make hotspots optional

Author: jjgao

AnnotatorCore.py

@@ -125,8 +125,9 @@ def inithotspots():
     curatedgenes |= set(_3dhotspots.keys())
 
 
-def processalterationevents(eventfile, outfile, previousoutfile, defaultCancerType, cancerTypeMap, retainonlycuratedgenes):
-    inithotspots()
+def processalterationevents(eventfile, outfile, previousoutfile, defaultCancerType, cancerTypeMap, retainonlycuratedgenes, annotatehotspots):
+    if annotatehotspots:
+        inithotspots()
     if os.path.isfile(previousoutfile):
         cacheannotated(previousoutfile, defaultCancerType, cancerTypeMap)
     outf = open(outfile, 'w+', 1000)
@@ -139,8 +140,9 @@ def processalterationevents(eventfile, outfile, previousoutfile, defaultCancerTy
 
         outf.write(headers['^-$'])
 
-        outf.write("\tis-a-hotspot")
-        outf.write("\tis-a-3d-hotspot")
+        if annotatehotspots:
+            outf.write("\tis-a-hotspot")
+            outf.write("\tis-a-3d-hotspot")
 
         outf.write("\tmutation_effect")
         outf.write("\toncogenic")
@@ -232,11 +234,12 @@ def processalterationevents(eventfile, outfile, previousoutfile, defaultCancerTy
             if start is not None and end is None:
                 end = start
 
-            hotspot = pullsinglehotspots(hugo, hgvs, None, consequence, start, end, cancertype)
-            row.append(hotspot)
+            if annotatehotspots:
+                hotspot = pullsinglehotspots(hugo, hgvs, None, consequence, start, end, cancertype)
+                row.append(hotspot)
 
-            _3dhotspot = pull3dhotspots(hugo, hgvs, None, consequence, start, end, cancertype)
-            row.append(_3dhotspot)
+                _3dhotspot = pull3dhotspots(hugo, hgvs, None, consequence, start, end, cancertype)
+                row.append(_3dhotspot)
 
             oncokbinfo = pulloncokb(hugo, hgvs, None, consequence, start, end, cancertype)
             row.append(oncokbinfo)

MafAnnotator.py

@@ -11,16 +11,17 @@ def main(argv):
     outputmaffile = ''
     previousresultfile = ''
     defaultcancertype = 'cancer'
+    annotatehotspots = False
 
     try:
-        opts, args = getopt.getopt(argv, "hi:o:p:c:s:t:u:v:")
+        opts, args = getopt.getopt(argv, "hi:o:p:c:s:t:u:v:a")
     except getopt.GetoptError:
         print 'for help: python MafAnnotator.py -h'
         sys.exit(2)
 
     for opt, arg in opts:
         if opt == '-h':
-            print 'MafAnnotator.py -i <input MAF file> -o <output MAF file> [-p previous results] [-c <input clinical file>] [-s sample list filter] [-t <default tumor type>] [-u oncokb-base-url] [-v cancerhotspots-base-url]'
+            print 'MafAnnotator.py -i <input MAF file> -o <output MAF file> [-p previous results] [-c <input clinical file>] [-s sample list filter] [-t <default tumor type>] [-u oncokb-base-url] [-a]'
             print '  Essential MAF columns (case insensitive):'
             print '    HUGO_SYMBOL: Hugo gene symbol'
             print '    VARIANT_CLASSIFICATION: Translational effect of variant allele'
@@ -37,6 +38,7 @@ def main(argv):
             print '     2) ONCOTREE_CODE exist in MAF'
             print '     3) default tumor type (-t)'
             print '  Default OncoKB base url is http://oncokb.org'
+            print '  use -a to annotate mutational hotspots'
             sys.exit()
         elif opt in ("-i"):
             inputmaffile = arg
@@ -52,6 +54,8 @@ def main(argv):
             defaultcancertype = arg
         elif opt in ("-u"):
             setoncokbbaseurl(arg)
+        elif opt in ("-a"):
+            annotatehotspots = True
         elif opt in ("-v"):
             setcancerhotspotsbaseurl(arg)
 
@@ -65,7 +69,7 @@ def main(argv):
 
     print 'annotating '+inputmaffile+"..."
 
-    processalterationevents(inputmaffile, outputmaffile, previousresultfile, defaultcancertype, cancertypemap, False)
+    processalterationevents(inputmaffile, outputmaffile, previousresultfile, defaultcancertype, cancertypemap, False, annotatehotspots)
 
     print 'done!'
 
@@ -74,6 +78,7 @@ def main(argv):
     #     '-i', 'data/example_maf.txt',
     #     '-o', 'data/example_maf.oncokb.txt',
     #     '-c', 'data/example_clinical.txt',
+    #     '-a'
     # ]
     # main(argv)