0
|
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)
|