changeset 9:ce984119f669 draft

planemo upload
author gandres
date Wed, 13 Apr 2016 03:32:59 -0400
parents 2b6bb9d5e4e9
children 2b7eb79f0ba0
files VCFToolFilter/find_indiv.py VCFToolsStats/vcfToolsStats.xml
diffstat 2 files changed, 4 insertions(+), 5 deletions(-) [+]
line wrap: on
line diff
--- a/VCFToolFilter/find_indiv.py	Tue Apr 12 05:43:01 2016 -0400
+++ b/VCFToolFilter/find_indiv.py	Wed Apr 13 03:32:59 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')
-        for line in chrs:
-		opt=re.search('^##contig=<ID=(\w+),length=',line).group(1)
+        chrs=os.popen("grep -v '#' %s | cut -f1 | sort -u "%dataset.file_name).read()[:-1].split('\n')
+        for opt in chrs:
                 options.append((opt,opt, True))
         return options
 
--- a/VCFToolsStats/vcfToolsStats.xml	Tue Apr 12 05:43:01 2016 -0400
+++ b/VCFToolsStats/vcfToolsStats.xml	Wed Apr 13 03:32:59 2016 -0400
@@ -67,8 +67,8 @@
 ---------------------------------------------------
 
 
-================
-VCF tools filter
+===============
+VCF tools Stats
 ================
 
 -----------