--- a/edena_ovl_wrapper.py	Mon Sep 09 05:44:31 2013 -0400
+++ b/edena_ovl_wrapper.py	Fri Oct 18 14:09:11 2013 -0400
@@ -13,11 +13,11 @@
     # load arguments
     print 'Parsing Edena (overlapping) input options...'
     parser = optparse.OptionParser()
-    parser.add_option('--unpaired_input', dest='unpaired_input', help='')
-    parser.add_option('--dr_pair_1', dest='dr_pair_1', help='')
-    parser.add_option('--dr_pair_2', dest='dr_pair_2', help='')
-    parser.add_option('--rd_pair_1', dest='rd_pair_1', help='')
-    parser.add_option('--rd_pair_2', dest='rd_pair_2', help='')
+    parser.add_option('--unpaired_input', action='append', dest='unpaired_input', help='')
+    parser.add_option('--dr_pair_1', action='append', dest='dr_pair_1', help='')
+    parser.add_option('--dr_pair_2', action='append', dest='dr_pair_2', help='')
+    parser.add_option('--rd_pair_1', action='append', dest='rd_pair_1', help='')
+    parser.add_option('--rd_pair_2', action='append', dest='rd_pair_2', help='')
     parser.add_option('--nThreads', dest='nThreads', type='int', help='')
     parser.add_option('--minOlap', dest='minOlap', type='int', help='')
     parser.add_option('--readsTruncation', dest='readsTruncation', type='int', help='')
@@ -26,71 +26,54 @@
     (options, args) = parser.parse_args()
     if len(args) > 0:
         parser.error('Wrong number of arguments')
-    
+
     # build Edena (overlapping) command to be executed
     # unpaired input(s)
     if options.unpaired_input:
-        unpaired_inputs = options.unpaired_input.split('+')[0:-1]
         unpaired_input = '-r'
-        for item in unpaired_inputs:
+        for item in options.unpaired_input:
             unpaired_input += ' %s' % (item)
     else:
         unpaired_input = ''
     # direct-reverse paired-end files
     if options.dr_pair_1 and options.dr_pair_2:
-        dr_pairs_1 = options.dr_pair_1.split('+')[0:-1]
-        dr_pairs_2 = options.dr_pair_2.split('+')[0:-1]
         dr_pairs = '-DRpairs'
-        for i in xrange(len(dr_pairs_1)):
-            dr_pairs += ' %s %s' % (dr_pairs_1[i], dr_pairs_2[i])
+        for i in range(len(options.dr_pair_1)):
+            dr_pairs += ' %s %s' % (options.dr_pair_1[i], options.dr_pair_2[i])
     else:
         dr_pairs = ''
      # reverse-direct paired-end files
     if options.rd_pair_1 and options.rd_pair_2:
-        rd_pairs_1 = options.rd_pair_1.split('+')[0:-1]
-        rd_pairs_2 = options.rd_pair_2.split('+')[0:-1]
         rd_pairs = '-RDpairs'
-        for i in xrange(len(rd_pairs_1)):
-            rd_pairs += ' %s %s' % (rd_pairs_1[i], rd_pairs_2[i])
+        for i in range(len(options.rd_pair_1)):
+            rd_pairs += ' %s %s' % (options.rd_pair_1[i], options.rd_pair_2[i])
     else:
         rd_pairs = ''
     # nThreads
-    if options.nThreads is not None:
-        nThreads = '-nThreads %d' % (options.nThreads)
-    else:
-        nThreads = ''
+    nThreads = '-nThreads %d' % (options.nThreads) if options.nThreads is not None else ''
     # minimum overlap
-    if options.minOlap is not None:
-        minOlap = '-M %d' % (options.minOlap)
-    else:
-        minOlap = ''
+    minOlap = '-M %d' % (options.minOlap) if options.minOlap is not None else ''
     # 3' end reads truncation
-    if options.readsTruncation is not None:
-        readsTruncation = '-t %d' % (options.readsTruncation)
-    else:
-        readsTruncation = ''
+    readsTruncation = '-t %d' % (options.readsTruncation) if options.readsTruncation is not None else ''
     # output file(s)
     output = options.output
     logfile = options.logfile
-    
+
     # Build Edena (overlapping) command
     cmd = 'edena %s %s %s %s %s %s -p galaxy_output' % (unpaired_input, dr_pairs, rd_pairs, nThreads, minOlap, readsTruncation)
-    print '\nEdena (overlapping) command to be executed: \n %s' % ( cmd )
-    
+    print '\nEdena (overlapping) command to be executed:\n %s' % (cmd)
+
     # Execution of Edena
     print 'Executing Edena (overlapping)...'
-    if logfile:
-        log = open(logfile, 'w')
-    else:
-        log = sys.stdout
+    log = open(logfile, 'w') if logfile else sys.stdout
     try:
         subprocess.check_call(cmd, stdout=log, stderr=subprocess.STDOUT, shell=True) # need to redirect stderr because edena writes some logging info there (e.g. "Computing overlaps >=30...")
     finally:
         if log != sys.stdout:
             log.close()
     print 'Edena (overlapping) executed!'
-    
-    shutil.move( "galaxy_output.ovl", output)
+
+    shutil.move('galaxy_output.ovl', output)
 
 
 if __name__ == "__main__":