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comparison reformat.py @ 0:20f12e7c279b draft

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Imported from capsule None
author bgruening
date Mon, 05 May 2014 04:23:26 -0400
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-1:000000000000 0:20f12e7c279b
1 #!/usr/bin/env python
2
3 """
4 Extract importent information from the standard output file and put it in some standard format, like BED and tabular.
5 """
6
7 import sys
8
9 bed = open(sys.argv[2], 'w+')
10 tabular = open(sys.argv[3], 'w+')
11
12 for line in open(sys.argv[1]):
13 # Sequence 'CRISPRs' (10798 bp)
14 if line.startswith('Sequence '):
15 organism = line.split("'")[1]
16 # CRISPR 1 Range: 679197 - 682529
17 if line.startswith('CRISPR '):
18 start,end = line.split('Range:')[1].strip().split('-')
19 start = start.strip()
20 end = end.strip()
21 bed.write('%s\t%s\t%s\n' % (organism, start, end))
22 if line.rstrip().endswith(']'):
23 cols = line.split()
24 tabular.write("%s\t%s\t%s\t%s\t%s\t%s\n" % (organism, cols[0], cols[1], cols[2], cols[4].rstrip(','), cols[5]))