Mercurial > repos > jowong > kwip
diff kwip_postprocess.py @ 22:89a88542f301 draft
planemo upload
author | jowong |
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date | Thu, 22 Nov 2018 09:46:09 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/kwip_postprocess.py Thu Nov 22 09:46:09 2018 -0500 @@ -0,0 +1,27 @@ +#!/usr/bin/env python + +import sys +import argparse as ap +import re +parser = ap.ArgumentParser(prog='kwip_postprocess', conflict_handler='resolve', + description="Postprocess galaxy kWIP output") + +input = parser.add_argument_group('Input', '') +input.add_argument('-i', '--input', nargs=1, required=True, help="kWIP galaxy OUTPUT") + + +if len(sys.argv) == 0: + parser.print_usage() + sys.exit(1) + +args = parser.parse_args() + + +with open(args.input[0]) as kwip_output: + with open('kwip_postprocess_output.txt', 'w') as output: + for line in kwip_output: + new_line = re.sub('(_1.fastq(.gz)*|_2.fastq(.gz)*|.fastq(.gz)*)', '', line) + output.write(new_line) + + +