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author oleg@oleg-desktop.times.labs.intellij.net
date Wed, 28 Oct 2015 19:02:21 +0300
parents 0eb50728861a
children 7d532e820976
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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 Usage: zinbra.py "${genome}" "${bed}" "${bin}" "${fdr}"
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5 """
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6
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7 import os
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8 import sys
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9 import subprocess
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10
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11 argv = sys.argv[1:]
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12 print 'Arguments {0}'.format(argv)
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13 genome, bed, bin, fdr = argv
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15 # Configure main jar path
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16 jar = os.environ.get("INTEGRATION_JAR")
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17 print 'Using JAR distributive file {0}'.format(jar)
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19 cmd = 'java -cp {0} org.jetbrains.bio.genestack.FastaToTwoBitCLA {1} reference.2bit'.format(jar, genome)
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20 print 'Converting reference genome fasta to 2bit: {0}'.format(cmd)
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21 subprocess.check_call(cmd, cwd=None, shell=True)
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23 # See https://github.com/JetBrains-Research/zinbra for command line options
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24 # cla.argument_string_list() is configured at ZinbraApplications#rebuildArgumentStringsFromVisualOptions
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25 cmd = 'java -cp {0} org.jetbrains.bio.zinbra.ZinbraCLA ' \
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26 'analyze -i {1} -bed result.bed -r reference.2bit -b {3} -fdr {4}'.format(jar,
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27 bed,
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28 bin, fdr)
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29 print 'Launching zinbra: {0}'.format(cmd)
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30 subprocess.check_call(cmd, cwd=None, shell=True)