Mercurial > repos > jetbrains > zinbra
annotate 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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1 #!/usr/bin/env python |
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2 |
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3 import os |
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4 import sys |
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5 import subprocess |
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6 |
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7 argv = sys.argv[1:] |
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8 print 'Arguments {0}'.format(argv) |
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9 |
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10 # Check command |
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11 if len(argv) == 5: |
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12 genome, bin, fdr, action, bed = argv |
617b5857ce96
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13 assert action == "analyze" |
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14 else: |
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15 genome, bin, fdr, action, bed1, bed2 = argv |
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16 assert action == "compare" |
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17 |
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18 # Configure main jar path |
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19 jar = os.environ.get("INTEGRATION_JAR") |
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20 print 'Using JAR distributive file {0}'.format(jar) |
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21 |
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22 cmd = 'java -cp {0} org.jetbrains.bio.genestack.FastaToTwoBitCLA {1} reference.2bit'.format(jar, genome) |
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23 print 'Converting reference genome fasta to 2bit: {0}'.format(cmd) |
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24 subprocess.check_call(cmd, cwd=None, shell=True) |
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25 |
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26 # See https://github.com/JetBrains-Research/zinbra for command line options |
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27 if action == "analyze": |
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28 cmd = 'java -cp {0} org.jetbrains.bio.zinbra.ZinbraCLA ' \ |
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29 'analyze -i {1} -bed result.bed -r reference.2bit -b {3} -fdr {4}'.format(jar, bed, bin, fdr) |
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30 else: |
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31 cmd = 'java -cp {0} org.jetbrains.bio.zinbra.ZinbraCLA ' \ |
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32 '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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33 print 'Launching zinbra: {0}'.format(cmd) |
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34 subprocess.check_call(cmd, cwd=None, shell=True) |