view VCFToolFilter/find_indiv.py @ 10:2b7eb79f0ba0 draft

planemo upload

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')
	if len(chr)>0:
		for line in chrs:
			opt=re.search('^##contig=<ID=(\w+),length=',line).group(1)
			options.append((opt,opt, True))
	else :
        	chrs=os.popen("perl GetChromOfVCF.pl %s | cut -f1 "%dataset.file_name).read()[:-1].split('\n')
        	for opt in chrs:
                	options.append((opt,opt, True))
        return options