Mercurial > repos > jowong > prince_galaxy

comparison prince_postprocess.py @ 4:82569b47df8d draft

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planemo upload
author jowong
date Mon, 29 Oct 2018 07:52:12 -0400
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children 63f3743c2ae4
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3:dde3036465de 4:82569b47df8d
1 #!/usr/bin/env python
2
3 import sys
4 import argparse as ap
5 import re
6 parser = ap.ArgumentParser(prog='prince_postprocess', conflict_handler='resolve',
7 description="Postprocess galaxy PRINCE output")
8
9 input = parser.add_argument_group('Input', '')
10 input.add_argument('-i', '--input', nargs=1, required=True, help="PRINCE OUTPUT")
11 input.add_argument('-s', '--sample', nargs='*', required=True, help="Sample names")
12
13 if len(sys.argv) == 0:
14 parser.print_usage()
15 sys.exit(1)
16
17 args = parser.parse_args()
18
19 #print(args.input)
20 #sample_name = re.sub('(_1.fastq(.gz)*|_2.fastq(.gz)*|.fastq(.gz)*)', '', args.label.rstrip().lstrip())
21
22 with open(args.input[0]) as prince_output:
23 with open('prince_postprocess_output.txt', 'w') as output:
24 x = 1
25 index = 0
26 for line in prince_output:
27 if x%2 == 0:
28 sample = re.sub('(_1.fastq(.gz)*|_2.fastq(.gz)*|.fastq(.gz)*)', '', args.sample[index])
29 output.write(re.sub('.*.dat', sample, line))
30 index += 1
31 else:
32 output.write(line)
33 x += 1
34 #output.write("\n")
35
36