Quick hack as proof of concept implementation

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/browser-link-branch@379 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

mutalyzer/parsers/genbank.py

@@ -454,6 +454,8 @@ class GBparser():
         record.seq = biorecord.seq
 
         record.version = biorecord.id.split('.')[1]
+        # Todo: also set organism in the LRG parser
+        record.organism = biorecord.annotations['organism']
 
         exonList = []
         geneDict = {}

mutalyzer/templates/check.html

@@ -264,6 +264,8 @@
             <a tal:content = "reference"
                tal:attributes = "href string:Reference/${reference}"></a>
             <br>
+            <a tal:condition = "browserLink" tal:attributes = "href browserLink">UCSC Genome Browser</a>
+            <br>
             <br>
           </div> <!-- interactive -->
         </div> <!-- reference -->

mutalyzer/variantchecker.py

@@ -1496,6 +1496,8 @@ def check_variant(description, config, output):
     # Add recordType to output for output formatting.
     output.addOutput('recordType', filetype)
 
+    output.addOutput('organism', retrieved_record.organism)
+
     output.addOutput('reference', record_id)
 
     # Note: geneSymbol[0] is used as a filter for batch runs.

mutalyzer/website.py

@@ -725,6 +725,24 @@ class Check:
                 link = urllib.quote(description)
             return description, link
 
+        # Create a link to the UCSC Genome Browser
+        # This is an ugly proof of concept.
+        browser_link = None
+        if output.getIndexedOutput('organism', 0) == 'Homo sapiens':
+            converter = Converter('hg19', config, output)
+            variant = converter.c2chrom(str(name))
+            if variant:
+                import re
+                match = re.match('NC_(\d+)\.\d+:g.(\d+)_?(\d*)[^_\d]', variant)
+                if match:
+                    # Todo: convert NC_0000XX to chr1...chrY
+                    chromosome, start, stop = match.groups()
+                    if stop:
+                        position = 'chr%i:%i-%i' % (int(chromosome), int(start), int(stop))
+                    else:
+                        position = 'chr%i:%i' % (int(chromosome), int(start))
+                    browser_link = 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&position=%s' % position
+
         # Todo: Generate the fancy HTML views for the proteins here instead
         # of in mutalyzer/variantchecker.py.
         args = {
@@ -752,7 +770,8 @@ class Check:
             'cdsStop_c'          : output.getIndexedOutput('cdsStop_c', 0),
             'restrictionSites'   : output.getOutput('restrictionSites'),
             'legends'            : output.getOutput('legends'),
-            'reference'          : reference
+            'reference'          : reference,
+            'browserLink'        : browser_link
         }
 
         return render.check(args, standalone=not interactive)