Mercurial > repos > bgruening > minced
view reformat.py @ 4:08e4ca411ea6 draft default tip
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/minced commit edee3afc7d729be9a224d21729bb7490a3761a0e-dirty
author | bgruening |
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date | Sun, 18 Sep 2016 06:18:17 -0400 |
parents | 5ead4a4f46bd |
children |
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#!/usr/bin/env python """ Extract importent information from the standard output file and put it in some standard format, like BED and tabular. """ import sys bed = open(sys.argv[2], 'w+') tabular = open(sys.argv[3], 'w+') for line in open(sys.argv[1]): # Sequence 'CRISPRs' (10798 bp) if line.startswith('Sequence '): organism = line.split("'")[1] # CRISPR 1 Range: 679197 - 682529 if line.startswith('CRISPR '): start,end = line.split('Range:')[1].strip().split('-') start = start.strip() end = end.strip() bed.write('%s\t%s\t%s\n' % (organism, start, end)) if line.rstrip().endswith(']'): cols = line.split() 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]))