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annotate zinbra.py @ 6:7d532e820976

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Support comparison in zinbra. 3fba761
author oleg@oleg-desktop.times.labs.intellij.net
date Wed, 28 Oct 2015 20:08:20 +0300
parents 0eb50728861a
children
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1 #!/usr/bin/env python
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2 """
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3 Python wrapper for zinbra.xml
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4 """
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5
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6 import os
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7 import sys
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8 import subprocess
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9
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10 argv = sys.argv[1:]
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11 print 'Arguments {0}'.format(argv)
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12
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13 # Check command
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14 if len(argv) == 5:
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15 genome, bin, fdr, action, bed = argv
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16 assert action == "analyze"
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17 else:
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18 genome, bin, fdr, action, bed1, bed2 = argv
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19 assert action == "compare"
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21 # Configure main jar path
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22 jar = os.environ.get("INTEGRATION_JAR")
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23 print 'Using JAR distributive file {0}'.format(jar)
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25 cmd = 'java -cp {0} org.jetbrains.bio.genestack.FastaToTwoBitCLA {1} reference.2bit'.format(jar, genome)
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26 print 'Converting reference genome fasta to 2bit: {0}'.format(cmd)
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27 subprocess.check_call(cmd, cwd=None, shell=True)
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29 # See https://github.com/JetBrains-Research/zinbra for command line options
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30 if action == "analyze":
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31 cmd = 'java -cp {0} org.jetbrains.bio.zinbra.ZinbraCLA ' \
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32 'analyze -i {1} -bed result.bed -r reference.2bit -b {3} -fdr {4}'.format(jar, bed, bin, fdr)
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33 else:
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34 cmd = 'java -cp {0} org.jetbrains.bio.zinbra.ZinbraCLA ' \
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35 'compare -1 {1} -2 {2} -bed result.bed -r reference.2bit -b {3} -fdr {4}'.format(jar, bed1, bed2, bin, fdr)
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36 print 'Launching zinbra: {0}'.format(cmd)
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37 subprocess.check_call(cmd, cwd=None, shell=True)