Mercurial > repos > jeremie > breakdancer_test

comparison breakdancer.py @ 16:0fb455068d3c draft

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Uploaded
author jeremie
date Fri, 27 Jun 2014 08:52:40 -0400
parents 00952c82ebc5
children 87a6ec1e2400
comparison
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15:743d75da4658 16:0fb455068d3c
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 = "bam2cfg.pl" 16 currentDir = os.path.dirname(os.path.abspath(__file__))
17 bam2cfg_path = currentDir+"/bam2cfg.pl"
17 # breakdancer_path = "/usr/bin/breakdancer-max" 18 # breakdancer_path = "/usr/bin/breakdancer-max"
18 breakdancer_path = "breakdancer-max" 19 breakdancer_path = "breakdancer-max"
19 breakdancer2vcf_path = "breakdancer2vcf.py" 20 breakdancer2vcf_path = currentDir+"/breakdancer2vcf.py"
20 21
21 22
22 def bam2cfg(args): 23 def bam2cfg(args):
23 config = tmp_dir+"/breakdancer_config" 24 config = tmp_dir+"/breakdancer_config"
24 cmd = 'perl %s %s' % (bam2cfg_path, args.input_bam) 25 cmd = 'perl %s %s' % (bam2cfg_path, args.input_bam)