diff edena_ass_wrapper.py @ 0:60609a9cef3b draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/edena_ass_wrapper.py	Mon Sep 09 05:44:31 2013 -0400
@@ -0,0 +1,103 @@
+# -*- coding: utf-8 -*-
+"""
+Edena (assembling)
+version 0.2.1 ([e-mail])
+"""
+
+import optparse
+import shutil
+import subprocess
+import sys
+
+def __main__():
+    # load arguments
+    print 'Parsing Edena (assembling) input options...'
+    parser = optparse.OptionParser(description='Edena assembly')
+    parser.add_option('--ovl_input', dest='ovl_input', help='')
+    parser.add_option('--overlapCutoff', dest='overlapCutoff', type='int', help='')
+    parser.add_option('--cc', action="store_true", dest='cc', help='')
+    parser.add_option('--discardNonUsable', action="store_true", dest='discardNonUsable', help='')
+    parser.add_option('--minContigSize', dest='minContigSize', type='int', help='')
+    parser.add_option('--minCoverage', dest='minCoverage', type='float', help='')
+    parser.add_option('--trim', dest='trim', type='int', help='')
+    parser.add_option('--peHorizon', dest='peHorizon', type='int', help='')
+    parser.add_option('--covStats', dest='covStats', help='')
+    parser.add_option('--out_contigs_cov', dest='out_contigs_cov', help='')
+    parser.add_option('--out_contigs_fasta', dest='out_contigs_fasta', help='')
+    parser.add_option('--out_contigs_lay', dest='out_contigs_lay', help='')
+    parser.add_option('--out_log_txt', dest='out_log_txt', help='')
+    parser.add_option('--out_nodesInfo', dest='out_nodesInfo', help='')
+    parser.add_option('--out_nodesPosition', dest='out_nodesPosition', help='')
+    parser.add_option('--logfile', dest='logfile', help='logfile')
+    (options, args) = parser.parse_args()
+    if len(args) > 0:
+        parser.error('Wrong number of arguments')
+    
+    # build Edena (assembling) command to be executed
+    ovl_input = '-e %s' % (options.ovl_input)
+    if options.overlapCutoff is not None:
+        overlapCutoff = '-m %d' % (options.overlapCutoff)
+    else:
+        overlapCutoff = ''
+    if options.cc:
+        cc = '-cc yes'
+    else:
+        cc = '-cc no'
+    if options.discardNonUsable:
+        discardNonUsable = '-discardNonUsable yes'
+    else:
+        discardNonUsable = '-discardNonUsable no'
+    if options.minContigSize is not None:
+        minContigSize = '-c %d' % (options.minContigSize)
+    else:
+        minContigSize = ''
+    if options.minCoverage is not None:
+        minCoverage = '-minCoverage %s' % (options.minCoverage)
+    else:
+        minCoverage = ''
+    if options.trim is not None:
+        trim = '-trim %d' % (options.trim)
+    else:
+        trim = ''
+    if options.peHorizon is not None:
+        peHorizon = '-peHorizon %d' % (options.peHorizon)
+    else:
+        peHorizon = ''
+    covStats = options.covStats
+    out_contigs_cov = options.out_contigs_cov
+    out_contigs_fasta = options.out_contigs_fasta
+    out_contigs_lay = options.out_contigs_lay
+    out_log_txt = options.out_log_txt
+    out_nodesInfo = options.out_nodesInfo
+    out_nodesPosition = options.out_nodesPosition
+    logfile = options.logfile
+    
+    # Build Edena (assembling) command
+    cmd1 = '%s %s %s %s %s %s %s %s' % (ovl_input, overlapCutoff, cc, discardNonUsable, minContigSize, minCoverage, trim, peHorizon)
+    cmd2 = 'edena %s' % ( cmd1 )
+    print '\nEdena (assembling) command to be executed: \n %s' % ( cmd2 )
+    
+    # Execution of Edena
+    print 'Executing Edena (assembling)...'
+    if logfile:
+        log = open(logfile, 'w')
+    else:
+        log = sys.stdout
+    try:
+        subprocess.check_call(cmd2, stdout=log, stderr=subprocess.STDOUT, shell=True) # need to redirect stderr because edena writes some logging info there (e.g. "Condensing overlaps graph...")
+    finally:
+        if log != sys.stdout:
+            log.close()
+    print 'Edena (assembling) executed!'
+
+    shutil.move("covStats", covStats)
+    shutil.move("out_contigs.cov", out_contigs_cov)
+    shutil.move("out_contigs.fasta", out_contigs_fasta)
+    shutil.move("out_contigs.lay", out_contigs_lay)
+    shutil.move("out_log.txt", out_log_txt)
+    shutil.move("out_nodesInfo", out_nodesInfo)
+    shutil.move("out_nodesPosition", out_nodesPosition)
+
+
+if __name__ == "__main__":
+    __main__()