Mercurial > repos > jetbrains > zinbra
diff zinbra.py @ 0:5f97f28e65ca
Initial commit
author | Oleg Shpynov <oleg.shpynov@gmail.com> |
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date | Tue, 27 Oct 2015 14:20:42 +0300 |
parents | |
children | 8cbb06892b62 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/zinbra.py Tue Oct 27 14:20:42 2015 +0300 @@ -0,0 +1,30 @@ +#!/usr/bin/env python +""" +Python wrapper for zinbra.xml +Usage: zinbra.py "${genome}" "${bed}" "${bin}" "${fdr}" +""" + +import os +import sys +import subprocess + +argv = sys.argv[1:] +print 'Arguments {0}'.format(argv) +genome, bed, bin, fdr = argv + +# Configure main jar path +epigenomeJar = os.environ.get("EPIGENOME_JAR") +print 'Using JAR distributive file {0}'.format(epigenomeJar) + +print 'Genome file {0}'.format(genome) + +# See https://github.com/JetBrains-Research/zinbra for command line options +# cla.argument_string_list() is configured at ZinbraApplications#rebuildArgumentStringsFromVisualOptions +cmd = 'java -cp {0} org.jetbrains.bio.zinbra.ZinbraCLA ' \ + 'analyze -i {1} -bed result.bed -r {2} -b {3} -fdr {4}'.format(epigenomeJar, + bed, + genome, + bin, fdr) +print 'Launching zinbra: {0}'.format(cmd) +subprocess.check_call(cmd, cwd=None, shell=True) +