leftGet=int(leftGet)
rightGet=int(rightGet)
colChr=getCol0ListFromCol1ListStringAdv(header,colChr)[0]
colCoordinate=getCol0ListFromCol1ListStringAdv(header,colCoordinate)[0]
colAlleleA=getCol0ListFromCol1ListStringAdv(header,colAlleleA)[0]
colAlleleB=getCol0ListFromCol1ListStringAdv(header,colAlleleB)[0]
labelASeq=header[colAlleleA]+".seq"
labelBSeq=header[colAlleleB]+".seq"
header+=[labelASeq,labelBSeq]
print >> stdout,fs.join(header)
bedSeqClient=BedSeqClient(seqDir,"bed")
lino=0
fil=open(SNPTable)
for lin in fil:
lino+=1
if lino<startRow:
continue
lin=lin.rstrip("\r\n")
fields=lin.split(fs)
chrom=fields[colChr]
if "chr" not in chrom:
def printUsageAndExit(programName):
print >> stderr,"Usage: %s seqdir pairedhitFile flankingLength" %(programName)
exit(1)
if __name__=='__main__':
programName=argv[0]
args=argv[1:]
try:
seqdir,filename,flankingLen=args
flankingLen=int(flankingLen)
except:
printUsageAndExit(programName)
bseq=BedSeqClient(seqdir,"bed")
fil=open(filename)
lino=0
for lin in fil:
lino+=1
lin=lin.rstrip("\r\n")
fields=lin.split("\t")
pair1Name=fields[4]
pair1Chrom=fields[1]
pair1Start0=int(fields[2])
pair1End1=int(fields[3])
pair1Strand=fields[6]
pair2Name=fields[11]
pair2Start0=int(fields[9])
