Merge pull request #11 from rhshah/master

Merge from Master
rhshah · Jul 13, 2017 · ee30aec · ee30aec
2 parents 5c2d802 + 228260c
commit ee30aec
Show file tree

Hide file tree

Showing 10 changed files with 32 additions and 36,915 deletions.
diff --git a/.project b/.project
diff --git a/.pydevproject b/.pydevproject
diff --git a/iAnnotateSV/AnnotateEachBreakpoint.py b/iAnnotateSV/AnnotateEachBreakpoint.py
@@ -22,10 +22,12 @@ def AnnotateEachBreakpoint(chromosome,position,strand,df,autoSelect):
         geneStart = df.iloc[index]['geneStart']
         geneEnd = df.iloc[index]['geneEnd']
         if((geneStart <= position) and (geneEnd >= position)):
+            #print position,geneStart,geneEnd
             transcriptIndex.append(index)
     desc = None
     intronnum = None
     intronframe = None
+    #print transcriptIndex
     if(transcriptIndex):
         coordData = pd.DataFrame(index=np.asarray(transcriptIndex),columns=['c', 'd', 'e', 'd1', 'd2', 'e1', 'e2','f'])
 
@@ -46,22 +48,23 @@ def AnnotateEachBreakpoint(chromosome,position,strand,df,autoSelect):
                 d = df.iloc[tindex]['txStart'] - position
                 apList = [c,d,e,d1,d2,e1,e2,f]
                 coordData.loc[tindex,['c', 'd', 'e', 'd1', 'd2', 'e1', 'e2','f']] = apList
-                #print "In Promoter","c=",c,"d=",d,"e=",e,"e1=",e1,"e2=",e2,"d1=",d1,"d2=",d2,"f=",f
+                #print "In Promoter 1",position,df.iloc[tindex]['txStart'],"c=",c,"d=",d,"e=",e,"e1=",e1,"e2=",e2,"d1=",d1,"d2=",d2,"f=",f
                 continue
             else:
                 c = None
                 d = None
             if position > df.iloc[tindex]['txEnd']:
                 c = 5 
-                d = position - df.iloc[tindex]['txStart']
+                d = position - df.iloc[tindex]['txEnd']
                 apList = [c,d,e,d1,d2,e1,e2,f]
                 #coordData.add(apList)
                 coordData.loc[tindex,['c', 'd', 'e', 'd1', 'd2', 'e1', 'e2','f']] = apList
-                #print "In Promoter","c=",c,"d=",d,"e=",e,"e1=",e1,"e2=",e2,"d1=",d1,"d2=",d2,"f=",f
+                #print "In Promoter 2","c=",c,"d=",d,"e=",e,"e1=",e1,"e2=",e2,"d1=",d1,"d2=",d2,"f=",f
                 continue
             else:
                 c = None
                 d = None 
+
             #in UTR region ?
             if(df.iloc[tindex]['strand'] == '+'):
                 if df.iloc[tindex]['cdsStart'] > position:
@@ -71,7 +74,10 @@ def AnnotateEachBreakpoint(chromosome,position,strand,df,autoSelect):
                     coordData.loc[tindex,['c', 'd', 'e', 'd1', 'd2', 'e1', 'e2','f']] = apList
                     #print "In 5'UTR","c=",c,"d=",d,"e=",e,"e1=",e1,"e2=",e2,"d1=",d1,"d2=",d2,"f=",f
                     continue
-                elif position > df.iloc[tindex]['cdsEnd']:
+                else:
+                    c = None
+                    d = None
+                if position > df.iloc[tindex]['cdsEnd']:
                     c = 3 
                     d = position - df.iloc[tindex]['cdsStart']
                     apList = [c,d,e,d1,d2,e1,e2,f]
@@ -89,7 +95,10 @@ def AnnotateEachBreakpoint(chromosome,position,strand,df,autoSelect):
                     coordData.loc[tindex,['c', 'd', 'e', 'd1', 'd2', 'e1', 'e2','f']] = apList
                     #print "In 3'UTR","c=",c,"d=",d,"e=",e,"e1=",e1,"e2=",e2,"d1=",d1,"d2=",d2,"f=",f
                     continue
-                elif position > df.iloc[tindex]['cdsEnd']:
+                else:
+                    c = None
+                    d = None
+                if position > df.iloc[tindex]['cdsEnd']:
                     c = 4
                     d = position - df.iloc[tindex]['cdsStart']
                     apList = [c,d,e,d1,d2,e1,e2,f]

diff --git a/iAnnotateSV/FindCanonicalTranscript.py b/iAnnotateSV/FindCanonicalTranscript.py
@@ -20,18 +20,22 @@ def FindCT(geneList,transcriptList,siteList,zoneList,strandList,intronnumList,in
     intronnum = None
     intronframe = None
     chkval = isinstance(geneList,list)
+    # print geneList,transcriptList
     if(chkval):
-        cts = []
+        cts = None
         minIndex = None
         for gene in geneList:
+            #print gene
             if gene in ctDict:
-                cts = ctDict[gene]
-        #print cts
+                cts = ctDict.get(gene)
+                break
         if(cts):
             if(len(cts) > 1 ):
                 minIndex = min(enumerate(zoneList), key=itemgetter(1))[0] 
             else:
+                #print "CTS",cts[0]
                 try:
+                    #print "I am here", transcriptList.index(cts[0])
                     minIndex = transcriptList.index(cts[0])
                 except ValueError:
                     logging.warn("iAnnotateSV::FindCanonicalTranscript: The given canonical transcript does not cover the coordinates.")