with open(readCountsFile,"rt") as IN:
while(True):
line=IN.readline()
if(line==""): break
if(rex.find("TOTAL MAPPED READS:\s*(\d+)",line)):
totalMappedReads=rex[1]
else:
fields=line.split()
(gene,count)=fields
readCounts[gene]=count
# Read GFF file to find annotated sites to exclude
gff={}
exclude={}
reader=GffTranscriptReader()
transcripts=reader.loadGFF(gffFile)
for transcript in transcripts:
if(transcript.getID()[0:3]=="ALT"): continue
if(rex.find("(\S+)_\d",transcript.getID())): gff[rex[1]]=transcript
substrate=transcript.getSubstrate()
exclusions=exclude.get(substrate,None)
if(exclusions is None): exclusions=exclude[substrate]={}
exons=transcript.getRawExons()
exons.sort(key=lambda exon:exon.begin)
numExons=len(exons)
for i in range(numExons-1):
key=str(exons[i].getEnd())+"-"+str(exons[i+1].getBegin())
exclusions[key]=True
# Read broken-sites file
brokenSubstrates={}
