--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/edena_ovl_wrapper.py	Mon Sep 09 05:44:31 2013 -0400
@@ -0,0 +1,97 @@
+# -*- coding: utf-8 -*-
+"""
+Edena (overlapping)
+version 0.2.1 (andrea.pinna@crs4.it)
+"""
+
+import optparse
+import shutil
+import subprocess
+import sys
+
+def __main__():
+    # 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('--nThreads', dest='nThreads', type='int', help='')
+    parser.add_option('--minOlap', dest='minOlap', type='int', help='')
+    parser.add_option('--readsTruncation', dest='readsTruncation', type='int', help='')
+    parser.add_option('--output', dest='output', help='')
+    parser.add_option('--logfile', dest='logfile', help='')
+    (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:
+            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])
+    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])
+    else:
+        rd_pairs = ''
+    # nThreads
+    if options.nThreads is not None:
+        nThreads = '-nThreads %d' % (options.nThreads)
+    else:
+        nThreads = ''
+    # minimum overlap
+    if options.minOlap is not None:
+        minOlap = '-M %d' % (options.minOlap)
+    else:
+        minOlap = ''
+    # 3' end reads truncation
+    if options.readsTruncation is not None:
+        readsTruncation = '-t %d' % (options.readsTruncation)
+    else:
+        readsTruncation = ''
+    # 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 )
+    
+    # Execution of Edena
+    print 'Executing Edena (overlapping)...'
+    if logfile:
+        log = open(logfile, 'w')
+    else:
+        log = 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)
+
+
+if __name__ == "__main__":
+    __main__()