break
return False
def main(overlap=10, minNReads=1):
for line in sys.stdin:
sampN, loc, exn, cnt = line.split('\t')
chrom, pos = loc.split(':')
strand = exn[0]
if int(cnt) < minNReads:
continue
if (strand == '+' and not exonInclusion(chrom, int(pos),
int(pos) + overlap)
) or (strand == '-'
and not exonInclusion(chrom,
int(pos) - overlap, int(pos))):
sys.stdout.write(line)
optL, argL = getopt.getopt(sys.argv[1:], 'i:o:s:', [])
optH = mybasic.parseParam(optL)
exonH = loadExonH()
main(10, 1)
for sampN in sampNameL:
# if sampN[7:-5] not in ['TCGA-28-5216-01A-01R-1850-01.4']:
# continue
if pbs:
os.system('echo "sort -k1,1 -k2,2n < %s/%s.bed > %s/%s.bed.sorted" | \
qsub -N %s -o %s/%s.sortBed.qlog -j oe' % (inputDirN,sampN, outputDirN,sampN, sampN, outputDirN,sampN))
else:
print sampN
os.system('(sort -k1,1 -k2,2n < %s/%s.bed > %s/%s.bed.sorted) 2> %s/%s.sortBed.qlog' % \
(inputDirN,sampN, outputDirN,sampN, outputDirN,sampN))
optL, argL = getopt.getopt(sys.argv[1:],'i:o:p',[])
optH = mybasic.parseParam(optL)
inputDirN = optH['-i']
if '-o' in optH:
outputDirN = optH['-o']
else:
outputDirN = inputDirN
sortBed_batch(inputDirN,outputDirN,'-p' in optH)
