Previous changeset 8:2b6bb9d5e4e9 (2016-04-12) Next changeset 10:2b7eb79f0ba0 (2016-04-13) |
Commit message:
planemo upload |
modified:
VCFToolFilter/find_indiv.py VCFToolsStats/vcfToolsStats.xml |
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diff -r 2b6bb9d5e4e9 -r ce984119f669 VCFToolFilter/find_indiv.py --- 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 |
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@@ -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 |
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diff -r 2b6bb9d5e4e9 -r ce984119f669 VCFToolsStats/vcfToolsStats.xml --- a/VCFToolsStats/vcfToolsStats.xml Tue Apr 12 05:43:01 2016 -0400 +++ b/VCFToolsStats/vcfToolsStats.xml Wed Apr 13 03:32:59 2016 -0400 |
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@@ -67,8 +67,8 @@ --------------------------------------------------- -================ -VCF tools filter +=============== +VCF tools Stats ================ ----------- |