Mercurial > repos > jetbrains > cmeth

annotate cmeth_wrapper.py @ 1:5efe658422eb

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Sadly XTransform not supported
author oleg@oleg-desktop.times.labs.intellij.net
date Thu, 29 Oct 2015 16:42:41 +0300
parents d7714f886224
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
d7714f886224 Initial commit. Snapshot 61f45be
oleg@oleg-desktop
parents:
diff changeset
1 #!/usr/bin/env python
d7714f886224 Initial commit. Snapshot 61f45be
oleg@oleg-desktop
parents:
diff changeset
2
d7714f886224 Initial commit. Snapshot 61f45be
oleg@oleg-desktop
parents:
diff changeset
3 import os
d7714f886224 Initial commit. Snapshot 61f45be
oleg@oleg-desktop
parents:
diff changeset
4 import sys
d7714f886224 Initial commit. Snapshot 61f45be
oleg@oleg-desktop
parents:
diff changeset
5 import subprocess
d7714f886224 Initial commit. Snapshot 61f45be
oleg@oleg-desktop
parents:
diff changeset
6
d7714f886224 Initial commit. Snapshot 61f45be
oleg@oleg-desktop
parents:
diff changeset
7 argv = sys.argv[1:]
d7714f886224 Initial commit. Snapshot 61f45be
oleg@oleg-desktop
parents:
diff changeset
8 print 'Arguments {0}'.format(argv)
d7714f886224 Initial commit. Snapshot 61f45be
oleg@oleg-desktop
parents:
diff changeset
9
d7714f886224 Initial commit. Snapshot 61f45be
oleg@oleg-desktop
parents:
diff changeset
10 # Check command
d7714f886224 Initial commit. Snapshot 61f45be
oleg@oleg-desktop
parents:
diff changeset
11 if len(argv) == 4:
d7714f886224 Initial commit. Snapshot 61f45be
oleg@oleg-desktop
parents:
diff changeset
12 genome, fdr, action, bam = argv
d7714f886224 Initial commit. Snapshot 61f45be
oleg@oleg-desktop
parents:
diff changeset
13 assert action == "analyze"
d7714f886224 Initial commit. Snapshot 61f45be
oleg@oleg-desktop
parents:
diff changeset
14 else:
d7714f886224 Initial commit. Snapshot 61f45be
oleg@oleg-desktop
parents:
diff changeset
15 genome, fdr, action, bam1, bam2 = argv
d7714f886224 Initial commit. Snapshot 61f45be
oleg@oleg-desktop
parents:
diff changeset
16 assert action == "compare"
d7714f886224 Initial commit. Snapshot 61f45be
oleg@oleg-desktop
parents:
diff changeset
17
d7714f886224 Initial commit. Snapshot 61f45be
oleg@oleg-desktop
parents:
diff changeset
18 # Configure main jar path
d7714f886224 Initial commit. Snapshot 61f45be
oleg@oleg-desktop
parents:
diff changeset
19 jar = os.environ.get("INTEGRATION_JAR")
d7714f886224 Initial commit. Snapshot 61f45be
oleg@oleg-desktop
parents:
diff changeset
20 print 'Using JAR distributive file {0}'.format(jar)
d7714f886224 Initial commit. Snapshot 61f45be
oleg@oleg-desktop
parents:
diff changeset
21
d7714f886224 Initial commit. Snapshot 61f45be
oleg@oleg-desktop
parents:
diff changeset
22 cmd = 'java -cp {0} org.jetbrains.bio.genestack.FastaToTwoBitCLA {1} reference.2bit'.format(jar, genome)
d7714f886224 Initial commit. Snapshot 61f45be
oleg@oleg-desktop
parents:
diff changeset
23 print 'Converting reference genome fasta to 2bit: {0}'.format(cmd)
d7714f886224 Initial commit. Snapshot 61f45be
oleg@oleg-desktop
parents:
diff changeset
24 subprocess.check_call(cmd, cwd=None, shell=True)
d7714f886224 Initial commit. Snapshot 61f45be
oleg@oleg-desktop
parents:
diff changeset
25
d7714f886224 Initial commit. Snapshot 61f45be
oleg@oleg-desktop
parents:
diff changeset
26 # See https://github.com/JetBrains-Research/cmeth for command line options
d7714f886224 Initial commit. Snapshot 61f45be
oleg@oleg-desktop
parents:
diff changeset
27 if action == "analyze":
d7714f886224 Initial commit. Snapshot 61f45be
oleg@oleg-desktop
parents:
diff changeset
28 cmd = 'java -cp {0} org.jetbrains.bio.cmeth.CmethCLA ' \
d7714f886224 Initial commit. Snapshot 61f45be
oleg@oleg-desktop
parents:
diff changeset
29 'analyze -i {1} -r reference.2bit -fdr {2}'.format(jar, bam, fdr)
d7714f886224 Initial commit. Snapshot 61f45be
oleg@oleg-desktop
parents:
diff changeset
30 else:
d7714f886224 Initial commit. Snapshot 61f45be
oleg@oleg-desktop
parents:
diff changeset
31 cmd = 'java -cp {0} org.jetbrains.bio.cmeth.CmethCLA ' \
d7714f886224 Initial commit. Snapshot 61f45be
oleg@oleg-desktop
parents:
diff changeset
32 'compare -1 {1} -2 {2} -r reference.2bit -fdr {3}'.format(jar, bam1, bam2, fdr)
d7714f886224 Initial commit. Snapshot 61f45be
oleg@oleg-desktop
parents:
diff changeset
33 print 'Launching cmeth: {0}'.format(cmd)
d7714f886224 Initial commit. Snapshot 61f45be
oleg@oleg-desktop
parents:
diff changeset
34 subprocess.check_call(cmd, cwd=None, shell=True)