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comparison 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
comparison
equal deleted inserted replaced
5:ae6878068d07 6:7d532e820976
1 #!/usr/bin/env python 1 #!/usr/bin/env python
2 """ 2 """
3 Python wrapper for zinbra.xml 3 Python wrapper for zinbra.xml
4 Usage: zinbra.py "${genome}" "${bed}" "${bin}" "${fdr}"
5 """ 4 """
6 5
7 import os 6 import os
8 import sys 7 import sys
9 import subprocess 8 import subprocess
10 9
11 argv = sys.argv[1:] 10 argv = sys.argv[1:]
12 print 'Arguments {0}'.format(argv) 11 print 'Arguments {0}'.format(argv)
13 genome, bed, bin, fdr = argv 12
13 # Check command
14 if len(argv) == 5:
15 genome, bin, fdr, action, bed = argv
16 assert action == "analyze"
17 else:
18 genome, bin, fdr, action, bed1, bed2 = argv
19 assert action == "compare"
14 20
15 # Configure main jar path 21 # Configure main jar path
16 jar = os.environ.get("INTEGRATION_JAR") 22 jar = os.environ.get("INTEGRATION_JAR")
17 print 'Using JAR distributive file {0}'.format(jar) 23 print 'Using JAR distributive file {0}'.format(jar)
18 24
19 cmd = 'java -cp {0} org.jetbrains.bio.genestack.FastaToTwoBitCLA {1} reference.2bit'.format(jar, genome) 25 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) 26 print 'Converting reference genome fasta to 2bit: {0}'.format(cmd)
21 subprocess.check_call(cmd, cwd=None, shell=True) 27 subprocess.check_call(cmd, cwd=None, shell=True)
22 28
23 # See https://github.com/JetBrains-Research/zinbra for command line options 29 # See https://github.com/JetBrains-Research/zinbra for command line options
24 # cla.argument_string_list() is configured at ZinbraApplications#rebuildArgumentStringsFromVisualOptions 30 if action == "analyze":
25 cmd = 'java -cp {0} org.jetbrains.bio.zinbra.ZinbraCLA ' \ 31 cmd = 'java -cp {0} org.jetbrains.bio.zinbra.ZinbraCLA ' \
26 'analyze -i {1} -bed result.bed -r reference.2bit -b {3} -fdr {4}'.format(jar, 32 'analyze -i {1} -bed result.bed -r reference.2bit -b {3} -fdr {4}'.format(jar, bed, bin, fdr)
27 bed, 33 else:
28 bin, fdr) 34 cmd = 'java -cp {0} org.jetbrains.bio.zinbra.ZinbraCLA ' \
35 'compare -1 {1} -2 {2} -bed result.bed -r reference.2bit -b {3} -fdr {4}'.format(jar, bed1, bed2, bin, fdr)
29 print 'Launching zinbra: {0}'.format(cmd) 36 print 'Launching zinbra: {0}'.format(cmd)
30 subprocess.check_call(cmd, cwd=None, shell=True) 37 subprocess.check_call(cmd, cwd=None, shell=True)