update html

minor location fixes version up
cas-bioinf · Oct 15, 2018 · cd997ff · cd997ff
1 parent d458780
commit cd997ff
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Showing 9 changed files with 74 additions and 45 deletions.
diff --git a/rna_blast_analyze/BA.py b/rna_blast_analyze/BA.py
@@ -154,7 +154,7 @@ def f_parser():
     misc_group.add_argument(
         '--version',
         action='version',
-        version='%(prog)s 0.0.4'
+        version='%(prog)s 0.0.5'
     )
     parameters_group.add_argument(
         '--config_file',

diff --git a/rna_blast_analyze/BR_core/BA_methods.py b/rna_blast_analyze/BR_core/BA_methods.py
@@ -306,6 +306,6 @@ def to_tab_delim_header(input_args):
 
 def add_loc_to_description(analyzed_hits):
     for hit in analyzed_hits.hits:
-        d2a = ' {}-{}'.format(hit.best_start, hit.best_end)
-        hit.source.description += d2a
+        d2a = '{}-{}'.format(hit.best_start, hit.best_end)
+        # hit.source.description += d2a
         hit.subs[hit.ret_keys[0]].description += d2a
diff --git a/rna_blast_analyze/BR_core/expand_by_BLAST.py b/rna_blast_analyze/BR_core/expand_by_BLAST.py
@@ -116,19 +116,18 @@ def trim_before(seqs):
 def compute_true_location_se(hit):
     hh = hit.subs[hit.ret_keys[0]]
     ann = hh.annotations
-    if ann['strand'] == -1:
+    if ann['strand'] == 1:
         if ann['trimmed_es']:
-            s = 0
+            s = 1
         else:
-            s = ann['blast'][1].sbjct_end - ann['blast'][1].query_start
-        e = s + len(hh.seq)
+            s = ann['blast'][1].sbjct_start - ann['blast'][1].query_start + 1
+        e = s + len(hh.seq) - 1
     else:
         if ann['trimmed_es']:
-            s = 0
+            s = 1
         else:
-            s = ann['blast'][1].sbjct_start - ann['blast'][1].query_start
-        e = s + len(hh.seq)
-
+            s = ann['blast'][1].sbjct_end - ann['blast'][1].query_start + 1
+        e = s + len(hh.seq) - 1
     return s, e
 
 

diff --git a/rna_blast_analyze/BR_core/expand_by_LOCARNA.py b/rna_blast_analyze/BR_core/expand_by_LOCARNA.py
@@ -400,12 +400,20 @@ def _select_refold_structure(refold_structures_, exp_hit_id):
 
 def compute_true_location_locarna(hit, match):
     start, end = match.span()
-    if hit.source.annotations['trimmed_ss']:
-        s = start
+    if hit.source.annotations['blast'][1].strand == 1:
+        if hit.source.annotations['trimmed_ss']:
+            s = start + 1
+        else:
+            s = hit.source.annotations['super_start'] + start
+
+        e = end - start + s + 1
     else:
-        s = hit.source.annotations['super_start'] + start
+        if hit.source.annotations['trimmed_ss']:
+            s = start + 1
+        else:
+            s = hit.source.annotations['super_start'] + start
 
-    e = end - start + s
+        e = end - start + s - 1
 
     return s, e
 

diff --git a/rna_blast_analyze/BR_core/expand_by_joined_pred_with_rsearch.py b/rna_blast_analyze/BR_core/expand_by_joined_pred_with_rsearch.py
@@ -139,6 +139,10 @@ def joined_wrapper_inner(args_inner, shared_list=None):
                 fah.write('>{}\n{}\n'.format(hit.subs[hit.ret_keys[0]].id,
                                            str(hit.subs[hit.ret_keys[0]].seq)))
 
+        # remove description from hits and sources
+        for hit in analyzed_hits.hits:
+            hit.subs[hit.ret_keys[0]].description = ''
+
         out_line = []
         # multiple prediction params
         if args_inner.dev_pred:

diff --git a/rna_blast_analyze/BR_core/output/onehit.html b/rna_blast_analyze/BR_core/output/onehit.html
@@ -4,7 +4,10 @@
 {% endblock %}
 {% block content %}
     {% macro create_onehit(data) %}
-    <div class="onehit" data-brna_sequence="{{data.sequence}}" data-brna_seqname="{{data.seqname}}"
+    <div class="onehit"
+         id="{{data.intid}}onehit"
+         data-brna_sequence="{{data.sequence}}"
+         data-brna_seqname="{{data.seqname}}"
          data-eval="{{data.eval}}">
         <h3 class="onehit_heading" style="background:{{data.h_color}};">
             Hit: {{data.source_seq_name}}
@@ -21,11 +24,11 @@ <h3 class="onehit_heading" style="background:{{data.h_color}};">
                     <table>
                         <tr>
                             <th class="left" scope="row">sequence start:</th>
-                            <td class="right">{{data.ext_start}}</td>
+                            <td class="right" id="{{data.intid}}SeqStart">{{data.ext_start}}</td>
                         </tr>
                         <tr>
                             <th class="left" scope="row">sequence end:</th>
-                            <td class="right">{{data.ext_end}}</td>
+                            <td class="right" id="{{data.intid}}SeqEnd">{{data.ext_end}}</td>
                         </tr>
                         <tr>
                             <th class="left" scope="row">RSEARCH bits score:</th>
@@ -39,26 +42,25 @@ <h3 class="onehit_heading" style="background:{{data.h_color}};">
                 </div>
                 <div class="repitem">
                     <div>
-                        <label for="indivSequenceCheckbox"><u>Extended sequence fasta:</u></label>
-                        <input type="checkbox" class="individualSequenceCheckbox" id="indivSequenceCheckbox">
+                        <label for="{{data.intid}}SeqCheck"><u>Extended sequence fasta:</u></label>
+                        <input type="checkbox" class="individualSequenceCheckbox" id="{{data.intid}}SeqCheck">
                     </div>
-                    <textarea readonly="true" rows="5" cols="65">{{data.formated_seq}}</textarea>
+                    <textarea id="{{data.intid}}FormSeq" readonly="true" rows="5" cols="65">{{data.formated_seq}}</textarea>
                 </div>
-                <!--</div>-->
             </div>
-        <div class="row">
-            {% for pic in data.pictures %}
-                <figure class="column" data-brna_secondary_structure="{{pic.secondary_structure}}">
-                    <a href onclick="mypicload(this)">
-                        <img class="rnapic" src="{{pic.pic}}" />
-                    </a>
-                    <figcaption>
-                        {{pic.picname}}
-                        <input type="checkbox" class="individualStructureCheckbox">
-                    </figcaption>
-                </figure>
-            {% endfor %}
-        </div>
+            <div class="row">
+                {% for pic in data.pictures %}
+                    <figure class="column" data-brna_secondary_structure="{{pic.secondary_structure}}" id="{{data.intid}}{{pic.picname}}">
+                        <a href onclick="mypicload(this)">
+                            <img class="rnapic" src="{{pic.pic}}" />
+                        </a>
+                        <figcaption>
+                            {{pic.picname}}
+                            <input type="checkbox" class="individualStructureCheckbox" id="{{data.intid}}{{data.picname}}StrCheck">
+                        </figcaption>
+                    </figure>
+                {% endfor %}
+            </div>
 
         {% if data.draw_seqview %}
 

diff --git a/rna_blast_analyze/BR_core/output/script.js b/rna_blast_analyze/BR_core/output/script.js
@@ -51,19 +51,33 @@ function buildFasta(seqname, sequence) {
   return ">" + seqname + "\n" + sequence + "\n";
 }
 
+function mySaveFile(uri, filename) {
+  var link = document.createElement('a');
+  if (typeof(link.download) === 'string') {
+    document.body.appendChild(link);
+    link.download = filename;
+    link.href = uri;
+    link.click();
+    document.body.removeChild(link);
+  } else {
+    window.open(uri, "_self");
+  }
+}
+
 function writeSelectionStructures() {
   console.log("write selection fasta");
   var sel = exportSelected("individualStructureCheckbox");
   var i;
   var exportdata = "";
 
   for (i = 0; i < sel.length; i++) {
-    var pnodedata = sel[i].parentNode.parentNode.parentNode.parentNode.dataset;
-    var structure = sel[i].parentNode.parentNode.dataset.brna_secondary_structure;
-
-    exportdata += buildFastaStructure(pnodedata.brna_seqname, pnodedata.brna_sequence, structure);
+    var intid = parseInt(sel[i].id)
+    var oh = document.getElementById(intid + "onehit");
+    var method = sel[i].parentNode.textContent.trim()
+    var seqname = oh.dataset.brna_seqname + "-" + method + " " + document.getElementById(intid + "SeqStart").textContent + "-" + document.getElementById(intid + "SeqEnd").textContent
+    exportdata += buildFastaStructure(seqname, oh.dataset.brna_sequence, document.getElementById(intid + method).dataset.brna_secondary_structure);
   }
-  window.open("data:application/txt," + encodeURIComponent(exportdata), "_self");
+  mySaveFile("data:application/txt," + encodeURIComponent(exportdata), "structures.txt");
 }
 
 function placeSelection(boxlist, val2place) {
@@ -106,10 +120,12 @@ function writeSelectionFasta() {
   var exportdata = "";
 
   for (i = 0; i < sel.length; i++) {
-    var pnodedata = sel[i].parentNode.parentNode.parentNode.dataset;
-    exportdata += buildFasta(pnodedata.brna_seqname, pnodedata.brna_sequence);
+    var intid = parseInt(sel[i].id)
+    var pnodedata = document.getElementById(intid + "FormSeq");
+
+    exportdata += pnodedata.textContent;
   }
-  window.open("data:application/txt," + encodeURIComponent(exportdata), "_self");
+  mySaveFile("data:application/txt," + encodeURIComponent(exportdata), "sequences.fasta");
 }
 
 function GetHits() {

diff --git a/setup.py b/setup.py
@@ -15,7 +15,7 @@
 
 setup(
     name='rna_blast_analyze',
-    version='0.0.4',
+    version='0.0.5',
     description='Analyze BLAST output for RNA query',
     author='Marek Schwarz',
     author_email='[email protected]',

diff --git a/test_func/test_data/RF00001_reference_output.html.md5 b/test_func/test_data/RF00001_reference_output.html.md5
@@ -1 +1 @@
-8d941ad1ea3912af31e4b3ce16c5d893
+87f65c91302e718fedddacadaea3b5f8