Mercurial > repos > jeremie > breakdancer_bin
changeset 19:b83483e9b1e8 draft
Uploaded
author | jeremie |
---|---|
date | Mon, 07 Jul 2014 04:04:13 -0400 |
parents | 0e73928aa0ca |
children | 93315e5d6420 |
files | breakdancer.py |
diffstat | 1 files changed, 5 insertions(+), 5 deletions(-) [+] |
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--- a/breakdancer.py Wed Jul 02 10:26:30 2014 -0400 +++ b/breakdancer.py Mon Jul 07 04:04:13 2014 -0400 @@ -26,10 +26,10 @@ -binPath = os.environ['BREAKDANCER_BIN'] +# binPath = os.environ['BREAKDANCER_BIN'] -bam2cfgPath = binPath+"/bam2cfg.pl" -breakdancer2vcfPath = binPath+"/breakdancer2vcf.py" +# bam2cfgPath = binPath+"/bam2cfg.pl" +# breakdancer2vcfPath = binPath+"/breakdancer2vcf.py" # def bam2cfg(args, tempDir): @@ -147,7 +147,7 @@ # bam2cfg config = tempDir+"/breakdancer_config" - cmd = 'perl %s %s' % (bam2cfgPath, args.inputBamFile) + cmd = 'bam2cfg.pl %s' % (args.inputBamFile) execute(cmd, output=config) # breakdancer @@ -171,7 +171,7 @@ # breakdancer2vcf if args.outputVcfFile: - cmd = "python %s -i %s -o %s" % (breakdancer2vcfPath, args.outputRawFile, args.outputVcfFile) + cmd = "breakdancer2vcf.py -i %s -o %s" % (args.outputRawFile, args.outputVcfFile) execute(cmd) # quelques tests