Mercurial > repos > jeremie > breakdancer_test

comparison breakdancer.py @ 22:b4f641515363 draft

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Uploaded
author jeremie
date Tue, 01 Jul 2014 10:14:06 -0400
parents 199c0c7d3093
children d05d0c77b021
comparison
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21:199c0c7d3093 22:b4f641515363
3 import argparse, optparse, os, shutil, subprocess, sys, tempfile, shlex, time 3 import argparse, optparse, os, shutil, subprocess, sys, tempfile, shlex, time
4 4
5 5
6 parser = argparse.ArgumentParser(description='') 6 parser = argparse.ArgumentParser(description='')
7 7
8 parser.add_argument('-x', dest='binPath')
9 parser.add_argument ( '-i1', dest='input_bam', help='the bam input file' ) 8 parser.add_argument ( '-i1', dest='input_bam', help='the bam input file' )
10 parser.add_argument ( '-o1', dest='output_raw', help='the output file' ) 9 parser.add_argument ( '-o1', dest='output_raw', help='the output file' )
11 parser.add_argument ( '-o2', dest='output_vcf', help='the output file' ) 10 parser.add_argument ( '-o2', dest='output_vcf', help='the output file' )
12 11
13 12
14 tmp_dir = tempfile.mkdtemp() 13 tmp_dir = tempfile.mkdtemp()
15 errorFile = tmp_dir+"/errorLog" 14 errorFile = tmp_dir+"/errorLog"
16 15
17 currentDir = os.path.dirname(os.path.abspath(__file__)) 16 currentDir = os.path.dirname(os.path.abspath(__file__))
18 17
19 binPath = args.binPath 18 binPath = os.environ['BREAKDANCER_BIN']
20 bam2cfg = binPath+"/bam2cfg.pl" 19 bam2cfg = binPath+"/bam2cfg.pl"
21 breakdancer = binPath+"/breakdancer-max" 20 breakdancer = binPath+"/breakdancer-max"
22 breakdancer2vcf = binPath+"/breakdancer2vcf.py" 21 breakdancer2vcf = binPath+"/breakdancer2vcf.py"
23 22
24 23