--- a/edena_ovl_wrapper.py	Fri Oct 18 14:09:11 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,80 +0,0 @@
-# -*- 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', 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='')
-    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_input = '-r'
-        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 = '-DRpairs'
-        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 = '-RDpairs'
-        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
-    nThreads = '-nThreads %d' % (options.nThreads) if options.nThreads is not None else ''
-    # minimum overlap
-    minOlap = '-M %d' % (options.minOlap) if options.minOlap is not None else ''
-    # 3' end reads truncation
-    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)
-
-    # Execution of Edena
-    print 'Executing Edena (overlapping)...'
-    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)
-
-
-if __name__ == "__main__":
-    __main__()