diff long-orfs_wrapper.py @ 0:9c8ffce71f7c draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/long-orfs_wrapper.py	Mon Sep 09 12:16:17 2013 -0400
@@ -0,0 +1,110 @@
+# -*- coding: utf-8 -*-
+"""
+Glimmer --> long-orfs
+version 0.2 ([e-mail])
+"""
+
+import optparse
+import subprocess
+import sys
+
+def __main__():
+    # load arguments
+    print 'Parsing Long-ORFs input options...'
+    parser = optparse.OptionParser()
+    parser.add_option('--loSequence', dest='sequence', help='')
+    parser.add_option('--loStartCodons', dest='start_codons', help='')
+    parser.add_option('--loEntropy', dest='entropy', help='')
+    parser.add_option('--loFixed', action='store_true', dest='fixed', help='')
+    parser.add_option('--loMinLen', dest='min_len', type='int', help='')
+    parser.add_option('--loIgnore', dest='ignore', help='')
+    parser.add_option('--loLinear', action='store_true', dest='linear', help='')
+    parser.add_option('--loLengthOpt', action='store_true', dest='length_opt', help='')
+    parser.add_option('--loNoHeader', action='store_true', dest='no_header', help='')
+    parser.add_option('--loMaxOverlap', dest='max_olap', type='int', help='')
+    parser.add_option('--loCutoff', dest='cutoff', type='float', help='')
+    parser.add_option('--loWithoutStops', action='store_true', dest='without_stops', help='')
+    parser.add_option('--loTransTable', dest='trans_table', type='int', help='')
+    parser.add_option('--loStopCodons', dest='stop_codons', help='')
+    parser.add_option('--loOutput', 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 Long-ORFs command to be executed
+    sequence = options.sequence
+    if options.start_codons:
+        start_codons = '--start_codons %s' % (options.start_codons)
+    else:
+        start_codons = ''
+    if options.entropy:
+        entropy = '--entropy %s' % (options.entropy)
+    else:
+        entropy = ''
+    if options.fixed:
+        fixed = '--fixed'
+    else:
+        fixed = ''
+    if options.min_len is not None:
+        min_len = '--min_len %d' % (options.min_len)
+    else:
+        min_len = ''
+    if options.ignore:
+        ignore = '--ignore %s' % (options.ignore)
+    else:
+        ignore = ''
+    if options.linear:
+        linear = '--linear'
+    else:
+        linear = ''
+    if options.length_opt:
+        length_opt = '--length_opt'
+    else:
+        length_opt = ''
+    if options.no_header:
+        no_header = '--no_header'
+    else:
+        no_header = ''
+    if options.max_olap is not None:
+        max_olap = '--max_olap %d' % (options.max_olap)
+    else:
+        max_olap = ''
+    if options.cutoff is not None:
+        cutoff = '--cutoff %s' % (options.cutoff)
+    else:
+        cutoff = ''
+    if options.without_stops:
+        without_stops = '--without_stops'
+    else:
+        without_stops = ''
+    if options.trans_table is not None:
+        trans_table = '--trans_table %s' % (options.trans_table)
+    else:
+        trans_table = ''
+    if options.stop_codons:
+        stop_codons = '--stop_codons %s' % (options.stop_codons)
+    else:
+        stop_codons = ''
+    output = options.output
+    logfile = options.logfile
+    
+    # Build Long-ORFs command
+    cmd = 'long-orfs %s %s %s %s %s %s %s %s %s %s %s %s %s %s %s' % (sequence, start_codons, entropy, fixed, min_len, ignore, linear, length_opt, no_header, max_olap, cutoff, without_stops, trans_table, stop_codons, output)
+    print '\nLong-ORFs command to be executed: \n %s' % (cmd)
+    
+    print 'Executing Long-ORFs...'
+    if logfile:
+        log = open(logfile, 'w')
+    else:
+        log = sys.stdout
+    try:
+        subprocess.check_call(cmd, stdout=log, stderr=subprocess.STDOUT, shell=True)
+    finally:
+        if log != sys.stdout:
+            log.close()
+    print 'Long-ORFs executed!'
+
+
+if __name__ == "__main__":
+    __main__()