Mercurial > repos > gandres > vcftools_filter_stats_diversity
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(-) [+] |
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--- 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 ================ -----------