Mercurial > repos > jeremie > breakdancer_test
changeset 19:87a6ec1e2400 draft
Uploaded
| author | jeremie |
|---|---|
| date | Tue, 01 Jul 2014 09:34:51 -0400 |
| parents | d26b184866b4 |
| children | b122ca66efc7 |
| files | breakdancer.py |
| diffstat | 1 files changed, 7 insertions(+), 7 deletions(-) [+] |
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--- a/breakdancer.py Tue Jul 01 09:28:30 2014 -0400 +++ b/breakdancer.py Tue Jul 01 09:34:51 2014 -0400 @@ -14,27 +14,27 @@ errorFile = tmp_dir+"/errorLog" currentDir = os.path.dirname(os.path.abspath(__file__)) -bam2cfg_path = currentDir+"/bam2cfg.pl" -# breakdancer_path = "/usr/bin/breakdancer-max" -breakdancer_path = "breakdancer-max" -breakdancer2vcf_path = currentDir+"/breakdancer2vcf.py" +bam2cfg = "./bam2cfg.pl" +# breakdancer = "/usr/bin/breakdancer-max" +breakdancer = "breakdancer-max" +breakdancer2vcf = "./breakdancer2vcf.py" def bam2cfg(args): config = tmp_dir+"/breakdancer_config" - cmd = 'perl %s %s' % (bam2cfg_path, args.input_bam) + cmd = 'perl %s %s' % (bam2cfg, args.input_bam) execute(cmd, output=config) print ("\ncmd = %s \n" ) %(cmd) return config def breakdancer(args, config): - cmd = '%s %s' % (breakdancer_path, config) + cmd = '%s %s' % (breakdancer, config) execute(cmd, output=args.output_raw) def breakdancer2vcf(args): - cmd = "python %s -i %s -o %s" % ( breakdancer2vcf_path, args.output_raw, args.output_vcf ) + cmd = "python %s -i %s -o %s" % ( breakdancer2vcf, args.output_raw, args.output_vcf ) execute(cmd)