Mercurial > repos > gandres > vcftools_filter_stats_diversity
changeset 5:18fdec90ed8c draft
planemo upload
| author | gandres |
|---|---|
| date | Wed, 13 Apr 2016 04:28:32 -0400 |
| parents | 2c6f8de56bc5 |
| children | b726ff436103 |
| files | VCFToolFilter/find_indiv.py VCFToolsStats/vcfToolsStats.xml |
| diffstat | 2 files changed, 11 insertions(+), 5 deletions(-) [+] |
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--- a/VCFToolFilter/find_indiv.py Tue Apr 12 11:24:28 2016 -0400 +++ b/VCFToolFilter/find_indiv.py Wed Apr 13 04:28:32 2016 -0400 @@ -12,8 +12,14 @@ def get_field_chrs_options(dataset): options = [] - 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)) + 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("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 11:24:28 2016 -0400 +++ b/VCFToolsStats/vcfToolsStats.xml Wed Apr 13 04:28:32 2016 -0400 @@ -67,8 +67,8 @@ --------------------------------------------------- -================ -VCF tools filter +=============== +VCF tools Stats ================ -----------