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Update grepfqparser.py #3

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Update grepfqparser.py #3

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8 changes: 6 additions & 2 deletions grepfqparser.py
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Original file line number Diff line number Diff line change
Expand Up @@ -43,13 +43,17 @@
def main():
#parse command line options
try:
opts, arg = getopt.getopt(sys.argv[1:],"h", ["help"])
opts, arg = getopt.getopt(sys.argv[1:],"ht:", ["help"])
except getopt.error, msg:
print msg
print "for help use --help"
sys.exit(2)
# process options
offset = 0
for o, a in opts:
if o == '-t':
offset = int(a)
print "Using offset", offset
if o in ("-h", "--help"):
print __doc__
sys.exit(0)
Expand Down Expand Up @@ -108,7 +112,7 @@ def main():
cmd = 'grep -B 1 -A 2 ^%s %s' % (barcode_up, fqFile)
subprocess.call(cmd, shell=True,stdout=parsed_file_step1, stderr=errlog)
#(note: pipe into sed to remove barcodes and associated quality scores from each line)
cmd = "grep -B 1 -A 2 ^%s %s | sed '2~2s/^%s//g'" % (barcode_up, fqFile, '.'*len(barcode_up))
cmd = "grep -B 1 -A 2 ^%s %s | sed '2~2s/^%s//g'" % (barcode_up, fqFile, '.'*(len(barcode_up)+offset))
subprocess.call(cmd, shell=True,stdout=parsed_file_step1, stderr=errlog)
errlog.close()
parsed_file_step1.close()
Expand Down