Mercurial > repos > jetbrains > cmeth
comparison cmeth_wrapper.py @ 0:d7714f886224
Initial commit. Snapshot 61f45be
author | oleg@oleg-desktop |
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date | Thu, 29 Oct 2015 12:04:47 +0300 |
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-1:000000000000 | 0:d7714f886224 |
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1 #!/usr/bin/env python | |
2 | |
3 import os | |
4 import sys | |
5 import subprocess | |
6 | |
7 argv = sys.argv[1:] | |
8 print 'Arguments {0}'.format(argv) | |
9 | |
10 # Check command | |
11 if len(argv) == 4: | |
12 genome, fdr, action, bam = argv | |
13 assert action == "analyze" | |
14 else: | |
15 genome, fdr, action, bam1, bam2 = argv | |
16 assert action == "compare" | |
17 | |
18 # Configure main jar path | |
19 jar = os.environ.get("INTEGRATION_JAR") | |
20 print 'Using JAR distributive file {0}'.format(jar) | |
21 | |
22 cmd = 'java -cp {0} org.jetbrains.bio.genestack.FastaToTwoBitCLA {1} reference.2bit'.format(jar, genome) | |
23 print 'Converting reference genome fasta to 2bit: {0}'.format(cmd) | |
24 subprocess.check_call(cmd, cwd=None, shell=True) | |
25 | |
26 # See https://github.com/JetBrains-Research/cmeth for command line options | |
27 if action == "analyze": | |
28 cmd = 'java -cp {0} org.jetbrains.bio.cmeth.CmethCLA ' \ | |
29 'analyze -i {1} -r reference.2bit -fdr {2}'.format(jar, bam, fdr) | |
30 else: | |
31 cmd = 'java -cp {0} org.jetbrains.bio.cmeth.CmethCLA ' \ | |
32 'compare -1 {1} -2 {2} -r reference.2bit -fdr {3}'.format(jar, bam1, bam2, fdr) | |
33 print 'Launching cmeth: {0}'.format(cmd) | |
34 subprocess.check_call(cmd, cwd=None, shell=True) |