Mercurial > repos > gandres > vcftools_filter_stats_diversity

changeset 3:13ef7e92cdf1 draft

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planemo upload
author gandres
date Tue, 12 Apr 2016 10:47:45 -0400
parents 4980ad57ee36
children 2c6f8de56bc5
files VCFToolFilter/find_indiv.py
diffstat 1 files changed, 1 insertions(+), 2 deletions(-) [+]
line wrap: on
line diff
--- a/VCFToolFilter/find_indiv.py	Tue Apr 12 05:40:26 2016 -0400
+++ b/VCFToolFilter/find_indiv.py	Tue Apr 12 10:47:45 2016 -0400
@@ -12,9 +12,8 @@
 
 def get_field_chrs_options(dataset):
         options = []
-        chrs=os.popen("grep '##contig' %s"%dataset.file_name).read()[:-1].split('\n')
+        chrs=os.popen("grep -v '#' %s | cut -f1 | sort -u "%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