Mercurial > repos > jowong > prince_galaxy

comparison prince_postprocess.py @ 0:88748989a22a draft default tip

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planemo upload
author jowong
date Tue, 13 Nov 2018 11:41:37 -0500
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-1:000000000000 0:88748989a22a
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 input.add_argument('-f', '--file', nargs='+', required=True, help="File of forward reads in galaxy convention")
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 sample_dict={}
22 path_index = 0
23 for path in args.file:
24 with open(path) as f:
25 for line in f:
26 sample_dict[re.sub(".*/","",line)] = sample[path_index]
27 path_index += 1
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34
35 with open(args.input[0]) as prince_output:
36 with open('prince_postprocess_output.txt', 'w') as output:
37 x = 1
38 index = 0
39 for line in prince_output:
40 if x%2 == 0:
41 entries =line.rstrip().split(',')
42 sample = re.sub('(_1.fastq(.gz)*|_2.fastq(.gz)*|.fastq(.gz)*)', '', sample_dict[entries[0]])
43 output.write(re.sub(entries[0], sample, line))
44 index += 1
45 else:
46 output.write(line)
47 x += 1
48 #output.write("\n")
49
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