o">=</span><span class="mi">90</span><span class="p">)</span></tt>
+            </div>
+            <div id="l230"
+               class="code sev- "><tt><i>230</i> &nbsp;</tt>
+            </div>
+            <div id="l231"
+               class="code sev- "><tt><i>231</i>         <span class="n">ylocs</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">arange</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">result_df</span><span class="o">.</span><span class="n">index</span><span class="p">))</span></tt>
+            </div>
+            <div id="l232"
+               class="code sev- "><tt><i>232</i>         <span class="n">_</span> <span class="o">=</span> <span class="n">ax</span><span class="o">.</span><span class="n">set_yticks</span><span class="p">(</span><span class="n">ylocs</span><span class="p">)</span></tt>
+            </div>
+            <div id="l233"
+               class="code sev- "><tt><i>233</i>         <span class="n">_</span> <span class="o">=</span> <span class="n">ax</span><span class="o">.</span><span class="n">set_yticklabels</span><span class="p">(</span><span class="n">result_df</span><span class="o">.</span><span class="n">index</span><span class="o">.</span><span class="n">to_list</span><span class="p">())</span>  <span class="c1"># type: ignore</span></tt>
+            </div>
+            <div id="l234"
+               class="code sev- "><tt><i>234</i> &nbsp;</tt>
+            </div>
+            <div id="l235"
+               class="code sev- "><tt><i>235</i>         <span class="n">ax</span><span class="o">.</span><span class="n">set_title</span><span class="p">(</span></tt>
+            </div>
+            <div id="l236"
+               class="code sev- "><tt><i>236</i>             <span class="s2">&quot;Correlation for neighboring basepairs &quot;</span> <span class="s2">&quot;and pairs of helical parameters&quot;</span></tt>
+            </div>
+            <div id="l237"
+               class="code sev- "><tt><i>237</i>         <span class="p">)</span></tt>
+            </div>
+            <div id="l238"
+               class="code sev- "><tt><i>238</i> &nbsp;</tt>
+            </div>
+            <div id="l239"
+               class="code sev- "><tt><i>239</i>         <span class="n">fig</span><span class="o">.</span><span class="n">tight_layout</span><span class="p">()</span></tt>
+            </div>
+            <div id="l240"
+               class="code sev- "><tt><i>240</i>         <span class="n">fig</span><span class="o">.</span><span class="n">savefig</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">stage_io_dict</span><span class="p">[</span><span class="s2">&quot;out&quot;</span><span class="p">][</span><span class="s2">&quot;output_jpg_path&quot;</span><span class="p">],</span> <span class="nb">format</span><span class="o">=</span><span class="s2">&quot;jpg&quot;</span><span class="p">)</span></tt>
+            </div>
+            <div id="l241"
+               class="code sev- "><tt><i>241</i>         <span class="n">plt</span><span class="o">.</span><span class="n">close</span><span class="p">()</span></tt>
+            </div>
+            <div id="l242"
+               class="code sev- "><tt><i>242</i> &nbsp;</tt>
+            </div>
+            <div id="l243"
+               class="code sev- "><tt><i>243</i>         <span class="c1"># Copy files to host</span></tt>
+            </div>
+            <div id="l244"
+               class="code sev- "><tt><i>244</i>         <span class="bp">self</span><span class="o">.</span><span class="n">copy_to_host</span><span class="p">()</span></tt>
+            </div>
+            <div id="l245"
+               class="code sev- "><tt><i>245</i> &nbsp;</tt>
+            </div>
+            <div id="l246"
+               class="code sev- "><tt><i>246</i>         <span class="c1"># Remove temporary file(s)</span></tt>
+            </div>
+            <div id="l247"
+               class="code sev- "><tt><i>247</i>         <span class="bp">self</span><span class="o">.</span><span class="n">tmp_files</span><span class="o">.</span><span class="n">extend</span><span class="p">([</span><span class="bp">self</span><span class="o">.</span><span class="n">stage_io_dict</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">&quot;unique_dir&quot;</span><span class="p">,</span> <span class="s2">&quot;&quot;</span><span class="p">)])</span></tt>
+            </div>
+            <div id="l248"
+               class="code sev- "><tt><i>248</i>         <span class="bp">self</span><span class="o">.</span><span class="n">remove_tmp_files</span><span class="p">()</span></tt>
+            </div>
+            <div id="l249"
+               class="code sev- "><tt><i>249</i> &nbsp;</tt>
+            </div>
+            <div id="l250"
+               class="code sev- "><tt><i>250</i>         <span class="bp">self</span><span class="o">.</span><span class="n">check_arguments</span><span class="p">(</span><span class="n">output_files_created</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">raise_exception</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span></tt>
+            </div>
+            <div id="l251"
+               class="code sev- "><tt><i>251</i> &nbsp;</tt>
+            </div>
+            <div id="l252"
+               class="code sev- "><tt><i>252</i>         <span class="k">return</span> <span class="mi">0</span></tt>
+            </div>
+            <div id="l253"
+               class="code sev- "><tt><i>253</i> &nbsp;</tt>
+            </div>
+            <div id="l254"
+               class="code sev- "><tt><i>254</i>     <span class="nd">@staticmethod</span></tt>
+            </div>
+            <div id="l255"
+               class="code sev- "><tt><i>255</i>     <span class="k">def</span> <span class="nf">circular</span><span class="p">(</span><span class="n">x1</span><span class="p">,</span> <span class="n">x2</span><span class="p">):</span></tt>
+            </div>
+            <div id="l256"
+               class="code sev- "><tt><i>256</i>         <span class="n">x1</span> <span class="o">=</span> <span class="n">x1</span> <span class="o">*</span> <span class="n">np</span><span class="o">.</span><span class="n">pi</span> <span class="o">/</span> <span class="mi">180</span></tt>
+            </div>
+            <div id="l257"
+               class="code sev- "><tt><i>257</i>         <span class="n">x2</span> <span class="o">=</span> <span class="n">x2</span> <span class="o">*</span> <span class="n">np</span><span class="o">.</span><span class="n">pi</span> <span class="o">/</span> <span class="mi">180</span></tt>
+            </div>
+            <div id="l258"
+               class="code sev- "><tt><i>258</i>         <span class="n">diff_1</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">sin</span><span class="p">(</span><span class="n">x1</span> <span class="o">-</span> <span class="n">x1</span><span class="o">.</span><span class="n">mean</span><span class="p">())</span></tt>
+            </div>
+            <div id="l259"
+               class="code sev- "><tt><i>259</i>         <span class="n">diff_2</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">sin</span><span class="p">(</span><span class="n">x2</span> <span class="o">-</span> <span class="n">x2</span><span class="o">.</span><span class="n">mean</span><span class="p">())</span></tt>
+            </div>
+            <div id="l260"
+               class="code sev- "><tt><i>260</i>         <span class="n">num</span> <span class="o">=</span> <span class="p">(</span><span class="n">diff_1</span> <span class="o">*</span> <span class="n">diff_2</span><span class="p">)</span><span class="o">.</span><span class="n">sum</span><span class="p">()</span></tt>
+            </div>
+            <div id="l261"
+               class="code sev- "><tt><i>261</i>         <span class="n">den</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">sqrt</span><span class="p">((</span><span class="n">diff_1</span><span class="o">**</span><span class="mi">2</span><span class="p">)</span><span class="o">.</span><span class="n">sum</span><span class="p">()</span> <span class="o">*</span> <span class="p">(</span><span class="n">diff_2</span><span class="o">**</span><span class="mi">2</span><span class="p">)</span><span class="o">.</span><span class="n">sum</span><span class="p">())</span></tt>
+            </div>
+            <div id="l262"
+               class="code sev- "><tt><i>262</i>         <span class="k">return</span> <span class="n">num</span> <span class="o">/</span> <span class="n">den</span></tt>
+            </div>
+            <div id="l263"
+               class="code sev- "><tt><i>263</i> &nbsp;</tt>
+            </div>
+            <div id="l264"
+               class="code sev- "><tt><i>264</i>     <span class="nd">@staticmethod</span></tt>
+            </div>
+            <div id="l265"
+               class="code sev- "><tt><i>265</i>     <span class="k">def</span> <span class="nf">circlineal</span><span class="p">(</span><span class="n">x1</span><span class="p">,</span> <span class="n">x2</span><span class="p">):</span></tt>
+            </div>
+            <div id="l266"
+               class="code sev- "><tt><i>266</i>         <span class="n">x2</span> <span class="o">=</span> <span class="n">x2</span> <span class="o">*</span> <span class="n">np</span><span class="o">.</span><span class="n">pi</span> <span class="o">/</span> <span class="mi">180</span></tt>
+            </div>
+            <div id="l267"
+               class="code sev- "><tt><i>267</i>         <span class="n">rc</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">corrcoef</span><span class="p">(</span><span class="n">x1</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">cos</span><span class="p">(</span><span class="n">x2</span><span class="p">))[</span><span class="mi">1</span><span class="p">,</span> <span class="mi">0</span><span class="p">]</span></tt>
+            </div>
+            <div id="l268"
+               class="code sev- "><tt><i>268</i>         <span class="n">rs</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">corrcoef</span><span class="p">(</span><span class="n">x1</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">sin</span><span class="p">(</span><span class="n">x2</span><span class="p">))[</span><span class="mi">1</span><span class="p">,</span> <span class="mi">0</span><span class="p">]</span></tt>
+            </div>
+            <div id="l269"
+               class="code sev- "><tt><i>269</i>         <span class="n">rcs</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">corrcoef</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">sin</span><span class="p">(</span><span class="n">x2</span><span class="p">),</span> <span class="n">np</span><span class="o">.</span><span class="n">cos</span><span class="p">(</span><span class="n">x2</span><span class="p">))[</span><span class="mi">1</span><span class="p">,</span> <span class="mi">0</span><span class="p">]</span></tt>
+            </div>
+            <div id="l270"
+               class="code sev- "><tt><i>270</i>         <span class="n">num</span> <span class="o">=</span> <span class="p">(</span><span class="n">rc</span><span class="o">**</span><span class="mi">2</span><span class="p">)</span> <span class="o">+</span> <span class="p">(</span><span class="n">rs</span><span class="o">**</span><span class="mi">2</span><span class="p">)</span> <span class="o">-</span> <span class="mi">2</span> <span class="o">*</span> <span class="n">rc</span> <span class="o">*</span> <span class="n">rs</span> <span class="o">*</span> <span class="n">rcs</span></tt>
+            </div>
+            <div id="l271"
+               class="code sev- "><tt><i>271</i>         <span class="n">den</span> <span class="o">=</span> <span class="mi">1</span> <span class="o">-</span> <span class="p">(</span><span class="n">rcs</span><span class="o">**</span><span class="mi">2</span><span class="p">)</span></tt>
+            </div>
+            <div id="l272"
+               class="code sev- "><tt><i>272</i>         <span class="n">correlation</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">sqrt</span><span class="p">(</span><span class="n">num</span> <span class="o">/</span> <span class="n">den</span><span class="p">)</span></tt>
+            </div>
+            <div id="l273"
+               class="code sev- "><tt><i>273</i>         <span class="k">if</span> <span class="n">np</span><span class="o">.</span><span class="n">corrcoef</span><span class="p">(</span><span class="n">x1</span><span class="p">,</span> <span class="n">x2</span><span class="p">)[</span><span class="mi">1</span><span class="p">,</span> <span class="mi">0</span><span class="p">]</span> <span class="o">&lt;</span> <span class="mi">0</span><span class="p">:</span></tt>
+            </div>
+            <div id="l274"
+               class="code sev- "><tt><i>274</i>             <span class="n">correlation</span> <span class="o">*=</span> <span class="o">-</span><span class="mi">1</span></tt>
+            </div>
+            <div id="l275"
+               class="code sev- "><tt><i>275</i>         <span class="k">return</span> <span class="n">correlation</span></tt>
+            </div>
+            <div id="l276"
+               class="code sev- "><tt><i>276</i> &nbsp;</tt>
+            </div>
+            <div id="l277"
+               class="code sev- "><tt><i>277</i> &nbsp;</tt>
+            </div>
+            <div id="l278"
+               class="code sev- "><tt><i>278</i> <span class="k">def</span> <span class="nf">intrabpcorr</span><span class="p">(</span></tt>
+            </div>
+            <div id="l279"
+               class="code sev- "><tt><i>279</i>     <span class="n">input_filename_shear</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span></tt>
+            </div>
+            <div id="l280"
+               class="code sev- "><tt><i>280</i>     <span class="n">input_filename_stretch</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span></tt>
+            </div>
+            <div id="l281"
+               class="code sev- "><tt><i>281</i>     <span class="n">input_filename_stagger</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span></tt>
+            </div>
+            <div id="l282"
+               class="code sev- "><tt><i>282</i>     <span class="n">input_filename_buckle</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span></tt>
+            </div>
+            <div id="l283"
+               class="code sev- "><tt><i>283</i>     <span class="n">input_filename_propel</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span></tt>
+            </div>
+            <div id="l284"
+               class="code sev- "><tt><i>284</i>     <span class="n">input_filename_opening</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span></tt>
+            </div>
+            <div id="l285"
+               class="code sev- "><tt><i>285</i>     <span class="n">output_csv_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span></tt>
+            </div>
+            <div id="l286"
+               class="code sev- "><tt><i>286</i>     <span class="n">output_jpg_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span></tt>
+            </div>
+            <div id="l287"
+               class="code sev- "><tt><i>287</i>     <span class="n">properties</span><span class="p">:</span> <span class="n">Optional</span><span class="p">[</span><span class="nb">dict</span><span class="p">]</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span></tt>
+            </div>
+            <div id="l288"
+               class="code sev- "><tt><i>288</i>     <span class="o">**</span><span class="n">kwargs</span><span class="p">,</span></tt>
+            </div>
+            <div id="l289"
+               class="code sev- "><tt><i>289</i> <span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">int</span><span class="p">:</span></tt>
+            </div>
+            <div id="l290"
+               class="code sev- "><tt><i>290</i> <span class="w">    </span><span class="sd">&quot;&quot;&quot;Create :class:`HelParCorrelation &lt;intrabp_correlations.intrabpcorr.IntraBasePairCorrelation&gt;` class and</span></tt>
+            </div>
+            <div id="l291"
+               class="code sev- "><tt><i>291</i> <span class="sd">    execute the :meth:`launch() &lt;intrabp_correlations.intrabpcorr.IntraBasePairCorrelation.launch&gt;` method.&quot;&quot;&quot;</span></tt>
+            </div>
+            <div id="l292"
+               class="code sev- "><tt><i>292</i> &nbsp;</tt>
+            </div>
+            <div id="l293"
+               class="code sev- "><tt><i>293</i>     <span class="k">return</span> <span class="n">IntraBasePairCorrelation</span><span class="p">(</span></tt>
+            </div>
+            <div id="l294"
+               class="code sev- "><tt><i>294</i>         <span class="n">input_filename_shear</span><span class="o">=</span><span class="n">input_filename_shear</span><span class="p">,</span></tt>
+            </div>
+            <div id="l295"
+               class="code sev- "><tt><i>295</i>         <span class="n">input_filename_stretch</span><span class="o">=</span><span class="n">input_filename_stretch</span><span class="p">,</span></tt>
+            </div>
+            <div id="l296"
+               class="code sev- "><tt><i>296</i>         <span class="n">input_filename_stagger</span><span class="o">=</span><span class="n">input_filename_stagger</span><span class="p">,</span></tt>
+            </div>
+            <div id="l297"
+               class="code sev- "><tt><i>297</i>         <span class="n">input_filename_buckle</span><span class="o">=</span><span class="n">input_filename_buckle</span><span class="p">,</span></tt>
+            </div>
+            <div id="l298"
+               class="code sev- "><tt><i>298</i>         <span class="n">input_filename_propel</span><span class="o">=</span><span class="n">input_filename_propel</span><span class="p">,</span></tt>
+            </div>
+            <div id="l299"
+               class="code sev- "><tt><i>299</i>         <span class="n">input_filename_opening</span><span class="o">=</span><span class="n">input_filename_opening</span><span class="p">,</span></tt>
+            </div>
+            <div id="l300"
+               class="code sev- "><tt><i>300</i>         <span class="n">output_csv_path</span><span class="o">=</span><span class="n">output_csv_path</span><span class="p">,</span></tt>
+            </div>
+            <div id="l301"
+               class="code sev- "><tt><i>301</i>         <span class="n">output_jpg_path</span><span class="o">=</span><span class="n">output_jpg_path</span><span class="p">,</span></tt>
+            </div>
+            <div id="l302"
+               class="code sev- "><tt><i>302</i>         <span class="n">properties</span><span class="o">=</span><span class="n">properties</span><span class="p">,</span></tt>
+            </div>
+            <div id="l303"
+               class="code sev- "><tt><i>303</i>         <span class="o">**</span><span class="n">kwargs</span><span class="p">,</span></tt>
+            </div>
+            <div id="l304"
+               class="code sev- "><tt><i>304</i>     <span class="p">)</span><span class="o">.</span><span class="n">launch</span><span class="p">()</span></tt>
+            </div>
+            <div id="l305"
+               class="code sev- "><tt><i>305</i> &nbsp;</tt>
+            </div>
+            <div id="l306"
+               class="code sev- "><tt><i>306</i> &nbsp;</tt>
+            </div>
+            <div id="l307"
+               class="code sev- "><tt><i>307</i> <span class="k">def</span> <span class="nf">main</span><span class="p">():</span></tt>
+            </div>
+            <div id="l308"
+               class="code sev- "><tt><i>308</i> <span class="w">    </span><span class="sd">&quot;&quot;&quot;Command line execution of this building block. Please check the command line documentation.&quot;&quot;&quot;</span></tt>
+            </div>
+            <div id="l309"
+               class="code sev- "><tt><i>309</i>     <span class="n">parser</span> <span class="o">=</span> <span class="n">argparse</span><span class="o">.</span><span class="n">ArgumentParser</span><span class="p">(</span></tt>
+            </div>
+            <div id="l310"
+               class="code sev- "><tt><i>310</i>         <span class="n">description</span><span class="o">=</span><span class="s2">&quot;Load .ser file from Canal output and calculate correlation between base pairs of the corresponding sequence.&quot;</span><span class="p">,</span></tt>
+            </div>
+            <div id="l311"
+               class="code sev- "><tt><i>311</i>         <span class="n">formatter_class</span><span class="o">=</span><span class="k">lambda</span> <span class="n">prog</span><span class="p">:</span> <span class="n">argparse</span><span class="o">.</span><span class="n">RawTextHelpFormatter</span><span class="p">(</span><span class="n">prog</span><span class="p">,</span> <span class="n">width</span><span class="o">=</span><span class="mi">99999</span><span class="p">),</span></tt>
+            </div>
+            <div id="l312"
+               class="code sev- "><tt><i>312</i>     <span class="p">)</span></tt>
+            </div>
+            <div id="l313"
+               class="code sev- "><tt><i>313</i>     <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s2">&quot;--config&quot;</span><span class="p">,</span> <span class="n">required</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s2">&quot;Configuration file&quot;</span><span class="p">)</span></tt>
+            </div>
+            <div id="l314"
+               class="code sev- "><tt><i>314</i> &nbsp;</tt>
+            </div>
+            <div id="l315"
+               class="code sev- "><tt><i>315</i>     <span class="n">required_args</span> <span class="o">=</span> <span class="n">parser</span><span class="o">.</span><span class="n">add_argument_group</span><span class="p">(</span><span class="s2">&quot;required arguments&quot;</span><span class="p">)</span></tt>
+            </div>
+            <div id="l316"
+               class="code sev- "><tt><i>316</i>     <span class="n">required_args</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span></tt>
+            </div>
+            <div id="l317"
+               class="code sev- "><tt><i>317</i>         <span class="s2">&quot;--input_filename_shear&quot;</span><span class="p">,</span></tt>
+            </div>
+            <div id="l318"
+               class="code sev- "><tt><i>318</i>         <span class="n">required</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span></tt>
+            </div>
+            <div id="l319"
+               class="code sev- "><tt><i>319</i>         <span class="n">help</span><span class="o">=</span><span class="s2">&quot;Path to ser file for helical parameter shear. Accepted formats: ser.&quot;</span><span class="p">,</span></tt>
+            </div>
+            <div id="l320"
+               class="code sev- "><tt><i>320</i>     <span class="p">)</span></tt>
+            </div>
+            <div id="l321"
+               class="code sev- "><tt><i>321</i>     <span class="n">required_args</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span></tt>
+            </div>
+            <div id="l322"
+               class="code sev- "><tt><i>322</i>         <span class="s2">&quot;--input_filename_stretch&quot;</span><span class="p">,</span></tt>
+            </div>
+            <div id="l323"
+               class="code sev- "><tt><i>323</i>         <span class="n">required</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span></tt>
+            </div>
+            <div id="l324"
+               class="code sev- "><tt><i>324</i>         <span class="n">help</span><span class="o">=</span><span class="s2">&quot;Path to ser file for helical parameter stretch. Accepted formats: ser.&quot;</span><span class="p">,</span></tt>
+            </div>
+            <div id="l325"
+               class="code sev- "><tt><i>325</i>     <span class="p">)</span></tt>
+            </div>
+            <div id="l326"
+               class="code sev- "><tt><i>326</i>     <span class="n">required_args</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span></tt>
+            </div>
+            <div id="l327"
+               class="code sev- "><tt><i>327</i>         <span class="s2">&quot;--input_filename_stagger&quot;</span><span class="p">,</span></tt>
+            </div>
+            <div id="l328"
+               class="code sev- "><tt><i>328</i>         <span class="n">required</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span></tt>
+            </div>
+            <div id="l329"
+               class="code sev- "><tt><i>329</i>         <span class="n">help</span><span class="o">=</span><span class="s2">&quot;Path to ser file for helical parameter stagger. Accepted formats: ser.&quot;</span><span class="p">,</span></tt>
+            </div>
+            <div id="l330"
+               class="code sev- "><tt><i>330</i>     <span class="p">)</span></tt>
+            </div>
+            <div id="l331"
+               class="code sev- "><tt><i>331</i>     <span class="n">required_args</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span></tt>
+            </div>
+            <div id="l332"
+               class="code sev- "><tt><i>332</i>         <span class="s2">&quot;--input_filename_buckle&quot;</span><span class="p">,</span></tt>
+            </div>
+            <div id="l333"
+               class="code sev- "><tt><i>333</i>         <span class="n">required</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span></tt>
+            </div>
+            <div id="l334"
+               class="code sev- "><tt><i>334</i>         <span class="n">help</span><span class="o">=</span><span class="s2">&quot;Path to ser file for helical parameter buckle. Accepted formats: ser.&quot;</span><span class="p">,</span></tt>
+            </div>
+            <div id="l335"
+               class="code sev- "><tt><i>335</i>     <span class="p">)</span></tt>
+            </div>
+            <div id="l336"
+               class="code sev- "><tt><i>336</i>     <span class="n">required_args</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span></tt>
+            </div>
+            <div id="l337"
+               class="code sev- "><tt><i>337</i>         <span class="s2">&quot;--input_filename_propel&quot;</span><span class="p">,</span></tt>
+            </div>
+            <div id="l338"
+               class="code sev- "><tt><i>338</i>         <span class="n">required</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span></tt>
+            </div>
+            <div id="l339"
+               class="code sev- "><tt><i>339</i>         <span class="n">help</span><span class="o">=</span><span class="s2">&quot;Path to ser file for helical parameter propel. Accepted formats: ser.&quot;</span><span class="p">,</span></tt>
+            </div>
+            <div id="l340"
+               class="code sev- "><tt><i>340</i>     <span class="p">)</span></tt>
+            </div>
+            <div id="l341"
+               class="code sev- "><tt><i>341</i>     <span class="n">required_args</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span></tt>
+            </div>
+            <div id="l342"
+               class="code sev- "><tt><i>342</i>         <span class="s2">&quot;--input_filename_opening&quot;</span><span class="p">,</span></tt>
+            </div>
+            <div id="l343"
+               class="code sev- "><tt><i>343</i>         <span class="n">required</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span></tt>
+            </div>
+            <div id="l344"
+               class="code sev- "><tt><i>344</i>         <span class="n">help</span><span class="o">=</span><span class="s2">&quot;Path to ser file for helical parameter opening. Accepted formats: ser.&quot;</span><span class="p">,</span></tt>
+            </div>
+            <div id="l345"
+               class="code sev- "><tt><i>345</i>     <span class="p">)</span></tt>
+            </div>
+            <div id="l346"
+               class="code sev- "><tt><i>346</i>     <span class="n">required_args</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span></tt>
+            </div>
+            <div id="l347"
+               class="code sev- "><tt><i>347</i>         <span class="s2">&quot;--output_csv_path&quot;</span><span class="p">,</span></tt>
+            </div>
+            <div id="l348"
+               class="code sev- "><tt><i>348</i>         <span class="n">required</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span></tt>
+            </div>
+            <div id="l349"
+               class="code sev- "><tt><i>349</i>         <span class="n">help</span><span class="o">=</span><span class="s2">&quot;Path to output file. Accepted formats: csv.&quot;</span><span class="p">,</span></tt>
+            </div>
+            <div id="l350"
+               class="code sev- "><tt><i>350</i>     <span class="p">)</span></tt>
+            </div>
+            <div id="l351"
+               class="code sev- "><tt><i>351</i>     <span class="n">required_args</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span></tt>
+            </div>
+            <div id="l352"
+               class="code sev- "><tt><i>352</i>         <span class="s2">&quot;--output_jpg_path&quot;</span><span class="p">,</span></tt>
+            </div>
+            <div id="l353"
+               class="code sev- "><tt><i>353</i>         <span class="n">required</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span></tt>
+            </div>
+            <div id="l354"
+               class="code sev- "><tt><i>354</i>         <span class="n">help</span><span class="o">=</span><span class="s2">&quot;Path to output plot. Accepted formats: jpg.&quot;</span><span class="p">,</span></tt>
+            </div>
+            <div id="l355"
+               class="code sev- "><tt><i>355</i>     <span class="p">)</span></tt>
+            </div>
+            <div id="l356"
+               class="code sev- "><tt><i>356</i> &nbsp;</tt>
+            </div>
+            <div id="l357"
+               class="code sev- "><tt><i>357</i>     <span class="n">args</span> <span class="o">=</span> <span class="n">parser</span><span class="o">.</span><span class="n">parse_args</span><span class="p">()</span></tt>
+            </div>
+            <div id="l358"
+               class="code sev- "><tt><i>358</i>     <span class="n">args</span><span class="o">.</span><span class="n">config</span> <span class="o">=</span> <span class="n">args</span><span class="o">.</span><span class="n">config</span> <span class="ow">or</span> <span class="s2">&quot;</span><span class="si">{}</span><span class="s2">&quot;</span></tt>
+            </div>
+            <div id="l359"
+               class="code sev- "><tt><i>359</i>     <span class="n">properties</span> <span class="o">=</span> <span class="n">settings</span><span class="o">.</span><span class="n">ConfReader</span><span class="p">(</span><span class="n">config</span><span class="o">=</span><span class="n">args</span><span class="o">.</span><span class="n">config</span><span class="p">)</span><span class="o">.</span><span class="n">get_prop_dic</span><span class="p">()</span></tt>
+            </div>
+            <div id="l360"
+               class="code sev- "><tt><i>360</i> &nbsp;</tt>
+            </div>
+            <div id="l361"
+               class="code sev- "><tt><i>361</i>     <span class="n">intrabpcorr</span><span class="p">(</span></tt>
+            </div>
+            <div id="l362"
+               class="code sev- "><tt><i>362</i>         <span class="n">input_filename_shear</span><span class="o">=</span><span class="n">args</span><span class="o">.</span><span class="n">input_filename_shear</span><span class="p">,</span></tt>
+            </div>
+            <div id="l363"
+               class="code sev- "><tt><i>363</i>         <span class="n">input_filename_stretch</span><span class="o">=</span><span class="n">args</span><span class="o">.</span><span class="n">input_filename_stretch</span><span class="p">,</span></tt>
+            </div>
+            <div id="l364"
+               class="code sev- "><tt><i>364</i>         <span class="n">input_filename_stagger</span><span class="o">=</span><span class="n">args</span><span class="o">.</span><span class="n">input_filename_stagger</span><span class="p">,</span></tt>
+            </div>
+            <div id="l365"
+               class="code sev- "><tt><i>365</i>         <span class="n">input_filename_buckle</span><span class="o">=</span><span class="n">args</span><span class="o">.</span><span class="n">input_filename_buckle</span><span class="p">,</span></tt>
+            </div>
+            <div id="l366"
+               class="code sev- "><tt><i>366</i>         <span class="n">input_filename_propel</span><span class="o">=</span><span class="n">args</span><span class="o">.</span><span class="n">input_filename_propel</span><span class="p">,</span></tt>
+            </div>
+            <div id="l367"
+               class="code sev- "><tt><i>367</i>         <span class="n">input_filename_opening</span><span class="o">=</span><span class="n">args</span><span class="o">.</span><span class="n">input_filename_opening</span><span class="p">,</span></tt>
+            </div>
+            <div id="l368"
+               class="code sev- "><tt><i>368</i>         <span class="n">output_csv_path</span><span class="o">=</span><span class="n">args</span><span class="o">.</span><span class="n">output_csv_path</span><span class="p">,</span></tt>
+            </div>
+            <div id="l369"
+               class="code sev- "><tt><i>369</i>         <span class="n">output_jpg_path</span><span class="o">=</span><span class="n">args</span><span class="o">.</span><span class="n">output_jpg_path</span><span class="p">,</span></tt>
+            </div>
+            <div id="l370"
+               class="code sev- "><tt><i>370</i>         <span class="n">properties</span><span class="o">=</span><span class="n">properties</span><span class="p">,</span></tt>
+            </div>
+            <div id="l371"
+               class="code sev- "><tt><i>371</i>     <span class="p">)</span></tt>
+            </div>
+            <div id="l372"
+               class="code sev- "><tt><i>372</i> &nbsp;</tt>
+            </div>
+            <div id="l373"
+               class="code sev- "><tt><i>373</i> &nbsp;</tt>
+            </div>
+            <div id="l374"
+               class="code sev- "><tt><i>374</i> <span class="k">if</span> <span class="vm">__name__</span> <span class="o">==</span> <span class="s2">&quot;__main__&quot;</span><span class="p">:</span></tt>
+            </div>
+            <div id="l375"
+               class="code sev- "><tt><i>375</i>     <span class="n">main</span><span class="p">()</span></tt>
+            </div>
+            
+         </div>
+      </div>
+   </body>
+</html>
\ No newline at end of file
diff --git a/flake8/flake8badge.svg b/flake8/flake8badge.svg
index 58d5817..55710d4 100644
--- a/flake8/flake8badge.svg
+++ b/flake8/flake8badge.svg
@@ -1 +1 @@
-<svg xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" width="128" height="20" role="img" aria-label="Flake8: 0 C, 0 W, 0 I"><title>Flake8: 0 C, 0 W, 0 I</title><linearGradient id="s" x2="0" y2="100%"><stop offset="0" stop-color="#bbb" stop-opacity=".1"/><stop offset="1" stop-opacity=".1"/></linearGradient><clipPath id="r"><rect width="128" height="20" rx="3" fill="#fff"/></clipPath><g clip-path="url(#r)"><rect width="47" height="20" fill="#555"/><rect x="47" width="81" height="20" fill="#4c1"/><rect width="128" height="20" fill="url(#s)"/></g><g fill="#fff" text-anchor="middle" font-family="Verdana,Geneva,DejaVu Sans,sans-serif" text-rendering="geometricPrecision" font-size="110"><text aria-hidden="true" x="245" y="150" fill="#010101" fill-opacity=".3" transform="scale(.1)" textLength="370">Flake8</text><text x="245" y="140" transform="scale(.1)" fill="#fff" textLength="370">Flake8</text><text aria-hidden="true" x="865" y="150" fill="#010101" fill-opacity=".3" transform="scale(.1)" textLength="710">0 C, 0 W, 0 I</text><text x="865" y="140" transform="scale(.1)" fill="#fff" textLength="710">0 C, 0 W, 0 I</text></g></svg>
\ No newline at end of file
+<svg xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" width="128" height="20" role="img" aria-label="Flake8: 0 C, 4 W, 0 I"><title>Flake8: 0 C, 4 W, 0 I</title><linearGradient id="s" x2="0" y2="100%"><stop offset="0" stop-color="#bbb" stop-opacity=".1"/><stop offset="1" stop-opacity=".1"/></linearGradient><clipPath id="r"><rect width="128" height="20" rx="3" fill="#fff"/></clipPath><g clip-path="url(#r)"><rect width="47" height="20" fill="#555"/><rect x="47" width="81" height="20" fill="#fe7d37"/><rect width="128" height="20" fill="url(#s)"/></g><g fill="#fff" text-anchor="middle" font-family="Verdana,Geneva,DejaVu Sans,sans-serif" text-rendering="geometricPrecision" font-size="110"><text aria-hidden="true" x="245" y="150" fill="#010101" fill-opacity=".3" transform="scale(.1)" textLength="370">Flake8</text><text x="245" y="140" transform="scale(.1)" fill="#fff" textLength="370">Flake8</text><text aria-hidden="true" x="865" y="150" fill="#010101" fill-opacity=".3" transform="scale(.1)" textLength="710">0 C, 4 W, 0 I</text><text x="865" y="140" transform="scale(.1)" fill="#fff" textLength="710">0 C, 4 W, 0 I</text></g></svg>
\ No newline at end of file
diff --git a/flake8/flake8stats.txt b/flake8/flake8stats.txt
index e69de29..883e4fd 100644
--- a/flake8/flake8stats.txt
+++ b/flake8/flake8stats.txt
@@ -0,0 +1 @@
+4     W503 line break before binary operator
diff --git a/flake8/index.html b/flake8/index.html
index f9ce797..ca1eaa6 100644
--- a/flake8/index.html
+++ b/flake8/index.html
@@ -6,22 +6,30 @@
       <link rel="stylesheet" href="styles.css">
    </head>
    <body>
-      <div id="masthead" class="sev-4"></div>
+      <div id="masthead" class="sev-2"></div>
       <div id="page">
           <h1>flake8 violations</h1>
-         <p id="versions">Generated on 2024-11-04 11:04
+         <p id="versions">Generated on 2024-11-15 12:06
             with Installed plugins: flake8-html: 0.4.3, mccabe: 0.7.0, pycodestyle: 2.12.1, pyflakes: 3.2.0
          </p>
          <ul id="index">
          
          <li>
-            <div id="all-good">
-               <span class="count sev-4">
-                  <span class="tick">&#x2713;</span>
+            <a href="biobb_dna.interbp_correlations.interbpcorr.report.html">
+               <span class="count sev-2">
+                  2
                </span>
-               <h2>All good!</h2>
-               <p>No flake8 errors found in 45 files scanned.</p>
-            </div>
+               biobb_dna/interbp_correlations/interbpcorr.py
+            </a>
+         </li>
+         
+         <li>
+            <a href="biobb_dna.intrabp_correlations.intrabpcorr.report.html">
+               <span class="count sev-2">
+                  2
+               </span>
+               biobb_dna/intrabp_correlations/intrabpcorr.py
+            </a>
          </li>
          
          </ul>
diff --git a/junit/junit.xml b/junit/junit.xml
index 8206fab..fe464a1 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="19" time="27.373" timestamp="2024-11-04T11:04:47.333699+00:00" hostname="biobb-runners"><testcase classname="biobb_dna.test.unitests.test_backbone.test_bipopulations.TestBIPopulations" name="test_bipopulations" time="0.513" /><testcase classname="biobb_dna.test.unitests.test_backbone.test_canonical_alpha_gamma.TestCanonicalAlphaGamma" name="test_canonicalag" time="0.458" /><testcase classname="biobb_dna.test.unitests.test_backbone.test_puckering.TestPuckering" name="test_puckering" time="0.553" /><testcase classname="biobb_dna.test.unitests.test_correlation.test_correlation.TestInterHelparCorrelation" name="test_helparcorrelation" time="0.341" /><testcase classname="biobb_dna.test.unitests.test_correlation.test_correlation.TestInterSequenceCorrelation" name="test_sequencecorrelation" time="0.348" /><testcase classname="biobb_dna.test.unitests.test_correlation.test_correlation.TestInterBasepairCorrelation" name="test_basepaircorrelation" time="0.856" /><testcase classname="biobb_dna.test.unitests.test_correlation.test_correlation.TestIntraHelparCorrelation" name="test_helparcorrelation" time="0.276" /><testcase classname="biobb_dna.test.unitests.test_correlation.test_correlation.TestIntraSequenceCorrelation" name="test_sequencecorrelation" time="0.348" /><testcase classname="biobb_dna.test.unitests.test_correlation.test_correlation.TestIntraBasepairCorrelation" name="test_basepaircorrelation" time="0.996" /><testcase classname="biobb_dna.test.unitests.test_curvesplus.test_canal.TestCanal" name="test_canal" time="7.206" /><testcase classname="biobb_dna.test.unitests.test_curvesplus.test_canal_unzip.TestCanalUnzip" name="test_canal_unzip" time="0.092" /><testcase classname="biobb_dna.test.unitests.test_curvesplus.test_canion.TestCanal" name="test_canion" time="0.373" /><testcase classname="biobb_dna.test.unitests.test_curvesplus.test_curves.TestCurves" name="test_curves" time="6.749" /><testcase classname="biobb_dna.test.unitests.test_dna.test_averages.TestAverages" name="test_helparaverages" time="0.332" /><testcase classname="biobb_dna.test.unitests.test_dna.test_bimodality.TestBimodality" name="test_helparbimodality" time="0.592" /><testcase classname="biobb_dna.test.unitests.test_dna.test_timeseries.TestTimeSeries" name="test_helpartimeseries" time="4.385" /><testcase classname="biobb_dna.test.unitests.test_dna.test_timeseries_unzip.TestCanalUnzip" name="test_dna_timeseries_unzip" time="0.151" /><testcase classname="biobb_dna.test.unitests.test_stiffness.test_stiffness.TestAvgStiffness" name="test_averagestiffness" time="0.262" /><testcase classname="biobb_dna.test.unitests.test_stiffness.test_stiffness.TestBasePairStiffness" name="test_basepairstiffness" time="0.270" /></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="19" time="26.992" timestamp="2024-11-15T12:07:04.585518+00:00" hostname="biobb-runners"><testcase classname="biobb_dna.test.unitests.test_backbone.test_bipopulations.TestBIPopulations" name="test_bipopulations" time="0.502" /><testcase classname="biobb_dna.test.unitests.test_backbone.test_canonical_alpha_gamma.TestCanonicalAlphaGamma" name="test_canonicalag" time="0.458" /><testcase classname="biobb_dna.test.unitests.test_backbone.test_puckering.TestPuckering" name="test_puckering" time="0.578" /><testcase classname="biobb_dna.test.unitests.test_correlation.test_correlation.TestInterHelparCorrelation" name="test_helparcorrelation" time="0.279" /><testcase classname="biobb_dna.test.unitests.test_correlation.test_correlation.TestInterSequenceCorrelation" name="test_sequencecorrelation" time="0.428" /><testcase classname="biobb_dna.test.unitests.test_correlation.test_correlation.TestInterBasepairCorrelation" name="test_basepaircorrelation" time="0.857" /><testcase classname="biobb_dna.test.unitests.test_correlation.test_correlation.TestIntraHelparCorrelation" name="test_helparcorrelation" time="0.277" /><testcase classname="biobb_dna.test.unitests.test_correlation.test_correlation.TestIntraSequenceCorrelation" name="test_sequencecorrelation" time="0.351" /><testcase classname="biobb_dna.test.unitests.test_correlation.test_correlation.TestIntraBasepairCorrelation" name="test_basepaircorrelation" time="0.859" /><testcase classname="biobb_dna.test.unitests.test_curvesplus.test_canal.TestCanal" name="test_canal" time="7.196" /><testcase classname="biobb_dna.test.unitests.test_curvesplus.test_canal_unzip.TestCanalUnzip" name="test_canal_unzip" time="0.086" /><testcase classname="biobb_dna.test.unitests.test_curvesplus.test_canion.TestCanal" name="test_canion" time="0.374" /><testcase classname="biobb_dna.test.unitests.test_curvesplus.test_curves.TestCurves" name="test_curves" time="6.805" /><testcase classname="biobb_dna.test.unitests.test_dna.test_averages.TestAverages" name="test_helparaverages" time="0.240" /><testcase classname="biobb_dna.test.unitests.test_dna.test_bimodality.TestBimodality" name="test_helparbimodality" time="0.501" /><testcase classname="biobb_dna.test.unitests.test_dna.test_timeseries.TestTimeSeries" name="test_helpartimeseries" time="4.310" /><testcase classname="biobb_dna.test.unitests.test_dna.test_timeseries_unzip.TestCanalUnzip" name="test_dna_timeseries_unzip" time="0.083" /><testcase classname="biobb_dna.test.unitests.test_stiffness.test_stiffness.TestAvgStiffness" name="test_averagestiffness" time="0.246" /><testcase classname="biobb_dna.test.unitests.test_stiffness.test_stiffness.TestBasePairStiffness" name="test_basepairstiffness" time="0.327" /></testsuite></testsuites>
\ No newline at end of file
diff --git a/junit/report.html b/junit/report.html
index e652fb3..7e9d864 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 04-Nov-2024 at 11:05:14 by <a href="https://pypi.python.org/pypi/pytest-html">pytest-html</a>
+    <p>Report generated on 15-Nov-2024 at 12:07:31 by <a href="https://pypi.python.org/pypi/pytest-html">pytest-html</a>
         v4.1.1</p>
     <div id="environment-header">
       <h2>Environment</h2>
@@ -108,7 +108,7 @@ <h2>Summary</h2>
     </table>
   </body>
   <footer>
-    <div id="data-container" data-jsonblob="{&#34;environment&#34;: {&#34;Python&#34;: &#34;3.9.20&#34;, &#34;Platform&#34;: &#34;Linux-5.4.0-200-generic-x86_64-with-glibc2.31&#34;, &#34;Packages&#34;: {&#34;pytest&#34;: &#34;8.3.3&#34;, &#34;pluggy&#34;: &#34;1.5.0&#34;}, &#34;Plugins&#34;: {&#34;metadata&#34;: &#34;3.1.1&#34;, &#34;cov&#34;: &#34;6.0.0&#34;, &#34;html&#34;: &#34;4.1.1&#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;513 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;513 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 -----------------------------\n2024-11-04 11:04:49,298 [MainThread  ] [INFO ]  Module: biobb_dna.backbone.bipopulations Version: 5.0.0\n2024-11-04 11:04:49,298 [MainThread  ] [INFO ]  /tmp/biobb/unitests_7/bipopulations/sandbox_c55c8281-cb67-4c77-83bd-7a15521532b8 directory successfully created\n2024-11-04 11:04:49,299 [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_7/bipopulations/sandbox_c55c8281-cb67-4c77-83bd-7a15521532b8\n2024-11-04 11:04:49,300 [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_7/bipopulations/sandbox_c55c8281-cb67-4c77-83bd-7a15521532b8\n2024-11-04 11:04:49,300 [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_7/bipopulations/sandbox_c55c8281-cb67-4c77-83bd-7a15521532b8\n2024-11-04 11:04:49,301 [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_7/bipopulations/sandbox_c55c8281-cb67-4c77-83bd-7a15521532b8\n2024-11-04 11:04:49,717 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_7/bipopulations/sandbox_c55c8281-cb67-4c77-83bd-7a15521532b8&amp;#x27;]\n2024-11-04 11:04:49,718 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_7/bipopulations/bipop.csv\nChecking if empty file: /tmp/biobb/unitests_7/bipopulations/bipop.jpg\nComparing images of both files:\n     IMAGE_A: /tmp/biobb/unitests_7/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: ff8981818180c9ff SIZE: 64 bits\n     TOLERANCE: 1.0%, ABS TOLERANCE: 1 bits, DIFFERENCE: 1 bits\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_7/bipopulations/bipopulations_log.out:file_utils.py:409 Module: biobb_dna.backbone.bipopulations Version: 5.0.0\nINFO     /tmp/biobb/unitests_7/bipopulations/bipopulations_log.out:file_utils.py:82 /tmp/biobb/unitests_7/bipopulations/sandbox_c55c8281-cb67-4c77-83bd-7a15521532b8 directory successfully created\nINFO     /tmp/biobb/unitests_7/bipopulations/bipopulations_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/backbone/canal_output_epsilC.ser to /tmp/biobb/unitests_7/bipopulations/sandbox_c55c8281-cb67-4c77-83bd-7a15521532b8\nINFO     /tmp/biobb/unitests_7/bipopulations/bipopulations_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/backbone/canal_output_epsilW.ser to /tmp/biobb/unitests_7/bipopulations/sandbox_c55c8281-cb67-4c77-83bd-7a15521532b8\nINFO     /tmp/biobb/unitests_7/bipopulations/bipopulations_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/backbone/canal_output_zetaC.ser to /tmp/biobb/unitests_7/bipopulations/sandbox_c55c8281-cb67-4c77-83bd-7a15521532b8\nINFO     /tmp/biobb/unitests_7/bipopulations/bipopulations_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/backbone/canal_output_zetaW.ser to /tmp/biobb/unitests_7/bipopulations/sandbox_c55c8281-cb67-4c77-83bd-7a15521532b8\nINFO     /tmp/biobb/unitests_7/bipopulations/bipopulations_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_7/bipopulations/sandbox_c55c8281-cb67-4c77-83bd-7a15521532b8&amp;#x27;]\nINFO     /tmp/biobb/unitests_7/bipopulations/bipopulations_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_7\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;458 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;458 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 -----------------------------\n2024-11-04 11:04:49,836 [MainThread  ] [INFO ]  Module: biobb_dna.backbone.canonicalag Version: 5.0.0\n2024-11-04 11:04:49,836 [MainThread  ] [INFO ]  /tmp/biobb/unitests_7/canonicalag/sandbox_9a52fa94-f826-48be-9fc3-35fb60c69a50 directory successfully created\n2024-11-04 11:04:49,837 [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_7/canonicalag/sandbox_9a52fa94-f826-48be-9fc3-35fb60c69a50\n2024-11-04 11:04:49,837 [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_7/canonicalag/sandbox_9a52fa94-f826-48be-9fc3-35fb60c69a50\n2024-11-04 11:04:49,838 [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_7/canonicalag/sandbox_9a52fa94-f826-48be-9fc3-35fb60c69a50\n2024-11-04 11:04:49,839 [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_7/canonicalag/sandbox_9a52fa94-f826-48be-9fc3-35fb60c69a50\n2024-11-04 11:04:50,206 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_7/canonicalag/sandbox_9a52fa94-f826-48be-9fc3-35fb60c69a50&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_7/canonicalag/canonag.csv\nChecking if empty file: /tmp/biobb/unitests_7/canonicalag/canonag.jpg\nComparing images of both files:\n     IMAGE_A: /tmp/biobb/unitests_7/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_7/canonicalag/canonicalag_log.out:file_utils.py:409 Module: biobb_dna.backbone.canonicalag Version: 5.0.0\nINFO     /tmp/biobb/unitests_7/canonicalag/canonicalag_log.out:file_utils.py:82 /tmp/biobb/unitests_7/canonicalag/sandbox_9a52fa94-f826-48be-9fc3-35fb60c69a50 directory successfully created\nINFO     /tmp/biobb/unitests_7/canonicalag/canonicalag_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/backbone/canal_output_alphaC.ser to /tmp/biobb/unitests_7/canonicalag/sandbox_9a52fa94-f826-48be-9fc3-35fb60c69a50\nINFO     /tmp/biobb/unitests_7/canonicalag/canonicalag_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/backbone/canal_output_alphaW.ser to /tmp/biobb/unitests_7/canonicalag/sandbox_9a52fa94-f826-48be-9fc3-35fb60c69a50\nINFO     /tmp/biobb/unitests_7/canonicalag/canonicalag_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/backbone/canal_output_gammaC.ser to /tmp/biobb/unitests_7/canonicalag/sandbox_9a52fa94-f826-48be-9fc3-35fb60c69a50\nINFO     /tmp/biobb/unitests_7/canonicalag/canonicalag_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/backbone/canal_output_gammaW.ser to /tmp/biobb/unitests_7/canonicalag/sandbox_9a52fa94-f826-48be-9fc3-35fb60c69a50\nINFO     /tmp/biobb/unitests_7/canonicalag/canonicalag_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_7/canonicalag/sandbox_9a52fa94-f826-48be-9fc3-35fb60c69a50&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_7\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;553 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;553 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 -----------------------------\n2024-11-04 11:04:50,295 [MainThread  ] [INFO ]  Module: biobb_dna.backbone.puckering Version: 5.0.0\n2024-11-04 11:04:50,296 [MainThread  ] [INFO ]  /tmp/biobb/unitests_7/puckering/sandbox_4835f042-89ce-4e7b-b25b-0889514c1d5d directory successfully created\n2024-11-04 11:04:50,296 [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_7/puckering/sandbox_4835f042-89ce-4e7b-b25b-0889514c1d5d\n2024-11-04 11:04:50,297 [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_7/puckering/sandbox_4835f042-89ce-4e7b-b25b-0889514c1d5d\n2024-11-04 11:04:50,761 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_7/puckering/sandbox_4835f042-89ce-4e7b-b25b-0889514c1d5d&amp;#x27;]\n2024-11-04 11:04:50,761 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_7/puckering/puckering.csv\nChecking if empty file: /tmp/biobb/unitests_7/puckering/puckering.jpg\nComparing images of both files:\n     IMAGE_A: /tmp/biobb/unitests_7/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: eb8181808081ffff SIZE: 64 bits\n     TOLERANCE: 20%, ABS TOLERANCE: 12.8 bits, DIFFERENCE: 0 bits\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_7/puckering/puckering_log.out:file_utils.py:409 Module: biobb_dna.backbone.puckering Version: 5.0.0\nINFO     /tmp/biobb/unitests_7/puckering/puckering_log.out:file_utils.py:82 /tmp/biobb/unitests_7/puckering/sandbox_4835f042-89ce-4e7b-b25b-0889514c1d5d directory successfully created\nINFO     /tmp/biobb/unitests_7/puckering/puckering_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/backbone/canal_output_phaseC.ser to /tmp/biobb/unitests_7/puckering/sandbox_4835f042-89ce-4e7b-b25b-0889514c1d5d\nINFO     /tmp/biobb/unitests_7/puckering/puckering_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/backbone/canal_output_phaseW.ser to /tmp/biobb/unitests_7/puckering/sandbox_4835f042-89ce-4e7b-b25b-0889514c1d5d\nINFO     /tmp/biobb/unitests_7/puckering/puckering_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_7/puckering/sandbox_4835f042-89ce-4e7b-b25b-0889514c1d5d&amp;#x27;]\nINFO     /tmp/biobb/unitests_7/puckering/puckering_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_7\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;341 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;341 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 -----------------------------\n2024-11-04 11:04:50,849 [MainThread  ] [INFO ]  Module: biobb_dna.interbp_correlations.interhpcorr Version: 5.0.0\n2024-11-04 11:04:50,849 [MainThread  ] [INFO ]  /tmp/biobb/unitests_7/interhpcorr/sandbox_b15f2a85-08f8-4da8-a2dd-98a19581add0 directory successfully created\n2024-11-04 11:04:50,850 [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_7/interhpcorr/sandbox_b15f2a85-08f8-4da8-a2dd-98a19581add0\n2024-11-04 11:04:50,850 [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_7/interhpcorr/sandbox_b15f2a85-08f8-4da8-a2dd-98a19581add0\n2024-11-04 11:04:50,850 [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_7/interhpcorr/sandbox_b15f2a85-08f8-4da8-a2dd-98a19581add0\n2024-11-04 11:04:50,850 [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_7/interhpcorr/sandbox_b15f2a85-08f8-4da8-a2dd-98a19581add0\n2024-11-04 11:04:50,851 [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_7/interhpcorr/sandbox_b15f2a85-08f8-4da8-a2dd-98a19581add0\n2024-11-04 11:04:50,851 [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_7/interhpcorr/sandbox_b15f2a85-08f8-4da8-a2dd-98a19581add0\n2024-11-04 11:04:51,108 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_7/interhpcorr/sandbox_b15f2a85-08f8-4da8-a2dd-98a19581add0&amp;#x27;]\n2024-11-04 11:04:51,109 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_7/interhpcorr/inter_hpcorr.csv\nChecking if empty file: /tmp/biobb/unitests_7/interhpcorr/inter_hpcorr.jpg\nComparing images of both files:\n     IMAGE_A: /tmp/biobb/unitests_7/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_7/interhpcorr/log.out:file_utils.py:409 Module: biobb_dna.interbp_correlations.interhpcorr Version: 5.0.0\nINFO     /tmp/biobb/unitests_7/interhpcorr/log.out:file_utils.py:82 /tmp/biobb/unitests_7/interhpcorr/sandbox_b15f2a85-08f8-4da8-a2dd-98a19581add0 directory successfully created\nINFO     /tmp/biobb/unitests_7/interhpcorr/log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_shift_AA.csv to /tmp/biobb/unitests_7/interhpcorr/sandbox_b15f2a85-08f8-4da8-a2dd-98a19581add0\nINFO     /tmp/biobb/unitests_7/interhpcorr/log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_slide_AA.csv to /tmp/biobb/unitests_7/interhpcorr/sandbox_b15f2a85-08f8-4da8-a2dd-98a19581add0\nINFO     /tmp/biobb/unitests_7/interhpcorr/log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_rise_AA.csv to /tmp/biobb/unitests_7/interhpcorr/sandbox_b15f2a85-08f8-4da8-a2dd-98a19581add0\nINFO     /tmp/biobb/unitests_7/interhpcorr/log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_tilt_AA.csv to /tmp/biobb/unitests_7/interhpcorr/sandbox_b15f2a85-08f8-4da8-a2dd-98a19581add0\nINFO     /tmp/biobb/unitests_7/interhpcorr/log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_roll_AA.csv to /tmp/biobb/unitests_7/interhpcorr/sandbox_b15f2a85-08f8-4da8-a2dd-98a19581add0\nINFO     /tmp/biobb/unitests_7/interhpcorr/log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_twist_AA.csv to /tmp/biobb/unitests_7/interhpcorr/sandbox_b15f2a85-08f8-4da8-a2dd-98a19581add0\nINFO     /tmp/biobb/unitests_7/interhpcorr/log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_7/interhpcorr/sandbox_b15f2a85-08f8-4da8-a2dd-98a19581add0&amp;#x27;]\nINFO     /tmp/biobb/unitests_7/interhpcorr/log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_7\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;348 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;348 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 -----------------------------\n2024-11-04 11:04:51,191 [MainThread  ] [INFO ]  Module: biobb_dna.interbp_correlations.interseqcorr Version: 5.0.0\n2024-11-04 11:04:51,191 [MainThread  ] [INFO ]  /tmp/biobb/unitests_7/interseqcorr/sandbox_5c928512-5f75-4f29-a463-01343c0326f2 directory successfully created\n2024-11-04 11:04:51,192 [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_7/interseqcorr/sandbox_5c928512-5f75-4f29-a463-01343c0326f2\n2024-11-04 11:04:51,455 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_7/interseqcorr/sandbox_5c928512-5f75-4f29-a463-01343c0326f2&amp;#x27;]\n2024-11-04 11:04:51,455 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_7/interseqcorr/inter_seqcorr.csv\nChecking if empty file: /tmp/biobb/unitests_7/interseqcorr/inter_seqcorr.jpg\nComparing images of both files:\n     IMAGE_A: /tmp/biobb/unitests_7/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_7/interseqcorr/interseqcorr_log.out:file_utils.py:409 Module: biobb_dna.interbp_correlations.interseqcorr Version: 5.0.0\nINFO     /tmp/biobb/unitests_7/interseqcorr/interseqcorr_log.out:file_utils.py:82 /tmp/biobb/unitests_7/interseqcorr/sandbox_5c928512-5f75-4f29-a463-01343c0326f2 directory successfully created\nINFO     /tmp/biobb/unitests_7/interseqcorr/interseqcorr_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_roll.ser to /tmp/biobb/unitests_7/interseqcorr/sandbox_5c928512-5f75-4f29-a463-01343c0326f2\nINFO     /tmp/biobb/unitests_7/interseqcorr/interseqcorr_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_7/interseqcorr/sandbox_5c928512-5f75-4f29-a463-01343c0326f2&amp;#x27;]\nINFO     /tmp/biobb/unitests_7/interseqcorr/interseqcorr_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_7\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;856 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;856 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 -----------------------------\n2024-11-04 11:04:51,541 [MainThread  ] [INFO ]  Module: biobb_dna.interbp_correlations.interbpcorr Version: 5.0.0\n2024-11-04 11:04:51,541 [MainThread  ] [INFO ]  /tmp/biobb/unitests_7/interbpcorr/sandbox_54d25f54-954d-4466-9239-2bf71eff964a directory successfully created\n2024-11-04 11:04:51,542 [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_7/interbpcorr/sandbox_54d25f54-954d-4466-9239-2bf71eff964a\n2024-11-04 11:04:51,542 [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_7/interbpcorr/sandbox_54d25f54-954d-4466-9239-2bf71eff964a\n2024-11-04 11:04:51,543 [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_7/interbpcorr/sandbox_54d25f54-954d-4466-9239-2bf71eff964a\n2024-11-04 11:04:51,544 [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_7/interbpcorr/sandbox_54d25f54-954d-4466-9239-2bf71eff964a\n2024-11-04 11:04:51,545 [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_7/interbpcorr/sandbox_54d25f54-954d-4466-9239-2bf71eff964a\n2024-11-04 11:04:51,545 [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_7/interbpcorr/sandbox_54d25f54-954d-4466-9239-2bf71eff964a\n2024-11-04 11:04:52,307 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_7/interbpcorr/sandbox_54d25f54-954d-4466-9239-2bf71eff964a&amp;#x27;]\n2024-11-04 11:04:52,307 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_7/interbpcorr/inter_bpcorr.csv\nChecking if empty file: /tmp/biobb/unitests_7/interbpcorr/inter_bpcorr.jpg\nComparing images of both files:\n     IMAGE_A: /tmp/biobb/unitests_7/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_7/interbpcorr/interbpcorr_log.out:file_utils.py:409 Module: biobb_dna.interbp_correlations.interbpcorr Version: 5.0.0\nINFO     /tmp/biobb/unitests_7/interbpcorr/interbpcorr_log.out:file_utils.py:82 /tmp/biobb/unitests_7/interbpcorr/sandbox_54d25f54-954d-4466-9239-2bf71eff964a directory successfully created\nINFO     /tmp/biobb/unitests_7/interbpcorr/interbpcorr_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_shift.ser to /tmp/biobb/unitests_7/interbpcorr/sandbox_54d25f54-954d-4466-9239-2bf71eff964a\nINFO     /tmp/biobb/unitests_7/interbpcorr/interbpcorr_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_slide.ser to /tmp/biobb/unitests_7/interbpcorr/sandbox_54d25f54-954d-4466-9239-2bf71eff964a\nINFO     /tmp/biobb/unitests_7/interbpcorr/interbpcorr_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_rise.ser to /tmp/biobb/unitests_7/interbpcorr/sandbox_54d25f54-954d-4466-9239-2bf71eff964a\nINFO     /tmp/biobb/unitests_7/interbpcorr/interbpcorr_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_tilt.ser to /tmp/biobb/unitests_7/interbpcorr/sandbox_54d25f54-954d-4466-9239-2bf71eff964a\nINFO     /tmp/biobb/unitests_7/interbpcorr/interbpcorr_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_roll.ser to /tmp/biobb/unitests_7/interbpcorr/sandbox_54d25f54-954d-4466-9239-2bf71eff964a\nINFO     /tmp/biobb/unitests_7/interbpcorr/interbpcorr_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_twist.ser to /tmp/biobb/unitests_7/interbpcorr/sandbox_54d25f54-954d-4466-9239-2bf71eff964a\nINFO     /tmp/biobb/unitests_7/interbpcorr/interbpcorr_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_7/interbpcorr/sandbox_54d25f54-954d-4466-9239-2bf71eff964a&amp;#x27;]\nINFO     /tmp/biobb/unitests_7/interbpcorr/interbpcorr_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_7\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;276 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;276 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 -----------------------------\n2024-11-04 11:04:52,398 [MainThread  ] [INFO ]  Module: biobb_dna.intrabp_correlations.intrahpcorr Version: 5.0.0\n2024-11-04 11:04:52,398 [MainThread  ] [INFO ]  /tmp/biobb/unitests_7/intrahpcorr/sandbox_0d31392d-84b3-41ff-b75d-2dae80ba08ae directory successfully created\n2024-11-04 11:04:52,398 [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_7/intrahpcorr/sandbox_0d31392d-84b3-41ff-b75d-2dae80ba08ae\n2024-11-04 11:04:52,399 [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_7/intrahpcorr/sandbox_0d31392d-84b3-41ff-b75d-2dae80ba08ae\n2024-11-04 11:04:52,399 [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_7/intrahpcorr/sandbox_0d31392d-84b3-41ff-b75d-2dae80ba08ae\n2024-11-04 11:04:52,399 [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_7/intrahpcorr/sandbox_0d31392d-84b3-41ff-b75d-2dae80ba08ae\n2024-11-04 11:04:52,399 [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_7/intrahpcorr/sandbox_0d31392d-84b3-41ff-b75d-2dae80ba08ae\n2024-11-04 11:04:52,400 [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_7/intrahpcorr/sandbox_0d31392d-84b3-41ff-b75d-2dae80ba08ae\n2024-11-04 11:04:52,592 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_7/intrahpcorr/sandbox_0d31392d-84b3-41ff-b75d-2dae80ba08ae&amp;#x27;]\n2024-11-04 11:04:52,593 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_7/intrahpcorr/intra_hpcorr.csv\nChecking if empty file: /tmp/biobb/unitests_7/intrahpcorr/intra_hpcorr.jpg\nComparing images of both files:\n     IMAGE_A: /tmp/biobb/unitests_7/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_7/intrahpcorr/log.out:file_utils.py:409 Module: biobb_dna.intrabp_correlations.intrahpcorr Version: 5.0.0\nINFO     /tmp/biobb/unitests_7/intrahpcorr/log.out:file_utils.py:82 /tmp/biobb/unitests_7/intrahpcorr/sandbox_0d31392d-84b3-41ff-b75d-2dae80ba08ae directory successfully created\nINFO     /tmp/biobb/unitests_7/intrahpcorr/log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/series_shear_A.csv to /tmp/biobb/unitests_7/intrahpcorr/sandbox_0d31392d-84b3-41ff-b75d-2dae80ba08ae\nINFO     /tmp/biobb/unitests_7/intrahpcorr/log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/series_stretch_A.csv to /tmp/biobb/unitests_7/intrahpcorr/sandbox_0d31392d-84b3-41ff-b75d-2dae80ba08ae\nINFO     /tmp/biobb/unitests_7/intrahpcorr/log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/series_stagger_A.csv to /tmp/biobb/unitests_7/intrahpcorr/sandbox_0d31392d-84b3-41ff-b75d-2dae80ba08ae\nINFO     /tmp/biobb/unitests_7/intrahpcorr/log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/series_buckle_A.csv to /tmp/biobb/unitests_7/intrahpcorr/sandbox_0d31392d-84b3-41ff-b75d-2dae80ba08ae\nINFO     /tmp/biobb/unitests_7/intrahpcorr/log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/series_propel_A.csv to /tmp/biobb/unitests_7/intrahpcorr/sandbox_0d31392d-84b3-41ff-b75d-2dae80ba08ae\nINFO     /tmp/biobb/unitests_7/intrahpcorr/log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/series_opening_A.csv to /tmp/biobb/unitests_7/intrahpcorr/sandbox_0d31392d-84b3-41ff-b75d-2dae80ba08ae\nINFO     /tmp/biobb/unitests_7/intrahpcorr/log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_7/intrahpcorr/sandbox_0d31392d-84b3-41ff-b75d-2dae80ba08ae&amp;#x27;]\nINFO     /tmp/biobb/unitests_7/intrahpcorr/log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_7\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;348 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;348 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 -----------------------------\n2024-11-04 11:04:52,674 [MainThread  ] [INFO ]  Module: biobb_dna.intrabp_correlations.intraseqcorr Version: 5.0.0\n2024-11-04 11:04:52,674 [MainThread  ] [INFO ]  /tmp/biobb/unitests_7/intraseqcorr/sandbox_887fce4c-8764-4e14-9d8a-31cef87d0e54 directory successfully created\n2024-11-04 11:04:52,675 [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_7/intraseqcorr/sandbox_887fce4c-8764-4e14-9d8a-31cef87d0e54\n2024-11-04 11:04:52,941 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_7/intraseqcorr/sandbox_887fce4c-8764-4e14-9d8a-31cef87d0e54&amp;#x27;]\n2024-11-04 11:04:52,941 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_7/intraseqcorr/intra_seqcorr.csv\nChecking if empty file: /tmp/biobb/unitests_7/intraseqcorr/intra_seqcorr.jpg\nComparing images of both files:\n     IMAGE_A: /tmp/biobb/unitests_7/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_7/intraseqcorr/intraseqcorr_log.out:file_utils.py:409 Module: biobb_dna.intrabp_correlations.intraseqcorr Version: 5.0.0\nINFO     /tmp/biobb/unitests_7/intraseqcorr/intraseqcorr_log.out:file_utils.py:82 /tmp/biobb/unitests_7/intraseqcorr/sandbox_887fce4c-8764-4e14-9d8a-31cef87d0e54 directory successfully created\nINFO     /tmp/biobb/unitests_7/intraseqcorr/intraseqcorr_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_buckle.ser to /tmp/biobb/unitests_7/intraseqcorr/sandbox_887fce4c-8764-4e14-9d8a-31cef87d0e54\nINFO     /tmp/biobb/unitests_7/intraseqcorr/intraseqcorr_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_7/intraseqcorr/sandbox_887fce4c-8764-4e14-9d8a-31cef87d0e54&amp;#x27;]\nINFO     /tmp/biobb/unitests_7/intraseqcorr/intraseqcorr_log.out:file_utils.py:409\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;996 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::TestIntraBasepairCorrelation::test_basepaircorrelation&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;996 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 -----------------------------\n2024-11-04 11:04:53,024 [MainThread  ] [INFO ]  Module: biobb_dna.intrabp_correlations.intrabpcorr Version: 5.0.0\n2024-11-04 11:04:53,024 [MainThread  ] [INFO ]  /tmp/biobb/unitests_8/intrabpcorr/sandbox_b2ade402-195f-4265-a4f7-e26087618c1b directory successfully created\n2024-11-04 11:04:53,025 [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_8/intrabpcorr/sandbox_b2ade402-195f-4265-a4f7-e26087618c1b\n2024-11-04 11:04:53,026 [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_8/intrabpcorr/sandbox_b2ade402-195f-4265-a4f7-e26087618c1b\n2024-11-04 11:04:53,027 [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_8/intrabpcorr/sandbox_b2ade402-195f-4265-a4f7-e26087618c1b\n2024-11-04 11:04:53,027 [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_8/intrabpcorr/sandbox_b2ade402-195f-4265-a4f7-e26087618c1b\n2024-11-04 11:04:53,028 [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_8/intrabpcorr/sandbox_b2ade402-195f-4265-a4f7-e26087618c1b\n2024-11-04 11:04:53,029 [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_8/intrabpcorr/sandbox_b2ade402-195f-4265-a4f7-e26087618c1b\n2024-11-04 11:04:53,926 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_8/intrabpcorr/sandbox_b2ade402-195f-4265-a4f7-e26087618c1b&amp;#x27;]\n2024-11-04 11:04:53,927 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_8/intrabpcorr/intra_bpcorr.csv\nChecking if empty file: /tmp/biobb/unitests_8/intrabpcorr/intra_bpcorr.jpg\nComparing images of both files:\n     IMAGE_A: /tmp/biobb/unitests_8/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_8/intrabpcorr/intrabpcorr_log.out:file_utils.py:409 Module: biobb_dna.intrabp_correlations.intrabpcorr Version: 5.0.0\nINFO     /tmp/biobb/unitests_8/intrabpcorr/intrabpcorr_log.out:file_utils.py:82 /tmp/biobb/unitests_8/intrabpcorr/sandbox_b2ade402-195f-4265-a4f7-e26087618c1b directory successfully created\nINFO     /tmp/biobb/unitests_8/intrabpcorr/intrabpcorr_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_shear.ser to /tmp/biobb/unitests_8/intrabpcorr/sandbox_b2ade402-195f-4265-a4f7-e26087618c1b\nINFO     /tmp/biobb/unitests_8/intrabpcorr/intrabpcorr_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_stretch.ser to /tmp/biobb/unitests_8/intrabpcorr/sandbox_b2ade402-195f-4265-a4f7-e26087618c1b\nINFO     /tmp/biobb/unitests_8/intrabpcorr/intrabpcorr_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_stagger.ser to /tmp/biobb/unitests_8/intrabpcorr/sandbox_b2ade402-195f-4265-a4f7-e26087618c1b\nINFO     /tmp/biobb/unitests_8/intrabpcorr/intrabpcorr_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_buckle.ser to /tmp/biobb/unitests_8/intrabpcorr/sandbox_b2ade402-195f-4265-a4f7-e26087618c1b\nINFO     /tmp/biobb/unitests_8/intrabpcorr/intrabpcorr_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_propel.ser to /tmp/biobb/unitests_8/intrabpcorr/sandbox_b2ade402-195f-4265-a4f7-e26087618c1b\nINFO     /tmp/biobb/unitests_8/intrabpcorr/intrabpcorr_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_opening.ser to /tmp/biobb/unitests_8/intrabpcorr/sandbox_b2ade402-195f-4265-a4f7-e26087618c1b\nINFO     /tmp/biobb/unitests_8/intrabpcorr/intrabpcorr_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_8/intrabpcorr/sandbox_b2ade402-195f-4265-a4f7-e26087618c1b&amp;#x27;]\nINFO     /tmp/biobb/unitests_8/intrabpcorr/intrabpcorr_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_8\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;00:00:07&#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_canal.py::TestCanal::test_canal&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 -----------------------------\n2024-11-04 11:04:54,021 [MainThread  ] [INFO ]  Module: biobb_dna.curvesplus.biobb_canal Version: 5.0.0\n2024-11-04 11:04:54,021 [MainThread  ] [INFO ]  /tmp/biobb/unitests_8/biobb_canal/sandbox_76f5f196-d9f5-4179-a4b8-575df25cec65 directory successfully created\n2024-11-04 11:04:54,034 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/curvesplus/curves_output.cda to /tmp/biobb/unitests_8/biobb_canal/sandbox_76f5f196-d9f5-4179-a4b8-575df25cec65\n2024-11-04 11:04:54,034 [MainThread  ] [INFO ]  Creating command line with instructions and required arguments\n2024-11-04 11:04:54,034 [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=.t.,\n  series=.t.,\n  corr=.t.,\n&amp;amp;end\ncurves_output.cda CGCGAATTCGCG\n!\n\n2024-11-04 11:05:01,019 [MainThread  ] [INFO ]  Executing: 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...\n2024-11-04 11:05:01,019 [MainThread  ] [INFO ]  Exit code: 0\n2024-11-04 11:05:01,174 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_8/biobb_canal/sandbox_76f5f196-d9f5-4179-a4b8-575df25cec65&amp;#x27;]\n2024-11-04 11:05:01,174 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_8/biobb_canal/canal_output.zip\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_8/biobb_canal/biobb_canal_log.out:file_utils.py:409 Module: biobb_dna.curvesplus.biobb_canal Version: 5.0.0\nINFO     /tmp/biobb/unitests_8/biobb_canal/biobb_canal_log.out:file_utils.py:82 /tmp/biobb/unitests_8/biobb_canal/sandbox_76f5f196-d9f5-4179-a4b8-575df25cec65 directory successfully created\nINFO     /tmp/biobb/unitests_8/biobb_canal/biobb_canal_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/curvesplus/curves_output.cda to /tmp/biobb/unitests_8/biobb_canal/sandbox_76f5f196-d9f5-4179-a4b8-575df25cec65\nINFO     /tmp/biobb/unitests_8/biobb_canal/biobb_canal_log.out:file_utils.py:409 Creating command line with instructions and required arguments\nINFO     /tmp/biobb/unitests_8/biobb_canal/biobb_canal_log.out:cmd_wrapper.py:63 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=.t.,\n  series=.t.,\n  corr=.t.,\n&amp;amp;end\ncurves_output.cda CGCGAATTCGCG\n!\n\nINFO     /tmp/biobb/unitests_8/biobb_canal/biobb_canal_log.out:cmd_wrapper.py:36 Executing: 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...\nINFO     /tmp/biobb/unitests_8/biobb_canal/biobb_canal_log.out:cmd_wrapper.py:37 Exit code: 0\nINFO     /tmp/biobb/unitests_8/biobb_canal/biobb_canal_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_8/biobb_canal/sandbox_76f5f196-d9f5-4179-a4b8-575df25cec65&amp;#x27;]\nINFO     /tmp/biobb/unitests_8/biobb_canal/biobb_canal_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_8\n&#34;}], &#34;biobb_dna/test/unitests/test_curvesplus/test_canal_unzip.py::TestCanalUnzip::test_canal_unzip&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_dna/test/unitests/test_curvesplus/test_canal_unzip.py::TestCanalUnzip::test_canal_unzip&#34;, &#34;duration&#34;: &#34;92 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_canal_unzip.py::TestCanalUnzip::test_canal_unzip&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;92 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 -----------------------------\n2024-11-04 11:05:01,233 [MainThread  ] [INFO ]  Module: biobb_dna.curvesplus.canal_unzip Version: 5.0.0\n2024-11-04 11:05:01,233 [MainThread  ] [INFO ]  /tmp/biobb/unitests_8/canal_unzip/sandbox_bfd9068a-bd18-4003-a03e-601b13efcd52 directory successfully created\n2024-11-04 11:05:01,264 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/curvesplus/canal_output.zip to /tmp/biobb/unitests_8/canal_unzip/sandbox_bfd9068a-bd18-4003-a03e-601b13efcd52\n2024-11-04 11:05:01,268 [MainThread  ] [INFO ]  canal_output_alphaC.his exists, copying into /tmp/biobb/unitests_8/canal_unzip/sandbox_bfd9068a-bd18-4003-a03e-601b13efcd52/canal_unzip_output.ser.\n2024-11-04 11:05:01,274 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_8/canal_unzip/sandbox_bfd9068a-bd18-4003-a03e-601b13efcd52&amp;#x27;]\n2024-11-04 11:05:01,274 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_8/canal_unzip/canal_unzip_output.ser\nChecking if empty file: /tmp/biobb/unitests_8/canal_unzip/canal_unzip_output.txt\nComparing: \n        File_A: /tmp/biobb/unitests_8/canal_unzip/canal_unzip_output.ser\n        File_B: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/reference/curvesplus/canal_unzip_output.ser\n        File_A hash: b&amp;#x27;\\r\\x84{\\xb8:rpBW\\xb4M\\x86\\xfd8I\\xfe\\xd3i\\x19CV_\\xd7\\x91\\xa5\\xf4\\xf4 \\xa6\\xed\\xc1\\xec&amp;#x27;\n        File_B hash: b&amp;#x27;\\r\\x84{\\xb8:rpBW\\xb4M\\x86\\xfd8I\\xfe\\xd3i\\x19CV_\\xd7\\x91\\xa5\\xf4\\xf4 \\xa6\\xed\\xc1\\xec&amp;#x27;\nComparing: \n        File_A: /tmp/biobb/unitests_8/canal_unzip/canal_unzip_output.txt\n        File_B: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/reference/curvesplus/canal_unzip_output.txt\n        File_A hash: b&amp;#x27;\\x00&amp;gt;\\x1f\\x86\\x87\\xae]^K\\t\\xa5\\x9a3\\x17\\xf1\\x91P\\x97O\\x04q\\xd6\\xd3d\\n\\xec4j\\x1d\\x1a\\x82\\xa5&amp;#x27;\n        File_B hash: b&amp;#x27;\\x00&amp;gt;\\x1f\\x86\\x87\\xae]^K\\t\\xa5\\x9a3\\x17\\xf1\\x91P\\x97O\\x04q\\xd6\\xd3d\\n\\xec4j\\x1d\\x1a\\x82\\xa5&amp;#x27;\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_8/canal_unzip/canal_unzip_log.out:file_utils.py:409 Module: biobb_dna.curvesplus.canal_unzip Version: 5.0.0\nINFO     /tmp/biobb/unitests_8/canal_unzip/canal_unzip_log.out:file_utils.py:82 /tmp/biobb/unitests_8/canal_unzip/sandbox_bfd9068a-bd18-4003-a03e-601b13efcd52 directory successfully created\nINFO     /tmp/biobb/unitests_8/canal_unzip/canal_unzip_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/curvesplus/canal_output.zip to /tmp/biobb/unitests_8/canal_unzip/sandbox_bfd9068a-bd18-4003-a03e-601b13efcd52\nINFO     /tmp/biobb/unitests_8/canal_unzip/canal_unzip_log.out:file_utils.py:409 canal_output_alphaC.his exists, copying into /tmp/biobb/unitests_8/canal_unzip/sandbox_bfd9068a-bd18-4003-a03e-601b13efcd52/canal_unzip_output.ser.\nINFO     /tmp/biobb/unitests_8/canal_unzip/canal_unzip_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_8/canal_unzip/sandbox_bfd9068a-bd18-4003-a03e-601b13efcd52&amp;#x27;]\nINFO     /tmp/biobb/unitests_8/canal_unzip/canal_unzip_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_8\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;373 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;373 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 -----------------------------\n2024-11-04 11:05:01,324 [MainThread  ] [INFO ]  Module: biobb_dna.curvesplus.biobb_canion Version: 5.0.0\n2024-11-04 11:05:01,324 [MainThread  ] [INFO ]  /tmp/biobb/unitests_8/biobb_canion/sandbox_a6847f49-6351-413b-ae2d-302936cab7b3 directory successfully created\n2024-11-04 11:05:01,593 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/curvesplus/THGA_K.cdi to /tmp/biobb/unitests_8/biobb_canion/sandbox_a6847f49-6351-413b-ae2d-302936cab7b3\n2024-11-04 11:05:01,593 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/curvesplus/THGA.afr to /tmp/biobb/unitests_8/biobb_canion/sandbox_a6847f49-6351-413b-ae2d-302936cab7b3\n2024-11-04 11:05:01,593 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/curvesplus/THGA_avg.pdb to /tmp/biobb/unitests_8/biobb_canion/sandbox_a6847f49-6351-413b-ae2d-302936cab7b3\n2024-11-04 11:05:01,594 [MainThread  ] [INFO ]  Creating command line with instructions and required arguments\n2024-11-04 11:05:01,594 [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  itst=0,\n  itnd=0,\n  itdel=1,\n  rmsf=.f.,\n  circ=.f.,\n&amp;amp;end\n!\n\n2024-11-04 11:05:01,605 [MainThread  ] [INFO ]  Executing: Canion &amp;lt;&amp;lt;! \n&amp;amp;inp\n  lis=canion_output,\n  dat=THGA_K,\n  axfrm=THGA,\n  solute=THGA_...\n2024-11-04 11:05:01,606 [MainThread  ] [INFO ]  Exit code: 0\n2024-11-04 11:05:01,648 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_8/biobb_canion/sandbox_a6847f49-6351-413b-ae2d-302936cab7b3&amp;#x27;]\n2024-11-04 11:05:01,648 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_8/biobb_canion/canion_output.zip\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_8/biobb_canion/biobb_canion_log.out:file_utils.py:409 Module: biobb_dna.curvesplus.biobb_canion Version: 5.0.0\nINFO     /tmp/biobb/unitests_8/biobb_canion/biobb_canion_log.out:file_utils.py:82 /tmp/biobb/unitests_8/biobb_canion/sandbox_a6847f49-6351-413b-ae2d-302936cab7b3 directory successfully created\nINFO     /tmp/biobb/unitests_8/biobb_canion/biobb_canion_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/curvesplus/THGA_K.cdi to /tmp/biobb/unitests_8/biobb_canion/sandbox_a6847f49-6351-413b-ae2d-302936cab7b3\nINFO     /tmp/biobb/unitests_8/biobb_canion/biobb_canion_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/curvesplus/THGA.afr to /tmp/biobb/unitests_8/biobb_canion/sandbox_a6847f49-6351-413b-ae2d-302936cab7b3\nINFO     /tmp/biobb/unitests_8/biobb_canion/biobb_canion_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/curvesplus/THGA_avg.pdb to /tmp/biobb/unitests_8/biobb_canion/sandbox_a6847f49-6351-413b-ae2d-302936cab7b3\nINFO     /tmp/biobb/unitests_8/biobb_canion/biobb_canion_log.out:file_utils.py:409 Creating command line with instructions and required arguments\nINFO     /tmp/biobb/unitests_8/biobb_canion/biobb_canion_log.out:cmd_wrapper.py:63 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  itst=0,\n  itnd=0,\n  itdel=1,\n  rmsf=.f.,\n  circ=.f.,\n&amp;amp;end\n!\n\nINFO     /tmp/biobb/unitests_8/biobb_canion/biobb_canion_log.out:cmd_wrapper.py:36 Executing: Canion &amp;lt;&amp;lt;! \n&amp;amp;inp\n  lis=canion_output,\n  dat=THGA_K,\n  axfrm=THGA,\n  solute=THGA_...\nINFO     /tmp/biobb/unitests_8/biobb_canion/biobb_canion_log.out:cmd_wrapper.py:37 Exit code: 0\nINFO     /tmp/biobb/unitests_8/biobb_canion/biobb_canion_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_8/biobb_canion/sandbox_a6847f49-6351-413b-ae2d-302936cab7b3&amp;#x27;]\nINFO     /tmp/biobb/unitests_8/biobb_canion/biobb_canion_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_8\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 -----------------------------\n2024-11-04 11:05:01,699 [MainThread  ] [INFO ]  Module: biobb_dna.curvesplus.biobb_curves Version: 5.0.0\n2024-11-04 11:05:01,700 [MainThread  ] [INFO ]  /tmp/biobb/unitests_8/biobb_curves/sandbox_0f93b7ef-0d24-4b1f-8467-78564a94c2bd directory successfully created\n2024-11-04 11:05:01,762 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/curvesplus/structure.stripped.trj to /tmp/biobb/unitests_8/biobb_curves/sandbox_0f93b7ef-0d24-4b1f-8467-78564a94c2bd\n2024-11-04 11:05:01,762 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/curvesplus/structure.stripped.top to /tmp/biobb/unitests_8/biobb_curves/sandbox_0f93b7ef-0d24-4b1f-8467-78564a94c2bd\n2024-11-04 11:05:01,763 [MainThread  ] [INFO ]  Appending provided topology to command\n2024-11-04 11:05:01,764 [MainThread  ] [INFO ]  Creating command line with instructions and required arguments\n2024-11-04 11:05:01,764 [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=.curvesplus/standard,\n  ions=.t.,\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\n2024-11-04 11:05:08,307 [MainThread  ] [INFO ]  Executing: Cur+ &amp;lt;&amp;lt;! \n&amp;amp;inp\n  file=structure.stripped.trj,\n  ftop=structure.stripped.top,\n  l...\n2024-11-04 11:05:08,307 [MainThread  ] [INFO ]  Exit code: 0\n2024-11-04 11:05:08,347 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_8/biobb_curves/sandbox_0f93b7ef-0d24-4b1f-8467-78564a94c2bd&amp;#x27;]\n2024-11-04 11:05:08,348 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_8/biobb_curves/curves_output.cda\nChecking if empty file: /tmp/biobb/unitests_8/biobb_curves/curves_output.lis\nChecking if empty file: /tmp/biobb/unitests_8/biobb_curves/curves_output.zip\nComparing ignoring lines containing this words: [2]\n     FILE_A: /tmp/biobb/unitests_8/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\nThis is a ZIP comparison!\nUnzipping:\nCreating a unique_dir for: /tmp/biobb/unitests_8/biobb_curves/curves_output.zip\nCreating a unique_dir for: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/reference/curvesplus/curves_trj_output.zip\nComparing: \n        File_A: 573988f9-3604-40e9-a4a8-1b1b97a6aed7/curves_output.cdi\n        File_B: a7b1c842-f506-4f8a-a23c-81368912b6b8/curves_output.cdi\n        File_A hash: b&amp;#x27;\\xbf\\x13\\x93\\xa0\\xc8\\xba\\x96\\xaa\\xd5sy\\xda\\x0f\\xe1m|\\xab\\xd4\\x9c z\\x9a\\x9d\\xde\\x07\\x7f\\xe3\\x1c\\x0cf_h&amp;#x27;\n        File_B hash: b&amp;#x27;\\xbf\\x13\\x93\\xa0\\xc8\\xba\\x96\\xaa\\xd5sy\\xda\\x0f\\xe1m|\\xab\\xd4\\x9c z\\x9a\\x9d\\xde\\x07\\x7f\\xe3\\x1c\\x0cf_h&amp;#x27;\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_8/biobb_curves/biobb_curves_log.out:file_utils.py:409 Module: biobb_dna.curvesplus.biobb_curves Version: 5.0.0\nINFO     /tmp/biobb/unitests_8/biobb_curves/biobb_curves_log.out:file_utils.py:82 /tmp/biobb/unitests_8/biobb_curves/sandbox_0f93b7ef-0d24-4b1f-8467-78564a94c2bd directory successfully created\nINFO     /tmp/biobb/unitests_8/biobb_curves/biobb_curves_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/curvesplus/structure.stripped.trj to /tmp/biobb/unitests_8/biobb_curves/sandbox_0f93b7ef-0d24-4b1f-8467-78564a94c2bd\nINFO     /tmp/biobb/unitests_8/biobb_curves/biobb_curves_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/curvesplus/structure.stripped.top to /tmp/biobb/unitests_8/biobb_curves/sandbox_0f93b7ef-0d24-4b1f-8467-78564a94c2bd\nINFO     /tmp/biobb/unitests_8/biobb_curves/biobb_curves_log.out:file_utils.py:409 Appending provided topology to command\nINFO     /tmp/biobb/unitests_8/biobb_curves/biobb_curves_log.out:file_utils.py:409 Creating command line with instructions and required arguments\nINFO     /tmp/biobb/unitests_8/biobb_curves/biobb_curves_log.out:cmd_wrapper.py:63 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=.curvesplus/standard,\n  ions=.t.,\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_8/biobb_curves/biobb_curves_log.out:cmd_wrapper.py:36 Executing: Cur+ &amp;lt;&amp;lt;! \n&amp;amp;inp\n  file=structure.stripped.trj,\n  ftop=structure.stripped.top,\n  l...\nINFO     /tmp/biobb/unitests_8/biobb_curves/biobb_curves_log.out:cmd_wrapper.py:37 Exit code: 0\nINFO     /tmp/biobb/unitests_8/biobb_curves/biobb_curves_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_8/biobb_curves/sandbox_0f93b7ef-0d24-4b1f-8467-78564a94c2bd&amp;#x27;]\nINFO     /tmp/biobb/unitests_8/biobb_curves/biobb_curves_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_8\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;332 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;332 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 -----------------------------\n2024-11-04 11:05:08,450 [MainThread  ] [INFO ]  Module: biobb_dna.dna.dna_averages Version: 5.0.0\n2024-11-04 11:05:08,450 [MainThread  ] [INFO ]  /tmp/biobb/unitests_8/dna_averages/sandbox_81b05254-f650-4a0b-9143-2667cac3de3a directory successfully created\n2024-11-04 11:05:08,451 [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_8/dna_averages/sandbox_81b05254-f650-4a0b-9143-2667cac3de3a\n2024-11-04 11:05:08,702 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_8/dna_averages/sandbox_81b05254-f650-4a0b-9143-2667cac3de3a&amp;#x27;]\n2024-11-04 11:05:08,703 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_8/dna_averages/avg_out.csv\nChecking if empty file: /tmp/biobb/unitests_8/dna_averages/avg_out.jpg\nComparing images of both files:\n     IMAGE_A: /tmp/biobb/unitests_8/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_8/dna_averages/dna_averages_log.out:file_utils.py:409 Module: biobb_dna.dna.dna_averages Version: 5.0.0\nINFO     /tmp/biobb/unitests_8/dna_averages/dna_averages_log.out:file_utils.py:82 /tmp/biobb/unitests_8/dna_averages/sandbox_81b05254-f650-4a0b-9143-2667cac3de3a directory successfully created\nINFO     /tmp/biobb/unitests_8/dna_averages/dna_averages_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/dna/canal_output_shift.ser to /tmp/biobb/unitests_8/dna_averages/sandbox_81b05254-f650-4a0b-9143-2667cac3de3a\nINFO     /tmp/biobb/unitests_8/dna_averages/dna_averages_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_8/dna_averages/sandbox_81b05254-f650-4a0b-9143-2667cac3de3a&amp;#x27;]\nINFO     /tmp/biobb/unitests_8/dna_averages/dna_averages_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_8\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;592 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;592 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 -----------------------------\n2024-11-04 11:05:08,783 [MainThread  ] [INFO ]  Module: biobb_dna.dna.dna_bimodality Version: 5.0.0\n2024-11-04 11:05:08,783 [MainThread  ] [INFO ]  /tmp/biobb/unitests_8/dna_bimodality/sandbox_f7e07aaf-536a-4fe3-a9dd-a5d930e1f72b directory successfully created\n2024-11-04 11:05:08,783 [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_8/dna_bimodality/sandbox_f7e07aaf-536a-4fe3-a9dd-a5d930e1f72b\n2024-11-04 11:05:09,328 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_8/dna_bimodality/sandbox_f7e07aaf-536a-4fe3-a9dd-a5d930e1f72b&amp;#x27;]\n2024-11-04 11:05:09,328 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_8/dna_bimodality/bimod_out.csv\nChecking if empty file: /tmp/biobb/unitests_8/dna_bimodality/bimod_out.jpg\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_8/dna_bimodality/dna_bimodality_log.out:file_utils.py:409 Module: biobb_dna.dna.dna_bimodality Version: 5.0.0\nINFO     /tmp/biobb/unitests_8/dna_bimodality/dna_bimodality_log.out:file_utils.py:82 /tmp/biobb/unitests_8/dna_bimodality/sandbox_f7e07aaf-536a-4fe3-a9dd-a5d930e1f72b directory successfully created\nINFO     /tmp/biobb/unitests_8/dna_bimodality/dna_bimodality_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/dna/series_shift_AT.csv to /tmp/biobb/unitests_8/dna_bimodality/sandbox_f7e07aaf-536a-4fe3-a9dd-a5d930e1f72b\nINFO     /tmp/biobb/unitests_8/dna_bimodality/dna_bimodality_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_8/dna_bimodality/sandbox_f7e07aaf-536a-4fe3-a9dd-a5d930e1f72b&amp;#x27;]\nINFO     /tmp/biobb/unitests_8/dna_bimodality/dna_bimodality_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_8\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 -----------------------------\n2024-11-04 11:05:09,378 [MainThread  ] [INFO ]  Module: biobb_dna.dna.dna_timeseries Version: 5.0.0\n2024-11-04 11:05:09,378 [MainThread  ] [INFO ]  /tmp/biobb/unitests_8/dna_timeseries/sandbox_4d47a45b-89b2-42fa-b6f8-92417b52f313 directory successfully created\n2024-11-04 11:05:09,379 [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_8/dna_timeseries/sandbox_4d47a45b-89b2-42fa-b6f8-92417b52f313\n2024-11-04 11:05:13,715 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_8/dna_timeseries/sandbox_4d47a45b-89b2-42fa-b6f8-92417b52f313&amp;#x27;]\n2024-11-04 11:05:13,716 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_8/dna_timeseries/timeseries_output.zip\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_8/dna_timeseries/dna_timeseries_log.out:file_utils.py:409 Module: biobb_dna.dna.dna_timeseries Version: 5.0.0\nINFO     /tmp/biobb/unitests_8/dna_timeseries/dna_timeseries_log.out:file_utils.py:82 /tmp/biobb/unitests_8/dna_timeseries/sandbox_4d47a45b-89b2-42fa-b6f8-92417b52f313 directory successfully created\nINFO     /tmp/biobb/unitests_8/dna_timeseries/dna_timeseries_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/dna/canal_output_shift.ser to /tmp/biobb/unitests_8/dna_timeseries/sandbox_4d47a45b-89b2-42fa-b6f8-92417b52f313\nINFO     /tmp/biobb/unitests_8/dna_timeseries/dna_timeseries_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_8/dna_timeseries/sandbox_4d47a45b-89b2-42fa-b6f8-92417b52f313&amp;#x27;]\nINFO     /tmp/biobb/unitests_8/dna_timeseries/dna_timeseries_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_8\n&#34;}], &#34;biobb_dna/test/unitests/test_dna/test_timeseries_unzip.py::TestCanalUnzip::test_dna_timeseries_unzip&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_dna/test/unitests/test_dna/test_timeseries_unzip.py::TestCanalUnzip::test_dna_timeseries_unzip&#34;, &#34;duration&#34;: &#34;151 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_timeseries_unzip.py::TestCanalUnzip::test_dna_timeseries_unzip&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;151 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 -----------------------------\n2024-11-04 11:05:13,830 [MainThread  ] [INFO ]  Module: biobb_dna.dna.dna_timeseries_unzip Version: 5.0.0\n2024-11-04 11:05:13,831 [MainThread  ] [INFO ]  /tmp/biobb/unitests_8/dna_timeseries_unzip/sandbox_0b774c1c-14fb-48b3-8053-490d0118c122 directory successfully created\n2024-11-04 11:05:13,832 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/dna/timeseries_output.zip to /tmp/biobb/unitests_8/dna_timeseries_unzip/sandbox_0b774c1c-14fb-48b3-8053-490d0118c122\n2024-11-04 11:05:13,832 [MainThread  ] [INFO ]  hist_shift_5_AA.csv exists, copying into /tmp/biobb/unitests_8/dna_timeseries_unzip/sandbox_0b774c1c-14fb-48b3-8053-490d0118c122/dna_timeseries_unzip.csv.\n2024-11-04 11:05:13,833 [MainThread  ] [INFO ]  hist_shift_5_AA.jpg exists, copying into /tmp/biobb/unitests_8/dna_timeseries_unzip/sandbox_0b774c1c-14fb-48b3-8053-490d0118c122/dna_timeseries_unzip.jpg.\n2024-11-04 11:05:13,834 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_8/dna_timeseries_unzip/sandbox_0b774c1c-14fb-48b3-8053-490d0118c122&amp;#x27;]\n2024-11-04 11:05:13,834 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_8/dna_timeseries_unzip/dna_timeseries_unzip.csv\nChecking if empty file: /tmp/biobb/unitests_8/dna_timeseries_unzip/dna_timeseries_unzip.jpg\nChecking if empty file: /tmp/biobb/unitests_8/dna_timeseries_unzip/dna_timeseries_unzip.txt\nComparing: \n        File_A: /tmp/biobb/unitests_8/dna_timeseries_unzip/dna_timeseries_unzip.csv\n        File_B: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/reference/dna/dna_timeseries_unzip.csv\n        File_A hash: b&amp;#x27;2\\xf3\\xc2\\xe4\\x137\\xc2\\xfc\\x98\\xc6A\\xe1\\x14T\\xeb\\xb2k\\xad\\xd5\\xe7y\\tx\\xd5\\xa1R\\xd1\\xd6\\xac\\xd1v\\xa8&amp;#x27;\n        File_B hash: b&amp;#x27;2\\xf3\\xc2\\xe4\\x137\\xc2\\xfc\\x98\\xc6A\\xe1\\x14T\\xeb\\xb2k\\xad\\xd5\\xe7y\\tx\\xd5\\xa1R\\xd1\\xd6\\xac\\xd1v\\xa8&amp;#x27;\nComparing: \n        File_A: /tmp/biobb/unitests_8/dna_timeseries_unzip/dna_timeseries_unzip.txt\n        File_B: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/reference/dna/dna_timeseries_unzip.txt\n        File_A hash: b&amp;#x27;\\xe3\\xbc\\x13{\\xa6\\r\\x807]\\x87\\x14|u\\xc6\\xbe\\x9d\\xca\\x8bl\\x96\\x86Z\\xd7\\x973+@+\\x1a\\xe4[\\x1b&amp;#x27;\n        File_B hash: b&amp;#x27;\\xe3\\xbc\\x13{\\xa6\\r\\x807]\\x87\\x14|u\\xc6\\xbe\\x9d\\xca\\x8bl\\x96\\x86Z\\xd7\\x973+@+\\x1a\\xe4[\\x1b&amp;#x27;\nComparing images of both files:\n     IMAGE_A: /tmp/biobb/unitests_8/dna_timeseries_unzip/dna_timeseries_unzip.jpg\n     IMAGE_B: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/reference/dna/dna_timeseries_unzip.jpg\n     IMAGE_A HASH: fff7f7e7e3e3c3f7 SIZE: 64 bits\n     IMAGE_B HASH: fff7f7e7e3e3c3f7 SIZE: 64 bits\n     TOLERANCE: 1.0%, ABS TOLERANCE: 1 bits, DIFFERENCE: 0 bits\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_8/dna_timeseries_unzip/dna_timeseries_unzip_log.out:file_utils.py:409 Module: biobb_dna.dna.dna_timeseries_unzip Version: 5.0.0\nINFO     /tmp/biobb/unitests_8/dna_timeseries_unzip/dna_timeseries_unzip_log.out:file_utils.py:82 /tmp/biobb/unitests_8/dna_timeseries_unzip/sandbox_0b774c1c-14fb-48b3-8053-490d0118c122 directory successfully created\nINFO     /tmp/biobb/unitests_8/dna_timeseries_unzip/dna_timeseries_unzip_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/dna/timeseries_output.zip to /tmp/biobb/unitests_8/dna_timeseries_unzip/sandbox_0b774c1c-14fb-48b3-8053-490d0118c122\nINFO     /tmp/biobb/unitests_8/dna_timeseries_unzip/dna_timeseries_unzip_log.out:file_utils.py:409 hist_shift_5_AA.csv exists, copying into /tmp/biobb/unitests_8/dna_timeseries_unzip/sandbox_0b774c1c-14fb-48b3-8053-490d0118c122/dna_timeseries_unzip.csv.\nINFO     /tmp/biobb/unitests_8/dna_timeseries_unzip/dna_timeseries_unzip_log.out:file_utils.py:409 hist_shift_5_AA.jpg exists, copying into /tmp/biobb/unitests_8/dna_timeseries_unzip/sandbox_0b774c1c-14fb-48b3-8053-490d0118c122/dna_timeseries_unzip.jpg.\nINFO     /tmp/biobb/unitests_8/dna_timeseries_unzip/dna_timeseries_unzip_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_8/dna_timeseries_unzip/sandbox_0b774c1c-14fb-48b3-8053-490d0118c122&amp;#x27;]\nINFO     /tmp/biobb/unitests_8/dna_timeseries_unzip/dna_timeseries_unzip_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_8\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;262 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;262 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 -----------------------------\n2024-11-04 11:05:13,923 [MainThread  ] [INFO ]  Module: biobb_dna.stiffness.average_stiffness Version: 5.0.0\n2024-11-04 11:05:13,923 [MainThread  ] [INFO ]  /tmp/biobb/unitests_8/average_stiffness/sandbox_93778497-97b0-40f1-a183-dc3cc5c4319b directory successfully created\n2024-11-04 11:05:13,924 [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_8/average_stiffness/sandbox_93778497-97b0-40f1-a183-dc3cc5c4319b\n2024-11-04 11:05:14,099 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_8/average_stiffness/sandbox_93778497-97b0-40f1-a183-dc3cc5c4319b&amp;#x27;]\n2024-11-04 11:05:14,100 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_8/average_stiffness/avgstiff.csv\nChecking if empty file: /tmp/biobb/unitests_8/average_stiffness/avgstiff.jpg\nComparing images of both files:\n     IMAGE_A: /tmp/biobb/unitests_8/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_8/average_stiffness/average_stiffness_log.out:file_utils.py:409 Module: biobb_dna.stiffness.average_stiffness Version: 5.0.0\nINFO     /tmp/biobb/unitests_8/average_stiffness/average_stiffness_log.out:file_utils.py:82 /tmp/biobb/unitests_8/average_stiffness/sandbox_93778497-97b0-40f1-a183-dc3cc5c4319b directory successfully created\nINFO     /tmp/biobb/unitests_8/average_stiffness/average_stiffness_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/canal_output_roll.ser to /tmp/biobb/unitests_8/average_stiffness/sandbox_93778497-97b0-40f1-a183-dc3cc5c4319b\nINFO     /tmp/biobb/unitests_8/average_stiffness/average_stiffness_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_8/average_stiffness/sandbox_93778497-97b0-40f1-a183-dc3cc5c4319b&amp;#x27;]\nINFO     /tmp/biobb/unitests_8/average_stiffness/average_stiffness_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_8\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;270 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;270 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 -----------------------------\n2024-11-04 11:05:14,183 [MainThread  ] [INFO ]  Module: biobb_dna.stiffness.basepair_stiffness Version: 5.0.0\n2024-11-04 11:05:14,184 [MainThread  ] [INFO ]  /tmp/biobb/unitests_8/basepair_stiffness/sandbox_fed545aa-fa54-47ff-a293-07df77b5a092 directory successfully created\n2024-11-04 11:05:14,184 [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_8/basepair_stiffness/sandbox_fed545aa-fa54-47ff-a293-07df77b5a092\n2024-11-04 11:05:14,184 [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_8/basepair_stiffness/sandbox_fed545aa-fa54-47ff-a293-07df77b5a092\n2024-11-04 11:05:14,185 [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_8/basepair_stiffness/sandbox_fed545aa-fa54-47ff-a293-07df77b5a092\n2024-11-04 11:05:14,185 [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_8/basepair_stiffness/sandbox_fed545aa-fa54-47ff-a293-07df77b5a092\n2024-11-04 11:05:14,185 [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_8/basepair_stiffness/sandbox_fed545aa-fa54-47ff-a293-07df77b5a092\n2024-11-04 11:05:14,185 [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_8/basepair_stiffness/sandbox_fed545aa-fa54-47ff-a293-07df77b5a092\n2024-11-04 11:05:14,366 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_8/basepair_stiffness/bpstiff.csv\nChecking if empty file: /tmp/biobb/unitests_8/basepair_stiffness/bpstiff.jpg\nComparing images of both files:\n     IMAGE_A: /tmp/biobb/unitests_8/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_8/basepair_stiffness/basepair_stiffness_log.out:file_utils.py:409 Module: biobb_dna.stiffness.basepair_stiffness Version: 5.0.0\nINFO     /tmp/biobb/unitests_8/basepair_stiffness/basepair_stiffness_log.out:file_utils.py:82 /tmp/biobb/unitests_8/basepair_stiffness/sandbox_fed545aa-fa54-47ff-a293-07df77b5a092 directory successfully created\nINFO     /tmp/biobb/unitests_8/basepair_stiffness/basepair_stiffness_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_shift_AA.csv to /tmp/biobb/unitests_8/basepair_stiffness/sandbox_fed545aa-fa54-47ff-a293-07df77b5a092\nINFO     /tmp/biobb/unitests_8/basepair_stiffness/basepair_stiffness_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_slide_AA.csv to /tmp/biobb/unitests_8/basepair_stiffness/sandbox_fed545aa-fa54-47ff-a293-07df77b5a092\nINFO     /tmp/biobb/unitests_8/basepair_stiffness/basepair_stiffness_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_rise_AA.csv to /tmp/biobb/unitests_8/basepair_stiffness/sandbox_fed545aa-fa54-47ff-a293-07df77b5a092\nINFO     /tmp/biobb/unitests_8/basepair_stiffness/basepair_stiffness_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_tilt_AA.csv to /tmp/biobb/unitests_8/basepair_stiffness/sandbox_fed545aa-fa54-47ff-a293-07df77b5a092\nINFO     /tmp/biobb/unitests_8/basepair_stiffness/basepair_stiffness_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_roll_AA.csv to /tmp/biobb/unitests_8/basepair_stiffness/sandbox_fed545aa-fa54-47ff-a293-07df77b5a092\nINFO     /tmp/biobb/unitests_8/basepair_stiffness/basepair_stiffness_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_twist_AA.csv to /tmp/biobb/unitests_8/basepair_stiffness/sandbox_fed545aa-fa54-47ff-a293-07df77b5a092\nINFO     /tmp/biobb/unitests_8/basepair_stiffness/basepair_stiffness_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_8\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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/tmp/biobb/unitests_60/bipopulations/bipop.jpg\nComparing images of both files:\n     IMAGE_A: /tmp/biobb/unitests_60/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: ff8981818180c9ff SIZE: 64 bits\n     TOLERANCE: 1.0%, ABS TOLERANCE: 1 bits, DIFFERENCE: 1 bits\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_60/bipopulations/bipopulations_log.out:file_utils.py:409 Module: biobb_dna.backbone.bipopulations Version: 5.0.0\nINFO     /tmp/biobb/unitests_60/bipopulations/bipopulations_log.out:file_utils.py:82 /tmp/biobb/unitests_60/bipopulations/sandbox_510b4f1b-d4bd-4b6b-bfa9-68a28491c74e directory successfully created\nINFO     /tmp/biobb/unitests_60/bipopulations/bipopulations_log.out:file_utils.py:409 Copy: 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/tmp/biobb/unitests_60/bipopulations/sandbox_510b4f1b-d4bd-4b6b-bfa9-68a28491c74e\nINFO     /tmp/biobb/unitests_60/bipopulations/bipopulations_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_60/bipopulations/sandbox_510b4f1b-d4bd-4b6b-bfa9-68a28491c74e&amp;#x27;]\nINFO     /tmp/biobb/unitests_60/bipopulations/bipopulations_log.out:file_utils.py:409\n\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;458 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td 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/home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/backbone/canal_output_alphaW.ser to /tmp/biobb/unitests_61/canonicalag/sandbox_c95c4d45-b9d6-4549-906c-659744ba9af4\n2024-11-15 12:07:07,059 [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_61/canonicalag/sandbox_c95c4d45-b9d6-4549-906c-659744ba9af4\n2024-11-15 12:07:07,060 [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_61/canonicalag/sandbox_c95c4d45-b9d6-4549-906c-659744ba9af4\n2024-11-15 12:07:07,429 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_61/canonicalag/sandbox_c95c4d45-b9d6-4549-906c-659744ba9af4&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_61/canonicalag/canonag.csv\nChecking if empty file: /tmp/biobb/unitests_61/canonicalag/canonag.jpg\nComparing images of both files:\n     IMAGE_A: /tmp/biobb/unitests_61/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_61/canonicalag/canonicalag_log.out:file_utils.py:409 Module: biobb_dna.backbone.canonicalag Version: 5.0.0\nINFO     /tmp/biobb/unitests_61/canonicalag/canonicalag_log.out:file_utils.py:82 /tmp/biobb/unitests_61/canonicalag/sandbox_c95c4d45-b9d6-4549-906c-659744ba9af4 directory successfully created\nINFO     /tmp/biobb/unitests_61/canonicalag/canonicalag_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/backbone/canal_output_alphaC.ser to /tmp/biobb/unitests_61/canonicalag/sandbox_c95c4d45-b9d6-4549-906c-659744ba9af4\nINFO     /tmp/biobb/unitests_61/canonicalag/canonicalag_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/backbone/canal_output_alphaW.ser to /tmp/biobb/unitests_61/canonicalag/sandbox_c95c4d45-b9d6-4549-906c-659744ba9af4\nINFO     /tmp/biobb/unitests_61/canonicalag/canonicalag_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/backbone/canal_output_gammaC.ser to /tmp/biobb/unitests_61/canonicalag/sandbox_c95c4d45-b9d6-4549-906c-659744ba9af4\nINFO     /tmp/biobb/unitests_61/canonicalag/canonicalag_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/backbone/canal_output_gammaW.ser to /tmp/biobb/unitests_61/canonicalag/sandbox_c95c4d45-b9d6-4549-906c-659744ba9af4\nINFO     /tmp/biobb/unitests_61/canonicalag/canonicalag_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_61/canonicalag/sandbox_c95c4d45-b9d6-4549-906c-659744ba9af4&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_61\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;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_puckering.py::TestPuckering::test_puckering&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 -----------------------------\n2024-11-15 12:07:07,515 [MainThread  ] [INFO ]  Module: biobb_dna.backbone.puckering Version: 5.0.0\n2024-11-15 12:07:07,515 [MainThread  ] [INFO ]  /tmp/biobb/unitests_61/puckering/sandbox_030af9fb-fd0e-4d8b-9d95-89830c4c9ec1 directory successfully created\n2024-11-15 12:07:07,516 [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_61/puckering/sandbox_030af9fb-fd0e-4d8b-9d95-89830c4c9ec1\n2024-11-15 12:07:07,517 [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_61/puckering/sandbox_030af9fb-fd0e-4d8b-9d95-89830c4c9ec1\n2024-11-15 12:07:08,006 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_61/puckering/sandbox_030af9fb-fd0e-4d8b-9d95-89830c4c9ec1&amp;#x27;]\n2024-11-15 12:07:08,006 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_61/puckering/puckering.csv\nChecking if empty file: /tmp/biobb/unitests_61/puckering/puckering.jpg\nComparing images of both files:\n     IMAGE_A: /tmp/biobb/unitests_61/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: eb8181808081ffff SIZE: 64 bits\n     TOLERANCE: 20%, ABS TOLERANCE: 12.8 bits, DIFFERENCE: 0 bits\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_61/puckering/puckering_log.out:file_utils.py:409 Module: biobb_dna.backbone.puckering Version: 5.0.0\nINFO     /tmp/biobb/unitests_61/puckering/puckering_log.out:file_utils.py:82 /tmp/biobb/unitests_61/puckering/sandbox_030af9fb-fd0e-4d8b-9d95-89830c4c9ec1 directory successfully created\nINFO     /tmp/biobb/unitests_61/puckering/puckering_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/backbone/canal_output_phaseC.ser to /tmp/biobb/unitests_61/puckering/sandbox_030af9fb-fd0e-4d8b-9d95-89830c4c9ec1\nINFO     /tmp/biobb/unitests_61/puckering/puckering_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/backbone/canal_output_phaseW.ser to /tmp/biobb/unitests_61/puckering/sandbox_030af9fb-fd0e-4d8b-9d95-89830c4c9ec1\nINFO     /tmp/biobb/unitests_61/puckering/puckering_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_61/puckering/sandbox_030af9fb-fd0e-4d8b-9d95-89830c4c9ec1&amp;#x27;]\nINFO     /tmp/biobb/unitests_61/puckering/puckering_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_61\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;279 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;279 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 -----------------------------\n2024-11-15 12:07:08,096 [MainThread  ] [INFO ]  Module: biobb_dna.interbp_correlations.interhpcorr Version: 5.0.0\n2024-11-15 12:07:08,096 [MainThread  ] [INFO ]  /tmp/biobb/unitests_61/interhpcorr/sandbox_c2db5378-e448-4fcd-9ea8-1ce0d80d43ad directory successfully created\n2024-11-15 12:07:08,097 [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_61/interhpcorr/sandbox_c2db5378-e448-4fcd-9ea8-1ce0d80d43ad\n2024-11-15 12:07:08,097 [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_61/interhpcorr/sandbox_c2db5378-e448-4fcd-9ea8-1ce0d80d43ad\n2024-11-15 12:07:08,097 [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_61/interhpcorr/sandbox_c2db5378-e448-4fcd-9ea8-1ce0d80d43ad\n2024-11-15 12:07:08,098 [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_61/interhpcorr/sandbox_c2db5378-e448-4fcd-9ea8-1ce0d80d43ad\n2024-11-15 12:07:08,098 [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_61/interhpcorr/sandbox_c2db5378-e448-4fcd-9ea8-1ce0d80d43ad\n2024-11-15 12:07:08,098 [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_61/interhpcorr/sandbox_c2db5378-e448-4fcd-9ea8-1ce0d80d43ad\n2024-11-15 12:07:08,292 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_61/interhpcorr/sandbox_c2db5378-e448-4fcd-9ea8-1ce0d80d43ad&amp;#x27;]\n2024-11-15 12:07:08,292 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_61/interhpcorr/inter_hpcorr.csv\nChecking if empty file: /tmp/biobb/unitests_61/interhpcorr/inter_hpcorr.jpg\nComparing images of both files:\n     IMAGE_A: /tmp/biobb/unitests_61/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_61/interhpcorr/log.out:file_utils.py:409 Module: biobb_dna.interbp_correlations.interhpcorr Version: 5.0.0\nINFO     /tmp/biobb/unitests_61/interhpcorr/log.out:file_utils.py:82 /tmp/biobb/unitests_61/interhpcorr/sandbox_c2db5378-e448-4fcd-9ea8-1ce0d80d43ad directory successfully created\nINFO     /tmp/biobb/unitests_61/interhpcorr/log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_shift_AA.csv to /tmp/biobb/unitests_61/interhpcorr/sandbox_c2db5378-e448-4fcd-9ea8-1ce0d80d43ad\nINFO     /tmp/biobb/unitests_61/interhpcorr/log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_slide_AA.csv to /tmp/biobb/unitests_61/interhpcorr/sandbox_c2db5378-e448-4fcd-9ea8-1ce0d80d43ad\nINFO     /tmp/biobb/unitests_61/interhpcorr/log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_rise_AA.csv to /tmp/biobb/unitests_61/interhpcorr/sandbox_c2db5378-e448-4fcd-9ea8-1ce0d80d43ad\nINFO     /tmp/biobb/unitests_61/interhpcorr/log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_tilt_AA.csv to /tmp/biobb/unitests_61/interhpcorr/sandbox_c2db5378-e448-4fcd-9ea8-1ce0d80d43ad\nINFO     /tmp/biobb/unitests_61/interhpcorr/log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_roll_AA.csv to /tmp/biobb/unitests_61/interhpcorr/sandbox_c2db5378-e448-4fcd-9ea8-1ce0d80d43ad\nINFO     /tmp/biobb/unitests_61/interhpcorr/log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_twist_AA.csv to /tmp/biobb/unitests_61/interhpcorr/sandbox_c2db5378-e448-4fcd-9ea8-1ce0d80d43ad\nINFO     /tmp/biobb/unitests_61/interhpcorr/log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_61/interhpcorr/sandbox_c2db5378-e448-4fcd-9ea8-1ce0d80d43ad&amp;#x27;]\nINFO     /tmp/biobb/unitests_61/interhpcorr/log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_61\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;428 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;428 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 -----------------------------\n2024-11-15 12:07:08,378 [MainThread  ] [INFO ]  Module: biobb_dna.interbp_correlations.interseqcorr Version: 5.0.0\n2024-11-15 12:07:08,378 [MainThread  ] [INFO ]  /tmp/biobb/unitests_61/interseqcorr/sandbox_15a17657-a994-4e66-9124-c24a27d5be71 directory successfully created\n2024-11-15 12:07:08,379 [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_61/interseqcorr/sandbox_15a17657-a994-4e66-9124-c24a27d5be71\n2024-11-15 12:07:08,713 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_61/interseqcorr/sandbox_15a17657-a994-4e66-9124-c24a27d5be71&amp;#x27;]\n2024-11-15 12:07:08,713 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_61/interseqcorr/inter_seqcorr.csv\nChecking if empty file: /tmp/biobb/unitests_61/interseqcorr/inter_seqcorr.jpg\nComparing images of both files:\n     IMAGE_A: /tmp/biobb/unitests_61/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_61/interseqcorr/interseqcorr_log.out:file_utils.py:409 Module: biobb_dna.interbp_correlations.interseqcorr Version: 5.0.0\nINFO     /tmp/biobb/unitests_61/interseqcorr/interseqcorr_log.out:file_utils.py:82 /tmp/biobb/unitests_61/interseqcorr/sandbox_15a17657-a994-4e66-9124-c24a27d5be71 directory successfully created\nINFO     /tmp/biobb/unitests_61/interseqcorr/interseqcorr_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_roll.ser to /tmp/biobb/unitests_61/interseqcorr/sandbox_15a17657-a994-4e66-9124-c24a27d5be71\nINFO     /tmp/biobb/unitests_61/interseqcorr/interseqcorr_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_61/interseqcorr/sandbox_15a17657-a994-4e66-9124-c24a27d5be71&amp;#x27;]\nINFO     /tmp/biobb/unitests_61/interseqcorr/interseqcorr_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_61\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;857 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;857 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 -----------------------------\n2024-11-15 12:07:08,804 [MainThread  ] [INFO ]  Module: biobb_dna.interbp_correlations.interbpcorr Version: 5.0.0\n2024-11-15 12:07:08,805 [MainThread  ] [INFO ]  /tmp/biobb/unitests_61/interbpcorr/sandbox_6630e7ef-966c-4a34-bf80-8e313a6f127d directory successfully created\n2024-11-15 12:07:08,805 [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_61/interbpcorr/sandbox_6630e7ef-966c-4a34-bf80-8e313a6f127d\n2024-11-15 12:07:08,806 [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_61/interbpcorr/sandbox_6630e7ef-966c-4a34-bf80-8e313a6f127d\n2024-11-15 12:07:08,807 [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_61/interbpcorr/sandbox_6630e7ef-966c-4a34-bf80-8e313a6f127d\n2024-11-15 12:07:08,807 [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_61/interbpcorr/sandbox_6630e7ef-966c-4a34-bf80-8e313a6f127d\n2024-11-15 12:07:08,808 [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_61/interbpcorr/sandbox_6630e7ef-966c-4a34-bf80-8e313a6f127d\n2024-11-15 12:07:08,809 [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_61/interbpcorr/sandbox_6630e7ef-966c-4a34-bf80-8e313a6f127d\n2024-11-15 12:07:09,572 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_61/interbpcorr/sandbox_6630e7ef-966c-4a34-bf80-8e313a6f127d&amp;#x27;]\n2024-11-15 12:07:09,573 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_61/interbpcorr/inter_bpcorr.csv\nChecking if empty file: /tmp/biobb/unitests_61/interbpcorr/inter_bpcorr.jpg\nComparing images of both files:\n     IMAGE_A: /tmp/biobb/unitests_61/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_61/interbpcorr/interbpcorr_log.out:file_utils.py:409 Module: biobb_dna.interbp_correlations.interbpcorr Version: 5.0.0\nINFO     /tmp/biobb/unitests_61/interbpcorr/interbpcorr_log.out:file_utils.py:82 /tmp/biobb/unitests_61/interbpcorr/sandbox_6630e7ef-966c-4a34-bf80-8e313a6f127d directory successfully created\nINFO     /tmp/biobb/unitests_61/interbpcorr/interbpcorr_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_shift.ser to /tmp/biobb/unitests_61/interbpcorr/sandbox_6630e7ef-966c-4a34-bf80-8e313a6f127d\nINFO     /tmp/biobb/unitests_61/interbpcorr/interbpcorr_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_slide.ser to /tmp/biobb/unitests_61/interbpcorr/sandbox_6630e7ef-966c-4a34-bf80-8e313a6f127d\nINFO     /tmp/biobb/unitests_61/interbpcorr/interbpcorr_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_rise.ser to /tmp/biobb/unitests_61/interbpcorr/sandbox_6630e7ef-966c-4a34-bf80-8e313a6f127d\nINFO     /tmp/biobb/unitests_61/interbpcorr/interbpcorr_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_tilt.ser to /tmp/biobb/unitests_61/interbpcorr/sandbox_6630e7ef-966c-4a34-bf80-8e313a6f127d\nINFO     /tmp/biobb/unitests_61/interbpcorr/interbpcorr_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_roll.ser to /tmp/biobb/unitests_61/interbpcorr/sandbox_6630e7ef-966c-4a34-bf80-8e313a6f127d\nINFO     /tmp/biobb/unitests_61/interbpcorr/interbpcorr_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_twist.ser to /tmp/biobb/unitests_61/interbpcorr/sandbox_6630e7ef-966c-4a34-bf80-8e313a6f127d\nINFO     /tmp/biobb/unitests_61/interbpcorr/interbpcorr_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_61/interbpcorr/sandbox_6630e7ef-966c-4a34-bf80-8e313a6f127d&amp;#x27;]\nINFO     /tmp/biobb/unitests_61/interbpcorr/interbpcorr_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_61\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;277 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;277 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 -----------------------------\n2024-11-15 12:07:09,663 [MainThread  ] [INFO ]  Module: biobb_dna.intrabp_correlations.intrahpcorr Version: 5.0.0\n2024-11-15 12:07:09,663 [MainThread  ] [INFO ]  /tmp/biobb/unitests_61/intrahpcorr/sandbox_e19deb03-bc0e-438e-9652-155c53815d06 directory successfully created\n2024-11-15 12:07:09,663 [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_61/intrahpcorr/sandbox_e19deb03-bc0e-438e-9652-155c53815d06\n2024-11-15 12:07:09,664 [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_61/intrahpcorr/sandbox_e19deb03-bc0e-438e-9652-155c53815d06\n2024-11-15 12:07:09,664 [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_61/intrahpcorr/sandbox_e19deb03-bc0e-438e-9652-155c53815d06\n2024-11-15 12:07:09,664 [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_61/intrahpcorr/sandbox_e19deb03-bc0e-438e-9652-155c53815d06\n2024-11-15 12:07:09,665 [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_61/intrahpcorr/sandbox_e19deb03-bc0e-438e-9652-155c53815d06\n2024-11-15 12:07:09,665 [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_61/intrahpcorr/sandbox_e19deb03-bc0e-438e-9652-155c53815d06\n2024-11-15 12:07:09,859 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_61/intrahpcorr/sandbox_e19deb03-bc0e-438e-9652-155c53815d06&amp;#x27;]\n2024-11-15 12:07:09,860 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_61/intrahpcorr/intra_hpcorr.csv\nChecking if empty file: /tmp/biobb/unitests_61/intrahpcorr/intra_hpcorr.jpg\nComparing images of both files:\n     IMAGE_A: /tmp/biobb/unitests_61/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_61/intrahpcorr/log.out:file_utils.py:409 Module: biobb_dna.intrabp_correlations.intrahpcorr Version: 5.0.0\nINFO     /tmp/biobb/unitests_61/intrahpcorr/log.out:file_utils.py:82 /tmp/biobb/unitests_61/intrahpcorr/sandbox_e19deb03-bc0e-438e-9652-155c53815d06 directory successfully created\nINFO     /tmp/biobb/unitests_61/intrahpcorr/log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/series_shear_A.csv to /tmp/biobb/unitests_61/intrahpcorr/sandbox_e19deb03-bc0e-438e-9652-155c53815d06\nINFO     /tmp/biobb/unitests_61/intrahpcorr/log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/series_stretch_A.csv to /tmp/biobb/unitests_61/intrahpcorr/sandbox_e19deb03-bc0e-438e-9652-155c53815d06\nINFO     /tmp/biobb/unitests_61/intrahpcorr/log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/series_stagger_A.csv to /tmp/biobb/unitests_61/intrahpcorr/sandbox_e19deb03-bc0e-438e-9652-155c53815d06\nINFO     /tmp/biobb/unitests_61/intrahpcorr/log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/series_buckle_A.csv to /tmp/biobb/unitests_61/intrahpcorr/sandbox_e19deb03-bc0e-438e-9652-155c53815d06\nINFO     /tmp/biobb/unitests_61/intrahpcorr/log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/series_propel_A.csv to /tmp/biobb/unitests_61/intrahpcorr/sandbox_e19deb03-bc0e-438e-9652-155c53815d06\nINFO     /tmp/biobb/unitests_61/intrahpcorr/log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/series_opening_A.csv to /tmp/biobb/unitests_61/intrahpcorr/sandbox_e19deb03-bc0e-438e-9652-155c53815d06\nINFO     /tmp/biobb/unitests_61/intrahpcorr/log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_61/intrahpcorr/sandbox_e19deb03-bc0e-438e-9652-155c53815d06&amp;#x27;]\nINFO     /tmp/biobb/unitests_61/intrahpcorr/log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_61\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;351 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;351 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 -----------------------------\n2024-11-15 12:07:09,942 [MainThread  ] [INFO ]  Module: biobb_dna.intrabp_correlations.intraseqcorr Version: 5.0.0\n2024-11-15 12:07:09,942 [MainThread  ] [INFO ]  /tmp/biobb/unitests_61/intraseqcorr/sandbox_7e1d0568-3fdc-4a01-9230-5942cb45a3e3 directory successfully created\n2024-11-15 12:07:09,943 [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_61/intraseqcorr/sandbox_7e1d0568-3fdc-4a01-9230-5942cb45a3e3\n2024-11-15 12:07:10,211 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_61/intraseqcorr/sandbox_7e1d0568-3fdc-4a01-9230-5942cb45a3e3&amp;#x27;]\n2024-11-15 12:07:10,212 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_61/intraseqcorr/intra_seqcorr.csv\nChecking if empty file: /tmp/biobb/unitests_61/intraseqcorr/intra_seqcorr.jpg\nComparing images of both files:\n     IMAGE_A: /tmp/biobb/unitests_61/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_61/intraseqcorr/intraseqcorr_log.out:file_utils.py:409 Module: biobb_dna.intrabp_correlations.intraseqcorr Version: 5.0.0\nINFO     /tmp/biobb/unitests_61/intraseqcorr/intraseqcorr_log.out:file_utils.py:82 /tmp/biobb/unitests_61/intraseqcorr/sandbox_7e1d0568-3fdc-4a01-9230-5942cb45a3e3 directory successfully created\nINFO     /tmp/biobb/unitests_61/intraseqcorr/intraseqcorr_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_buckle.ser to /tmp/biobb/unitests_61/intraseqcorr/sandbox_7e1d0568-3fdc-4a01-9230-5942cb45a3e3\nINFO     /tmp/biobb/unitests_61/intraseqcorr/intraseqcorr_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_61/intraseqcorr/sandbox_7e1d0568-3fdc-4a01-9230-5942cb45a3e3&amp;#x27;]\nINFO     /tmp/biobb/unitests_61/intraseqcorr/intraseqcorr_log.out:file_utils.py:409\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;859 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::TestIntraBasepairCorrelation::test_basepaircorrelation&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;859 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 -----------------------------\n2024-11-15 12:07:10,294 [MainThread  ] [INFO ]  Module: biobb_dna.intrabp_correlations.intrabpcorr Version: 5.0.0\n2024-11-15 12:07:10,294 [MainThread  ] [INFO ]  /tmp/biobb/unitests_62/intrabpcorr/sandbox_72585158-5797-43d0-8d16-4c7330ed2557 directory successfully created\n2024-11-15 12:07:10,295 [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_62/intrabpcorr/sandbox_72585158-5797-43d0-8d16-4c7330ed2557\n2024-11-15 12:07:10,296 [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_62/intrabpcorr/sandbox_72585158-5797-43d0-8d16-4c7330ed2557\n2024-11-15 12:07:10,297 [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_62/intrabpcorr/sandbox_72585158-5797-43d0-8d16-4c7330ed2557\n2024-11-15 12:07:10,297 [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_62/intrabpcorr/sandbox_72585158-5797-43d0-8d16-4c7330ed2557\n2024-11-15 12:07:10,298 [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_62/intrabpcorr/sandbox_72585158-5797-43d0-8d16-4c7330ed2557\n2024-11-15 12:07:10,299 [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_62/intrabpcorr/sandbox_72585158-5797-43d0-8d16-4c7330ed2557\n2024-11-15 12:07:11,061 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_62/intrabpcorr/sandbox_72585158-5797-43d0-8d16-4c7330ed2557&amp;#x27;]\n2024-11-15 12:07:11,062 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_62/intrabpcorr/intra_bpcorr.csv\nChecking if empty file: /tmp/biobb/unitests_62/intrabpcorr/intra_bpcorr.jpg\nComparing images of both files:\n     IMAGE_A: /tmp/biobb/unitests_62/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_62/intrabpcorr/intrabpcorr_log.out:file_utils.py:409 Module: biobb_dna.intrabp_correlations.intrabpcorr Version: 5.0.0\nINFO     /tmp/biobb/unitests_62/intrabpcorr/intrabpcorr_log.out:file_utils.py:82 /tmp/biobb/unitests_62/intrabpcorr/sandbox_72585158-5797-43d0-8d16-4c7330ed2557 directory successfully created\nINFO     /tmp/biobb/unitests_62/intrabpcorr/intrabpcorr_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_shear.ser to /tmp/biobb/unitests_62/intrabpcorr/sandbox_72585158-5797-43d0-8d16-4c7330ed2557\nINFO     /tmp/biobb/unitests_62/intrabpcorr/intrabpcorr_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_stretch.ser to /tmp/biobb/unitests_62/intrabpcorr/sandbox_72585158-5797-43d0-8d16-4c7330ed2557\nINFO     /tmp/biobb/unitests_62/intrabpcorr/intrabpcorr_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_stagger.ser to /tmp/biobb/unitests_62/intrabpcorr/sandbox_72585158-5797-43d0-8d16-4c7330ed2557\nINFO     /tmp/biobb/unitests_62/intrabpcorr/intrabpcorr_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_buckle.ser to /tmp/biobb/unitests_62/intrabpcorr/sandbox_72585158-5797-43d0-8d16-4c7330ed2557\nINFO     /tmp/biobb/unitests_62/intrabpcorr/intrabpcorr_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_propel.ser to /tmp/biobb/unitests_62/intrabpcorr/sandbox_72585158-5797-43d0-8d16-4c7330ed2557\nINFO     /tmp/biobb/unitests_62/intrabpcorr/intrabpcorr_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_opening.ser to /tmp/biobb/unitests_62/intrabpcorr/sandbox_72585158-5797-43d0-8d16-4c7330ed2557\nINFO     /tmp/biobb/unitests_62/intrabpcorr/intrabpcorr_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_62/intrabpcorr/sandbox_72585158-5797-43d0-8d16-4c7330ed2557&amp;#x27;]\nINFO     /tmp/biobb/unitests_62/intrabpcorr/intrabpcorr_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_62\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;00:00:07&#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_canal.py::TestCanal::test_canal&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 -----------------------------\n2024-11-15 12:07:11,157 [MainThread  ] [INFO ]  Module: biobb_dna.curvesplus.biobb_canal Version: 5.0.0\n2024-11-15 12:07:11,157 [MainThread  ] [INFO ]  /tmp/biobb/unitests_62/biobb_canal/sandbox_8cf46469-9b91-49d4-b0d8-a29e4b7e87ad directory successfully created\n2024-11-15 12:07:11,169 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/curvesplus/curves_output.cda to /tmp/biobb/unitests_62/biobb_canal/sandbox_8cf46469-9b91-49d4-b0d8-a29e4b7e87ad\n2024-11-15 12:07:11,169 [MainThread  ] [INFO ]  Creating command line with instructions and required arguments\n2024-11-15 12:07:11,169 [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=.t.,\n  series=.t.,\n  corr=.t.,\n&amp;amp;end\ncurves_output.cda CGCGAATTCGCG\n!\n\n2024-11-15 12:07:18,151 [MainThread  ] [INFO ]  Executing: 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...\n2024-11-15 12:07:18,151 [MainThread  ] [INFO ]  Exit code: 0\n2024-11-15 12:07:18,302 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_62/biobb_canal/sandbox_8cf46469-9b91-49d4-b0d8-a29e4b7e87ad&amp;#x27;]\n2024-11-15 12:07:18,303 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_62/biobb_canal/canal_output.zip\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_62/biobb_canal/biobb_canal_log.out:file_utils.py:409 Module: biobb_dna.curvesplus.biobb_canal Version: 5.0.0\nINFO     /tmp/biobb/unitests_62/biobb_canal/biobb_canal_log.out:file_utils.py:82 /tmp/biobb/unitests_62/biobb_canal/sandbox_8cf46469-9b91-49d4-b0d8-a29e4b7e87ad directory successfully created\nINFO     /tmp/biobb/unitests_62/biobb_canal/biobb_canal_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/curvesplus/curves_output.cda to /tmp/biobb/unitests_62/biobb_canal/sandbox_8cf46469-9b91-49d4-b0d8-a29e4b7e87ad\nINFO     /tmp/biobb/unitests_62/biobb_canal/biobb_canal_log.out:file_utils.py:409 Creating command line with instructions and required arguments\nINFO     /tmp/biobb/unitests_62/biobb_canal/biobb_canal_log.out:cmd_wrapper.py:63 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=.t.,\n  series=.t.,\n  corr=.t.,\n&amp;amp;end\ncurves_output.cda CGCGAATTCGCG\n!\n\nINFO     /tmp/biobb/unitests_62/biobb_canal/biobb_canal_log.out:cmd_wrapper.py:36 Executing: 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...\nINFO     /tmp/biobb/unitests_62/biobb_canal/biobb_canal_log.out:cmd_wrapper.py:37 Exit code: 0\nINFO     /tmp/biobb/unitests_62/biobb_canal/biobb_canal_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_62/biobb_canal/sandbox_8cf46469-9b91-49d4-b0d8-a29e4b7e87ad&amp;#x27;]\nINFO     /tmp/biobb/unitests_62/biobb_canal/biobb_canal_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_62\n&#34;}], &#34;biobb_dna/test/unitests/test_curvesplus/test_canal_unzip.py::TestCanalUnzip::test_canal_unzip&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_dna/test/unitests/test_curvesplus/test_canal_unzip.py::TestCanalUnzip::test_canal_unzip&#34;, &#34;duration&#34;: &#34;86 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_canal_unzip.py::TestCanalUnzip::test_canal_unzip&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;86 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 -----------------------------\n2024-11-15 12:07:18,356 [MainThread  ] [INFO ]  Module: biobb_dna.curvesplus.canal_unzip Version: 5.0.0\n2024-11-15 12:07:18,356 [MainThread  ] [INFO ]  /tmp/biobb/unitests_62/canal_unzip/sandbox_744acb21-4e0c-4a03-af97-ed834d6f89d6 directory successfully created\n2024-11-15 12:07:18,385 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/curvesplus/canal_output.zip to /tmp/biobb/unitests_62/canal_unzip/sandbox_744acb21-4e0c-4a03-af97-ed834d6f89d6\n2024-11-15 12:07:18,388 [MainThread  ] [INFO ]  canal_output_alphaC.his exists, copying into /tmp/biobb/unitests_62/canal_unzip/sandbox_744acb21-4e0c-4a03-af97-ed834d6f89d6/canal_unzip_output.ser.\n2024-11-15 12:07:18,394 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_62/canal_unzip/sandbox_744acb21-4e0c-4a03-af97-ed834d6f89d6&amp;#x27;]\n2024-11-15 12:07:18,394 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_62/canal_unzip/canal_unzip_output.ser\nChecking if empty file: /tmp/biobb/unitests_62/canal_unzip/canal_unzip_output.txt\nComparing: \n        File_A: /tmp/biobb/unitests_62/canal_unzip/canal_unzip_output.ser\n        File_B: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/reference/curvesplus/canal_unzip_output.ser\n        File_A hash: b&amp;#x27;\\r\\x84{\\xb8:rpBW\\xb4M\\x86\\xfd8I\\xfe\\xd3i\\x19CV_\\xd7\\x91\\xa5\\xf4\\xf4 \\xa6\\xed\\xc1\\xec&amp;#x27;\n        File_B hash: b&amp;#x27;\\r\\x84{\\xb8:rpBW\\xb4M\\x86\\xfd8I\\xfe\\xd3i\\x19CV_\\xd7\\x91\\xa5\\xf4\\xf4 \\xa6\\xed\\xc1\\xec&amp;#x27;\nComparing: \n        File_A: /tmp/biobb/unitests_62/canal_unzip/canal_unzip_output.txt\n        File_B: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/reference/curvesplus/canal_unzip_output.txt\n        File_A hash: b&amp;#x27;\\x00&amp;gt;\\x1f\\x86\\x87\\xae]^K\\t\\xa5\\x9a3\\x17\\xf1\\x91P\\x97O\\x04q\\xd6\\xd3d\\n\\xec4j\\x1d\\x1a\\x82\\xa5&amp;#x27;\n        File_B hash: b&amp;#x27;\\x00&amp;gt;\\x1f\\x86\\x87\\xae]^K\\t\\xa5\\x9a3\\x17\\xf1\\x91P\\x97O\\x04q\\xd6\\xd3d\\n\\xec4j\\x1d\\x1a\\x82\\xa5&amp;#x27;\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_62/canal_unzip/canal_unzip_log.out:file_utils.py:409 Module: biobb_dna.curvesplus.canal_unzip Version: 5.0.0\nINFO     /tmp/biobb/unitests_62/canal_unzip/canal_unzip_log.out:file_utils.py:82 /tmp/biobb/unitests_62/canal_unzip/sandbox_744acb21-4e0c-4a03-af97-ed834d6f89d6 directory successfully created\nINFO     /tmp/biobb/unitests_62/canal_unzip/canal_unzip_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/curvesplus/canal_output.zip to /tmp/biobb/unitests_62/canal_unzip/sandbox_744acb21-4e0c-4a03-af97-ed834d6f89d6\nINFO     /tmp/biobb/unitests_62/canal_unzip/canal_unzip_log.out:file_utils.py:409 canal_output_alphaC.his exists, copying into /tmp/biobb/unitests_62/canal_unzip/sandbox_744acb21-4e0c-4a03-af97-ed834d6f89d6/canal_unzip_output.ser.\nINFO     /tmp/biobb/unitests_62/canal_unzip/canal_unzip_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_62/canal_unzip/sandbox_744acb21-4e0c-4a03-af97-ed834d6f89d6&amp;#x27;]\nINFO     /tmp/biobb/unitests_62/canal_unzip/canal_unzip_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_62\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;374 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;374 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 -----------------------------\n2024-11-15 12:07:18,446 [MainThread  ] [INFO ]  Module: biobb_dna.curvesplus.biobb_canion Version: 5.0.0\n2024-11-15 12:07:18,447 [MainThread  ] [INFO ]  /tmp/biobb/unitests_62/biobb_canion/sandbox_dbdc0404-9caa-4d5b-9fa8-44ad34a62c3a directory successfully created\n2024-11-15 12:07:18,722 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/curvesplus/THGA_K.cdi to /tmp/biobb/unitests_62/biobb_canion/sandbox_dbdc0404-9caa-4d5b-9fa8-44ad34a62c3a\n2024-11-15 12:07:18,722 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/curvesplus/THGA.afr to /tmp/biobb/unitests_62/biobb_canion/sandbox_dbdc0404-9caa-4d5b-9fa8-44ad34a62c3a\n2024-11-15 12:07:18,723 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/curvesplus/THGA_avg.pdb to /tmp/biobb/unitests_62/biobb_canion/sandbox_dbdc0404-9caa-4d5b-9fa8-44ad34a62c3a\n2024-11-15 12:07:18,723 [MainThread  ] [INFO ]  Creating command line with instructions and required arguments\n2024-11-15 12:07:18,723 [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  itst=0,\n  itnd=0,\n  itdel=1,\n  rmsf=.f.,\n  circ=.f.,\n&amp;amp;end\n!\n\n2024-11-15 12:07:18,729 [MainThread  ] [INFO ]  Executing: Canion &amp;lt;&amp;lt;! \n&amp;amp;inp\n  lis=canion_output,\n  dat=THGA_K,\n  axfrm=THGA,\n  solute=THGA_...\n2024-11-15 12:07:18,729 [MainThread  ] [INFO ]  Exit code: 0\n2024-11-15 12:07:18,771 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_62/biobb_canion/sandbox_dbdc0404-9caa-4d5b-9fa8-44ad34a62c3a&amp;#x27;]\n2024-11-15 12:07:18,772 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_62/biobb_canion/canion_output.zip\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_62/biobb_canion/biobb_canion_log.out:file_utils.py:409 Module: biobb_dna.curvesplus.biobb_canion Version: 5.0.0\nINFO     /tmp/biobb/unitests_62/biobb_canion/biobb_canion_log.out:file_utils.py:82 /tmp/biobb/unitests_62/biobb_canion/sandbox_dbdc0404-9caa-4d5b-9fa8-44ad34a62c3a directory successfully created\nINFO     /tmp/biobb/unitests_62/biobb_canion/biobb_canion_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/curvesplus/THGA_K.cdi to /tmp/biobb/unitests_62/biobb_canion/sandbox_dbdc0404-9caa-4d5b-9fa8-44ad34a62c3a\nINFO     /tmp/biobb/unitests_62/biobb_canion/biobb_canion_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/curvesplus/THGA.afr to /tmp/biobb/unitests_62/biobb_canion/sandbox_dbdc0404-9caa-4d5b-9fa8-44ad34a62c3a\nINFO     /tmp/biobb/unitests_62/biobb_canion/biobb_canion_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/curvesplus/THGA_avg.pdb to /tmp/biobb/unitests_62/biobb_canion/sandbox_dbdc0404-9caa-4d5b-9fa8-44ad34a62c3a\nINFO     /tmp/biobb/unitests_62/biobb_canion/biobb_canion_log.out:file_utils.py:409 Creating command line with instructions and required arguments\nINFO     /tmp/biobb/unitests_62/biobb_canion/biobb_canion_log.out:cmd_wrapper.py:63 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  itst=0,\n  itnd=0,\n  itdel=1,\n  rmsf=.f.,\n  circ=.f.,\n&amp;amp;end\n!\n\nINFO     /tmp/biobb/unitests_62/biobb_canion/biobb_canion_log.out:cmd_wrapper.py:36 Executing: Canion &amp;lt;&amp;lt;! \n&amp;amp;inp\n  lis=canion_output,\n  dat=THGA_K,\n  axfrm=THGA,\n  solute=THGA_...\nINFO     /tmp/biobb/unitests_62/biobb_canion/biobb_canion_log.out:cmd_wrapper.py:37 Exit code: 0\nINFO     /tmp/biobb/unitests_62/biobb_canion/biobb_canion_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_62/biobb_canion/sandbox_dbdc0404-9caa-4d5b-9fa8-44ad34a62c3a&amp;#x27;]\nINFO     /tmp/biobb/unitests_62/biobb_canion/biobb_canion_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_62\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 -----------------------------\n2024-11-15 12:07:18,823 [MainThread  ] [INFO ]  Module: biobb_dna.curvesplus.biobb_curves Version: 5.0.0\n2024-11-15 12:07:18,823 [MainThread  ] [INFO ]  /tmp/biobb/unitests_62/biobb_curves/sandbox_59faf4cd-d73f-40c3-9b50-ab4cdd6dfb36 directory successfully created\n2024-11-15 12:07:18,883 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/curvesplus/structure.stripped.trj to /tmp/biobb/unitests_62/biobb_curves/sandbox_59faf4cd-d73f-40c3-9b50-ab4cdd6dfb36\n2024-11-15 12:07:18,884 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/curvesplus/structure.stripped.top to /tmp/biobb/unitests_62/biobb_curves/sandbox_59faf4cd-d73f-40c3-9b50-ab4cdd6dfb36\n2024-11-15 12:07:18,885 [MainThread  ] [INFO ]  Appending provided topology to command\n2024-11-15 12:07:18,885 [MainThread  ] [INFO ]  Creating command line with instructions and required arguments\n2024-11-15 12:07:18,885 [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=.curvesplus/standard,\n  ions=.t.,\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\n2024-11-15 12:07:25,484 [MainThread  ] [INFO ]  Executing: Cur+ &amp;lt;&amp;lt;! \n&amp;amp;inp\n  file=structure.stripped.trj,\n  ftop=structure.stripped.top,\n  l...\n2024-11-15 12:07:25,484 [MainThread  ] [INFO ]  Exit code: 0\n2024-11-15 12:07:25,527 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_62/biobb_curves/sandbox_59faf4cd-d73f-40c3-9b50-ab4cdd6dfb36&amp;#x27;]\n2024-11-15 12:07:25,528 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_62/biobb_curves/curves_output.cda\nChecking if empty file: /tmp/biobb/unitests_62/biobb_curves/curves_output.lis\nChecking if empty file: /tmp/biobb/unitests_62/biobb_curves/curves_output.zip\nComparing ignoring lines containing this words: [2]\n     FILE_A: /tmp/biobb/unitests_62/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\nThis is a ZIP comparison!\nUnzipping:\nCreating a unique_dir for: /tmp/biobb/unitests_62/biobb_curves/curves_output.zip\nCreating a unique_dir for: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/reference/curvesplus/curves_trj_output.zip\nComparing: \n        File_A: b24519eb-fff3-4549-8478-3735dd857616/curves_output.cdi\n        File_B: 8c42d88c-898e-4327-b2b7-9afdd8fd1c5e/curves_output.cdi\n        File_A hash: b&amp;#x27;\\xbf\\x13\\x93\\xa0\\xc8\\xba\\x96\\xaa\\xd5sy\\xda\\x0f\\xe1m|\\xab\\xd4\\x9c z\\x9a\\x9d\\xde\\x07\\x7f\\xe3\\x1c\\x0cf_h&amp;#x27;\n        File_B hash: b&amp;#x27;\\xbf\\x13\\x93\\xa0\\xc8\\xba\\x96\\xaa\\xd5sy\\xda\\x0f\\xe1m|\\xab\\xd4\\x9c z\\x9a\\x9d\\xde\\x07\\x7f\\xe3\\x1c\\x0cf_h&amp;#x27;\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_62/biobb_curves/biobb_curves_log.out:file_utils.py:409 Module: biobb_dna.curvesplus.biobb_curves Version: 5.0.0\nINFO     /tmp/biobb/unitests_62/biobb_curves/biobb_curves_log.out:file_utils.py:82 /tmp/biobb/unitests_62/biobb_curves/sandbox_59faf4cd-d73f-40c3-9b50-ab4cdd6dfb36 directory successfully created\nINFO     /tmp/biobb/unitests_62/biobb_curves/biobb_curves_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/curvesplus/structure.stripped.trj to /tmp/biobb/unitests_62/biobb_curves/sandbox_59faf4cd-d73f-40c3-9b50-ab4cdd6dfb36\nINFO     /tmp/biobb/unitests_62/biobb_curves/biobb_curves_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/curvesplus/structure.stripped.top to /tmp/biobb/unitests_62/biobb_curves/sandbox_59faf4cd-d73f-40c3-9b50-ab4cdd6dfb36\nINFO     /tmp/biobb/unitests_62/biobb_curves/biobb_curves_log.out:file_utils.py:409 Appending provided topology to command\nINFO     /tmp/biobb/unitests_62/biobb_curves/biobb_curves_log.out:file_utils.py:409 Creating command line with instructions and required arguments\nINFO     /tmp/biobb/unitests_62/biobb_curves/biobb_curves_log.out:cmd_wrapper.py:63 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=.curvesplus/standard,\n  ions=.t.,\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_62/biobb_curves/biobb_curves_log.out:cmd_wrapper.py:36 Executing: Cur+ &amp;lt;&amp;lt;! \n&amp;amp;inp\n  file=structure.stripped.trj,\n  ftop=structure.stripped.top,\n  l...\nINFO     /tmp/biobb/unitests_62/biobb_curves/biobb_curves_log.out:cmd_wrapper.py:37 Exit code: 0\nINFO     /tmp/biobb/unitests_62/biobb_curves/biobb_curves_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_62/biobb_curves/sandbox_59faf4cd-d73f-40c3-9b50-ab4cdd6dfb36&amp;#x27;]\nINFO     /tmp/biobb/unitests_62/biobb_curves/biobb_curves_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_62\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;240 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;240 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 -----------------------------\n2024-11-15 12:07:25,629 [MainThread  ] [INFO ]  Module: biobb_dna.dna.dna_averages Version: 5.0.0\n2024-11-15 12:07:25,629 [MainThread  ] [INFO ]  /tmp/biobb/unitests_62/dna_averages/sandbox_540a4b5c-63d9-4f04-b1e4-40e4560437d2 directory successfully created\n2024-11-15 12:07:25,630 [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_62/dna_averages/sandbox_540a4b5c-63d9-4f04-b1e4-40e4560437d2\n2024-11-15 12:07:25,785 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_62/dna_averages/sandbox_540a4b5c-63d9-4f04-b1e4-40e4560437d2&amp;#x27;]\n2024-11-15 12:07:25,785 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_62/dna_averages/avg_out.csv\nChecking if empty file: /tmp/biobb/unitests_62/dna_averages/avg_out.jpg\nComparing images of both files:\n     IMAGE_A: /tmp/biobb/unitests_62/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_62/dna_averages/dna_averages_log.out:file_utils.py:409 Module: biobb_dna.dna.dna_averages Version: 5.0.0\nINFO     /tmp/biobb/unitests_62/dna_averages/dna_averages_log.out:file_utils.py:82 /tmp/biobb/unitests_62/dna_averages/sandbox_540a4b5c-63d9-4f04-b1e4-40e4560437d2 directory successfully created\nINFO     /tmp/biobb/unitests_62/dna_averages/dna_averages_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/dna/canal_output_shift.ser to /tmp/biobb/unitests_62/dna_averages/sandbox_540a4b5c-63d9-4f04-b1e4-40e4560437d2\nINFO     /tmp/biobb/unitests_62/dna_averages/dna_averages_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_62/dna_averages/sandbox_540a4b5c-63d9-4f04-b1e4-40e4560437d2&amp;#x27;]\nINFO     /tmp/biobb/unitests_62/dna_averages/dna_averages_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_62\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;501 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;501 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 -----------------------------\n2024-11-15 12:07:25,873 [MainThread  ] [INFO ]  Module: biobb_dna.dna.dna_bimodality Version: 5.0.0\n2024-11-15 12:07:25,873 [MainThread  ] [INFO ]  /tmp/biobb/unitests_62/dna_bimodality/sandbox_847f4549-92be-444d-b3e4-bd8f7d938b25 directory successfully created\n2024-11-15 12:07:25,873 [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_62/dna_bimodality/sandbox_847f4549-92be-444d-b3e4-bd8f7d938b25\n2024-11-15 12:07:26,326 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_62/dna_bimodality/sandbox_847f4549-92be-444d-b3e4-bd8f7d938b25&amp;#x27;]\n2024-11-15 12:07:26,326 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_62/dna_bimodality/bimod_out.csv\nChecking if empty file: /tmp/biobb/unitests_62/dna_bimodality/bimod_out.jpg\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_62/dna_bimodality/dna_bimodality_log.out:file_utils.py:409 Module: biobb_dna.dna.dna_bimodality Version: 5.0.0\nINFO     /tmp/biobb/unitests_62/dna_bimodality/dna_bimodality_log.out:file_utils.py:82 /tmp/biobb/unitests_62/dna_bimodality/sandbox_847f4549-92be-444d-b3e4-bd8f7d938b25 directory successfully created\nINFO     /tmp/biobb/unitests_62/dna_bimodality/dna_bimodality_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/dna/series_shift_AT.csv to /tmp/biobb/unitests_62/dna_bimodality/sandbox_847f4549-92be-444d-b3e4-bd8f7d938b25\nINFO     /tmp/biobb/unitests_62/dna_bimodality/dna_bimodality_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_62/dna_bimodality/sandbox_847f4549-92be-444d-b3e4-bd8f7d938b25&amp;#x27;]\nINFO     /tmp/biobb/unitests_62/dna_bimodality/dna_bimodality_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_62\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 -----------------------------\n2024-11-15 12:07:26,375 [MainThread  ] [INFO ]  Module: biobb_dna.dna.dna_timeseries Version: 5.0.0\n2024-11-15 12:07:26,375 [MainThread  ] [INFO ]  /tmp/biobb/unitests_62/dna_timeseries/sandbox_53d17ebe-7ac8-421e-92b2-e6ef86fb1e80 directory successfully created\n2024-11-15 12:07:26,376 [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_62/dna_timeseries/sandbox_53d17ebe-7ac8-421e-92b2-e6ef86fb1e80\n2024-11-15 12:07:30,639 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_62/dna_timeseries/sandbox_53d17ebe-7ac8-421e-92b2-e6ef86fb1e80&amp;#x27;]\n2024-11-15 12:07:30,639 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_62/dna_timeseries/timeseries_output.zip\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_62/dna_timeseries/dna_timeseries_log.out:file_utils.py:409 Module: biobb_dna.dna.dna_timeseries Version: 5.0.0\nINFO     /tmp/biobb/unitests_62/dna_timeseries/dna_timeseries_log.out:file_utils.py:82 /tmp/biobb/unitests_62/dna_timeseries/sandbox_53d17ebe-7ac8-421e-92b2-e6ef86fb1e80 directory successfully created\nINFO     /tmp/biobb/unitests_62/dna_timeseries/dna_timeseries_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/dna/canal_output_shift.ser to /tmp/biobb/unitests_62/dna_timeseries/sandbox_53d17ebe-7ac8-421e-92b2-e6ef86fb1e80\nINFO     /tmp/biobb/unitests_62/dna_timeseries/dna_timeseries_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_62/dna_timeseries/sandbox_53d17ebe-7ac8-421e-92b2-e6ef86fb1e80&amp;#x27;]\nINFO     /tmp/biobb/unitests_62/dna_timeseries/dna_timeseries_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_62\n&#34;}], &#34;biobb_dna/test/unitests/test_dna/test_timeseries_unzip.py::TestCanalUnzip::test_dna_timeseries_unzip&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_dna/test/unitests/test_dna/test_timeseries_unzip.py::TestCanalUnzip::test_dna_timeseries_unzip&#34;, &#34;duration&#34;: &#34;83 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_timeseries_unzip.py::TestCanalUnzip::test_dna_timeseries_unzip&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;83 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 -----------------------------\n2024-11-15 12:07:30,688 [MainThread  ] [INFO ]  Module: biobb_dna.dna.dna_timeseries_unzip Version: 5.0.0\n2024-11-15 12:07:30,688 [MainThread  ] [INFO ]  /tmp/biobb/unitests_62/dna_timeseries_unzip/sandbox_b701b584-55e2-4bae-8744-0d77ecd6f738 directory successfully created\n2024-11-15 12:07:30,689 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/dna/timeseries_output.zip to /tmp/biobb/unitests_62/dna_timeseries_unzip/sandbox_b701b584-55e2-4bae-8744-0d77ecd6f738\n2024-11-15 12:07:30,690 [MainThread  ] [INFO ]  hist_shift_5_AA.csv exists, copying into /tmp/biobb/unitests_62/dna_timeseries_unzip/sandbox_b701b584-55e2-4bae-8744-0d77ecd6f738/dna_timeseries_unzip.csv.\n2024-11-15 12:07:30,690 [MainThread  ] [INFO ]  hist_shift_5_AA.jpg exists, copying into /tmp/biobb/unitests_62/dna_timeseries_unzip/sandbox_b701b584-55e2-4bae-8744-0d77ecd6f738/dna_timeseries_unzip.jpg.\n2024-11-15 12:07:30,691 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_62/dna_timeseries_unzip/sandbox_b701b584-55e2-4bae-8744-0d77ecd6f738&amp;#x27;]\n2024-11-15 12:07:30,691 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_62/dna_timeseries_unzip/dna_timeseries_unzip.csv\nChecking if empty file: /tmp/biobb/unitests_62/dna_timeseries_unzip/dna_timeseries_unzip.jpg\nChecking if empty file: /tmp/biobb/unitests_62/dna_timeseries_unzip/dna_timeseries_unzip.txt\nComparing: \n        File_A: /tmp/biobb/unitests_62/dna_timeseries_unzip/dna_timeseries_unzip.csv\n        File_B: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/reference/dna/dna_timeseries_unzip.csv\n        File_A hash: b&amp;#x27;2\\xf3\\xc2\\xe4\\x137\\xc2\\xfc\\x98\\xc6A\\xe1\\x14T\\xeb\\xb2k\\xad\\xd5\\xe7y\\tx\\xd5\\xa1R\\xd1\\xd6\\xac\\xd1v\\xa8&amp;#x27;\n        File_B hash: b&amp;#x27;2\\xf3\\xc2\\xe4\\x137\\xc2\\xfc\\x98\\xc6A\\xe1\\x14T\\xeb\\xb2k\\xad\\xd5\\xe7y\\tx\\xd5\\xa1R\\xd1\\xd6\\xac\\xd1v\\xa8&amp;#x27;\nComparing: \n        File_A: /tmp/biobb/unitests_62/dna_timeseries_unzip/dna_timeseries_unzip.txt\n        File_B: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/reference/dna/dna_timeseries_unzip.txt\n        File_A hash: b&amp;#x27;\\xe3\\xbc\\x13{\\xa6\\r\\x807]\\x87\\x14|u\\xc6\\xbe\\x9d\\xca\\x8bl\\x96\\x86Z\\xd7\\x973+@+\\x1a\\xe4[\\x1b&amp;#x27;\n        File_B hash: b&amp;#x27;\\xe3\\xbc\\x13{\\xa6\\r\\x807]\\x87\\x14|u\\xc6\\xbe\\x9d\\xca\\x8bl\\x96\\x86Z\\xd7\\x973+@+\\x1a\\xe4[\\x1b&amp;#x27;\nComparing images of both files:\n     IMAGE_A: /tmp/biobb/unitests_62/dna_timeseries_unzip/dna_timeseries_unzip.jpg\n     IMAGE_B: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/reference/dna/dna_timeseries_unzip.jpg\n     IMAGE_A HASH: fff7f7e7e3e3c3f7 SIZE: 64 bits\n     IMAGE_B HASH: fff7f7e7e3e3c3f7 SIZE: 64 bits\n     TOLERANCE: 1.0%, ABS TOLERANCE: 1 bits, DIFFERENCE: 0 bits\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_62/dna_timeseries_unzip/dna_timeseries_unzip_log.out:file_utils.py:409 Module: biobb_dna.dna.dna_timeseries_unzip Version: 5.0.0\nINFO     /tmp/biobb/unitests_62/dna_timeseries_unzip/dna_timeseries_unzip_log.out:file_utils.py:82 /tmp/biobb/unitests_62/dna_timeseries_unzip/sandbox_b701b584-55e2-4bae-8744-0d77ecd6f738 directory successfully created\nINFO     /tmp/biobb/unitests_62/dna_timeseries_unzip/dna_timeseries_unzip_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/dna/timeseries_output.zip to /tmp/biobb/unitests_62/dna_timeseries_unzip/sandbox_b701b584-55e2-4bae-8744-0d77ecd6f738\nINFO     /tmp/biobb/unitests_62/dna_timeseries_unzip/dna_timeseries_unzip_log.out:file_utils.py:409 hist_shift_5_AA.csv exists, copying into /tmp/biobb/unitests_62/dna_timeseries_unzip/sandbox_b701b584-55e2-4bae-8744-0d77ecd6f738/dna_timeseries_unzip.csv.\nINFO     /tmp/biobb/unitests_62/dna_timeseries_unzip/dna_timeseries_unzip_log.out:file_utils.py:409 hist_shift_5_AA.jpg exists, copying into /tmp/biobb/unitests_62/dna_timeseries_unzip/sandbox_b701b584-55e2-4bae-8744-0d77ecd6f738/dna_timeseries_unzip.jpg.\nINFO     /tmp/biobb/unitests_62/dna_timeseries_unzip/dna_timeseries_unzip_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_62/dna_timeseries_unzip/sandbox_b701b584-55e2-4bae-8744-0d77ecd6f738&amp;#x27;]\nINFO     /tmp/biobb/unitests_62/dna_timeseries_unzip/dna_timeseries_unzip_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_62\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;246 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;246 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 -----------------------------\n2024-11-15 12:07:30,772 [MainThread  ] [INFO ]  Module: biobb_dna.stiffness.average_stiffness Version: 5.0.0\n2024-11-15 12:07:30,772 [MainThread  ] [INFO ]  /tmp/biobb/unitests_62/average_stiffness/sandbox_bc0455b1-b020-4a3c-b643-729ce0d929de directory successfully created\n2024-11-15 12:07:30,773 [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_62/average_stiffness/sandbox_bc0455b1-b020-4a3c-b643-729ce0d929de\n2024-11-15 12:07:30,938 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_62/average_stiffness/sandbox_bc0455b1-b020-4a3c-b643-729ce0d929de&amp;#x27;]\n2024-11-15 12:07:30,938 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_62/average_stiffness/avgstiff.csv\nChecking if empty file: /tmp/biobb/unitests_62/average_stiffness/avgstiff.jpg\nComparing images of both files:\n     IMAGE_A: /tmp/biobb/unitests_62/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_62/average_stiffness/average_stiffness_log.out:file_utils.py:409 Module: biobb_dna.stiffness.average_stiffness Version: 5.0.0\nINFO     /tmp/biobb/unitests_62/average_stiffness/average_stiffness_log.out:file_utils.py:82 /tmp/biobb/unitests_62/average_stiffness/sandbox_bc0455b1-b020-4a3c-b643-729ce0d929de directory successfully created\nINFO     /tmp/biobb/unitests_62/average_stiffness/average_stiffness_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/canal_output_roll.ser to /tmp/biobb/unitests_62/average_stiffness/sandbox_bc0455b1-b020-4a3c-b643-729ce0d929de\nINFO     /tmp/biobb/unitests_62/average_stiffness/average_stiffness_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_62/average_stiffness/sandbox_bc0455b1-b020-4a3c-b643-729ce0d929de&amp;#x27;]\nINFO     /tmp/biobb/unitests_62/average_stiffness/average_stiffness_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_62\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;327 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;327 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 -----------------------------\n2024-11-15 12:07:31,018 [MainThread  ] [INFO ]  Module: biobb_dna.stiffness.basepair_stiffness Version: 5.0.0\n2024-11-15 12:07:31,018 [MainThread  ] [INFO ]  /tmp/biobb/unitests_62/basepair_stiffness/sandbox_a5996574-d36a-4d53-a243-449ca3077624 directory successfully created\n2024-11-15 12:07:31,019 [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_62/basepair_stiffness/sandbox_a5996574-d36a-4d53-a243-449ca3077624\n2024-11-15 12:07:31,019 [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_62/basepair_stiffness/sandbox_a5996574-d36a-4d53-a243-449ca3077624\n2024-11-15 12:07:31,019 [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_62/basepair_stiffness/sandbox_a5996574-d36a-4d53-a243-449ca3077624\n2024-11-15 12:07:31,019 [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_62/basepair_stiffness/sandbox_a5996574-d36a-4d53-a243-449ca3077624\n2024-11-15 12:07:31,020 [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_62/basepair_stiffness/sandbox_a5996574-d36a-4d53-a243-449ca3077624\n2024-11-15 12:07:31,020 [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_62/basepair_stiffness/sandbox_a5996574-d36a-4d53-a243-449ca3077624\n2024-11-15 12:07:31,266 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_62/basepair_stiffness/bpstiff.csv\nChecking if empty file: /tmp/biobb/unitests_62/basepair_stiffness/bpstiff.jpg\nComparing images of both files:\n     IMAGE_A: /tmp/biobb/unitests_62/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_62/basepair_stiffness/basepair_stiffness_log.out:file_utils.py:409 Module: biobb_dna.stiffness.basepair_stiffness Version: 5.0.0\nINFO     /tmp/biobb/unitests_62/basepair_stiffness/basepair_stiffness_log.out:file_utils.py:82 /tmp/biobb/unitests_62/basepair_stiffness/sandbox_a5996574-d36a-4d53-a243-449ca3077624 directory successfully created\nINFO     /tmp/biobb/unitests_62/basepair_stiffness/basepair_stiffness_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_shift_AA.csv to /tmp/biobb/unitests_62/basepair_stiffness/sandbox_a5996574-d36a-4d53-a243-449ca3077624\nINFO     /tmp/biobb/unitests_62/basepair_stiffness/basepair_stiffness_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_slide_AA.csv to /tmp/biobb/unitests_62/basepair_stiffness/sandbox_a5996574-d36a-4d53-a243-449ca3077624\nINFO     /tmp/biobb/unitests_62/basepair_stiffness/basepair_stiffness_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_rise_AA.csv to /tmp/biobb/unitests_62/basepair_stiffness/sandbox_a5996574-d36a-4d53-a243-449ca3077624\nINFO     /tmp/biobb/unitests_62/basepair_stiffness/basepair_stiffness_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_tilt_AA.csv to /tmp/biobb/unitests_62/basepair_stiffness/sandbox_a5996574-d36a-4d53-a243-449ca3077624\nINFO     /tmp/biobb/unitests_62/basepair_stiffness/basepair_stiffness_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_roll_AA.csv to /tmp/biobb/unitests_62/basepair_stiffness/sandbox_a5996574-d36a-4d53-a243-449ca3077624\nINFO     /tmp/biobb/unitests_62/basepair_stiffness/basepair_stiffness_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_twist_AA.csv to 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