Mercurial > repos > jetbrains > zinbra
diff zinbra_wrapper.py @ 7:617b5857ce96
Snapshot 61f45be of dev repo
author | oleg@oleg-desktop.times.labs.intellij.net |
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date | Thu, 29 Oct 2015 11:57:02 +0300 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/zinbra_wrapper.py Thu Oct 29 11:57:02 2015 +0300 @@ -0,0 +1,34 @@ +#!/usr/bin/env python + +import os +import sys +import subprocess + +argv = sys.argv[1:] +print 'Arguments {0}'.format(argv) + +# Check command +if len(argv) == 5: + genome, bin, fdr, action, bed = argv + assert action == "analyze" +else: + genome, bin, fdr, action, bed1, bed2 = argv + assert action == "compare" + +# Configure main jar path +jar = os.environ.get("INTEGRATION_JAR") +print 'Using JAR distributive file {0}'.format(jar) + +cmd = 'java -cp {0} org.jetbrains.bio.genestack.FastaToTwoBitCLA {1} reference.2bit'.format(jar, genome) +print 'Converting reference genome fasta to 2bit: {0}'.format(cmd) +subprocess.check_call(cmd, cwd=None, shell=True) + +# See https://github.com/JetBrains-Research/zinbra for command line options +if action == "analyze": + cmd = 'java -cp {0} org.jetbrains.bio.zinbra.ZinbraCLA ' \ + 'analyze -i {1} -bed result.bed -r reference.2bit -b {3} -fdr {4}'.format(jar, bed, bin, fdr) +else: + cmd = 'java -cp {0} org.jetbrains.bio.zinbra.ZinbraCLA ' \ + 'compare -1 {1} -2 {2} -bed result.bed -r reference.2bit -b {3} -fdr {4}'.format(jar, bed1, bed2, bin, fdr) +print 'Launching zinbra: {0}'.format(cmd) +subprocess.check_call(cmd, cwd=None, shell=True)