Mercurial > repos > jowong > kwip

comparison kwip_postprocess.py @ 22:89a88542f301 draft

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planemo upload
author jowong
date Thu, 22 Nov 2018 09:46:09 -0500
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21:12b9a42289c2 22:89a88542f301
1 #!/usr/bin/env python
2
3 import sys
4 import argparse as ap
5 import re
6 parser = ap.ArgumentParser(prog='kwip_postprocess', conflict_handler='resolve',
7 description="Postprocess galaxy kWIP output")
8
9 input = parser.add_argument_group('Input', '')
10 input.add_argument('-i', '--input', nargs=1, required=True, help="kWIP galaxy OUTPUT")
11
12
13 if len(sys.argv) == 0:
14 parser.print_usage()
15 sys.exit(1)
16
17 args = parser.parse_args()
18
19
20 with open(args.input[0]) as kwip_output:
21 with open('kwip_postprocess_output.txt', 'w') as output:
22 for line in kwip_output:
23 new_line = re.sub('(_1.fastq(.gz)*|_2.fastq(.gz)*|.fastq(.gz)*)', '', line)
24 output.write(new_line)
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