Mercurial > repos > jeremie > breakdancer_test
changeset 27:463a9ed9655b draft
Uploaded
author | jeremie |
---|---|
date | Tue, 01 Jul 2014 10:51:36 -0400 |
parents | acec6ba9884a |
children | abca53dd8b7b |
files | breakdancer.py |
diffstat | 1 files changed, 6 insertions(+), 6 deletions(-) [+] |
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--- a/breakdancer.py Tue Jul 01 10:39:41 2014 -0400 +++ b/breakdancer.py Tue Jul 01 10:51:36 2014 -0400 @@ -21,26 +21,26 @@ binPath=binPath[:-1] print("--"+binPath+"--") -bam2cfg = str(binPath)+"/bam2cfg.pl" -breakdancer = binPath+"/breakdancer-max" -breakdancer2vcf = binPath+"/breakdancer2vcf.py" +bam2cfgPath = str(binPath)+"/bam2cfg.pl" +breakdancerPath = binPath+"/breakdancer-max" +breakdancer2vcfPath = binPath+"/breakdancer2vcf.py" def bam2cfg(args): config = tmp_dir+"/breakdancer_config" - cmd = 'perl %s %s' % (bam2cfg, args.input_bam) + cmd = 'perl %s %s' % (bam2cfgPath, args.input_bam) execute(cmd, output=config) print ("\ncmd = %s \n" ) %(cmd) return config def breakdancer(args, config): - cmd = '%s %s' % (breakdancer, config) + cmd = '%s %s' % (breakdancerPath, config) execute(cmd, output=args.output_raw) def breakdancer2vcf(args): - cmd = "python %s -i %s -o %s" % ( breakdancer2vcf, args.output_raw, args.output_vcf ) + cmd = "python %s -i %s -o %s" % ( breakdancer2vcfPath, args.output_raw, args.output_vcf ) execute(cmd)