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comparison find_indiv.py @ 0:fe39a4677281 draft

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author dereeper
date Fri, 05 Aug 2016 09:46:55 -0400
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-1:000000000000 0:fe39a4677281
1 import sys
2 import os
3 import re
4
5 def get_field_samples_options(dataset):
6 options = []
7 line=os.popen("grep '#CHROM' %s"%dataset.file_name).read()[:-1].split('\t')
8 index=line.index('FORMAT')
9 for opt in line[index+1:] :
10 options.append((opt,opt, True))
11 return options
12
13 def get_field_chrs_options(dataset):
14 options = []
15 chrs=os.popen("grep '##contig' %s"%dataset.file_name).read()[:-1].split('\n')
16 for line in chrs:
17 opt=re.search('^##contig=<ID=(\w+),length=',line).group(1)
18 options.append((opt,opt, True))
19 return options
20