Mercurial > repos > jetbrains > zinbra
comparison zinbra.py @ 1:8cbb06892b62
Release version:
https://github.com/JetBrains-Research/galaxy/commit/a138a0b8f1d471d464a09a95daf5791f41fa0ec5
author | Oleg Shpynov <oleg.shpynov@gmail.com> |
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date | Wed, 28 Oct 2015 11:28:49 +0300 |
parents | 5f97f28e65ca |
children | 0eb50728861a |
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0:5f97f28e65ca | 1:8cbb06892b62 |
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11 argv = sys.argv[1:] | 11 argv = sys.argv[1:] |
12 print 'Arguments {0}'.format(argv) | 12 print 'Arguments {0}'.format(argv) |
13 genome, bed, bin, fdr = argv | 13 genome, bed, bin, fdr = argv |
14 | 14 |
15 # Configure main jar path | 15 # Configure main jar path |
16 epigenomeJar = os.environ.get("EPIGENOME_JAR") | 16 jar = os.environ.get("EPIGENOME_JAR") |
17 print 'Using JAR distributive file {0}'.format(epigenomeJar) | 17 print 'Using JAR distributive file {0}'.format(jar) |
18 | 18 |
19 print 'Genome file {0}'.format(genome) | 19 cmd = 'java -cp {0} org.jetbrains.bio.genestack.FastaToTwoBitCLA {1} reference.2bit'.format(jar, genome) |
20 print 'Converting reference genome fasta to 2bit: {0}'.format(cmd) | |
21 subprocess.check_call(cmd, cwd=None, shell=True) | |
20 | 22 |
21 # See https://github.com/JetBrains-Research/zinbra for command line options | 23 # See https://github.com/JetBrains-Research/zinbra for command line options |
22 # cla.argument_string_list() is configured at ZinbraApplications#rebuildArgumentStringsFromVisualOptions | 24 # cla.argument_string_list() is configured at ZinbraApplications#rebuildArgumentStringsFromVisualOptions |
23 cmd = 'java -cp {0} org.jetbrains.bio.zinbra.ZinbraCLA ' \ | 25 cmd = 'java -cp {0} org.jetbrains.bio.zinbra.ZinbraCLA ' \ |
24 'analyze -i {1} -bed result.bed -r {2} -b {3} -fdr {4}'.format(epigenomeJar, | 26 'analyze -i {1} -bed result.bed -r reference.2bit -b {3} -fdr {4}'.format(jar, |
25 bed, | 27 bed, |
26 genome, | 28 bin, fdr) |
27 bin, fdr) | |
28 print 'Launching zinbra: {0}'.format(cmd) | 29 print 'Launching zinbra: {0}'.format(cmd) |
29 subprocess.check_call(cmd, cwd=None, shell=True) | 30 subprocess.check_call(cmd, cwd=None, shell=True) |
30 |