Mercurial > repos > gandres > vcftools_filter_stats_diversity
view VCFToolFilter/find_indiv.py @ 6:1420a55ca72b draft
planemo upload
author | gandres |
---|---|
date | Mon, 21 Mar 2016 10:22:36 -0400 |
parents | |
children | ce984119f669 |
line wrap: on
line source
import sys import os import re def get_field_samples_options(dataset): options = [] line=os.popen("grep '#CHROM' %s"%dataset.file_name).read()[:-1].split('\t') index=line.index('FORMAT') for opt in line[index+1:] : options.append((opt,opt, True)) return options def get_field_chrs_options(dataset): options = [] chrs=os.popen("grep '##contig' %s"%dataset.file_name).read()[:-1].split('\n') for line in chrs: opt=re.search('^##contig=<ID=(\w+),length=',line).group(1) options.append((opt,opt, True)) return options