Mercurial > repos > jeremie > package_breakdancer_1_2_6

comparison breakdancer.py @ 6:88209fdd378d draft

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Uploaded
author jeremie
date Thu, 26 Jun 2014 09:16:55 -0400
parents caa1e0052ea6
children
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5:af25cf67aa0b 6:88209fdd378d
11 11
12 12
13 tmp_dir = tempfile.mkdtemp() 13 tmp_dir = tempfile.mkdtemp()
14 errorFile = tmp_dir+"/errorLog" 14 errorFile = tmp_dir+"/errorLog"
15 15
16 bam2cfg_path = "/home/jeremie/Tools/breakdancer-1.1.2/perl/bam2cfg.pl" 16 bam2cfg_path = "bam2cfg.pl"
17 breakdancer_path = "/usr/bin/breakdancer-max" 17 # breakdancer_path = "/usr/bin/breakdancer-max"
18 breakdancer2vcf_path = "/home/jeremie/Tools/breakdancer-1.1.2/breakdancer2vcf.py" 18 breakdancer_path = "breakdancer-max"
19 breakdancer2vcf_path = "breakdancer2vcf.py"
19 20
20 21
21 def bam2cfg(args): 22 def bam2cfg(args):
22 config = tmp_dir+"/breakdancer_config" 23 config = tmp_dir+"/breakdancer_config"
23 cmd = 'perl %s %s' % (bam2cfg_path, args.input_bam) 24 cmd = 'perl %s %s' % (bam2cfg_path, args.input_bam)