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Few bug fix #4

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ffdb1e0
Update python.calculateReadsDepthOfAmp.py
leefall Nov 26, 2021
8265502
Update python.getCNVPerSample.py
leefall Nov 26, 2021
25e472f
Update python.scoreCNV.py
leefall Nov 26, 2021
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4 changes: 2 additions & 2 deletions Code_v1.5.1/python.calculateReadsDepthOfAmp.py
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Original file line number Diff line number Diff line change
Expand Up @@ -177,7 +177,7 @@ def MapReadinBamPCR(inBamFile, ampliconDic, ampTree, dedupOp, MQList):
if(read.is_duplicate):
if(dedupOp=="true"):
continue
overlapAmpTreeList=ampTree[inBam.getrname(read.rname).replace("chr","")].search(read.pos+1, read.pos+read.alen+1) ## [start, end)
overlapAmpTreeList=ampTree[inBam.getrname(read.rname).replace("chr","")].overlap(read.pos+1, read.pos+read.alen+1) ## [start, end)
if(len(overlapAmpTreeList)==0):
pass
else:
Expand Down Expand Up @@ -242,7 +242,7 @@ def MapReadinBamHYB(inBamFile, ampliconDic, ampTree, dedupOp, MQList):
if(read.is_duplicate):
if(dedupOp=="true"):
continue
overlapAmpTreeList=ampTree[inBam.getrname(read.rname).replace("chr","")].search(read.pos+1, read.pos+read.alen+1) ## [start, end)
overlapAmpTreeList=ampTree[inBam.getrname(read.rname).replace("chr","")].overlap(read.pos+1, read.pos+read.alen+1) ## [start, end)
if(len(overlapAmpTreeList)==0):
pass
else:
Expand Down
8 changes: 4 additions & 4 deletions Code_v1.5.1/python.getCNVPerSample.py
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Original file line number Diff line number Diff line change
Expand Up @@ -137,20 +137,20 @@ def getCandidateRegion(self, qType, CBSTree):
#### UnifiedRegions ##############################
UnifiedRegion={}
ID=1
segmentList=CBSTree[self.chrom].search(self.start, self.end+1)
segmentList=CBSTree[self.chrom].overlap(self.start, self.end+1)
segmentList=sorted(segmentList,key=itemgetter(1))
for segment in segmentList:
[segChr, segStart, segEnd, segNo, segMean]=segment[-1]
if(self.qType=="dup"):
dupList=[]
for overlapAmps in list(self.dupTree[segChr].search(segStart, segEnd)):
for overlapAmps in list(self.dupTree[segChr].overlap(segStart, segEnd)):
dupList.append(overlapAmps[-1])
if(dupList!=[] and len(dupList)>=minAmpCntInRegion):
dupList=sorted(dupList,key=attrgetter('inS'))
UnifiedRegion[self.sample+"_"+self.gene+"_"+"dup"+":"+str(ID)]=dupList
if(self.qType=="del"):
delList=[]
for overlapAmps in list(self.delTree[segChr].search(segStart, segEnd)):
for overlapAmps in list(self.delTree[segChr].overlap(segStart, segEnd)):
delList.append(overlapAmps[-1])
if(delList!=[] and len(delList)>=minAmpCntInRegion):
delList=sorted(delList,key=attrgetter('inS'))
Expand Down Expand Up @@ -519,4 +519,4 @@ def readCBSFile(inFileName, dupTh, delTh):
getRegionCandidate(genePerSampleDic, outFileName, pTh, CBSTree,minAmpCntInRegion, dupTh, delTh, MQ)
#except:
# print("Unexpected error:", sys.exc_info()[0])
# print("Maybe all values are nan for "+inSample)
# print("Maybe all values are nan for "+inSample)
2 changes: 1 addition & 1 deletion Code_v1.5.1/python.scoreCNV.py
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Original file line number Diff line number Diff line change
Expand Up @@ -260,7 +260,7 @@ def filterOutSmallCNVs(outVDic, sampleCNVDic):
if(score1>=score2 and cnvType1==cnvType2 and sample1==sample2 and chr1==chr2 and start1<=start2 and end1>=end2):
if (score1==score2 and cnvType1==cnvType2 and sample1==sample2 and chr1==chr2 and start1==start2 and end1==end2):
if(idx1<idx2):
FalseIDList.append(ID2)
FalseIDList.append(ID2)

outVsList=[]
for ID in outVDic.keys():
Expand Down