diff zinbra_wrapper.py @ 10:eccf47de1192 draft default tip

Deleted selected files

--- a/zinbra_wrapper.py	Thu Nov 12 12:03:47 2015 +0300
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,34 +0,0 @@
-#!/usr/bin/env python
-
-import os
-import sys
-import subprocess
-
-argv = sys.argv[1:]
-print 'Arguments {0}'.format(argv)
-
-# Check command
-if len(argv) == 5:
-    genome, bin, fdr, action, bed = argv
-    assert action == "analyze"
-else:
-    genome, bin, fdr, action, bed1, bed2 = argv
-    assert action == "compare"
-
-# Configure main jar path
-jar = os.environ.get("INTEGRATION_JAR")
-print 'Using JAR distributive file {0}'.format(jar)
-
-cmd = 'java -cp {0} org.jetbrains.bio.genestack.FastaToTwoBitCLA {1} reference.2bit'.format(jar, genome)
-print 'Converting reference genome fasta to 2bit: {0}'.format(cmd)
-subprocess.check_call(cmd, cwd=None, shell=True)
-
-# See https://github.com/JetBrains-Research/zinbra for command line options
-if action == "analyze":
-    cmd = 'java -cp {0} org.jetbrains.bio.zinbra.ZinbraCLA ' \
-          'analyze -i {1} -bed result.bed -r reference.2bit -b {3} -fdr {4}'.format(jar, bed, bin, fdr)
-else:
-    cmd = 'java -cp {0} org.jetbrains.bio.zinbra.ZinbraCLA ' \
-          'compare -1 {1} -2 {2} -bed result.bed -r reference.2bit -b {3} -fdr {4}'.format(jar, bed1, bed2, bin, fdr)
-print 'Launching zinbra: {0}'.format(cmd)
-subprocess.check_call(cmd, cwd=None, shell=True)