--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/anomaly_wrapper.py	Mon Sep 09 12:16:17 2013 -0400
@@ -0,0 +1,68 @@
+# -*- coding: utf-8 -*-
+"""
+Glimmer --> anomaly
+version 0.2 (andrea.pinna@crs4.it)
+"""
+
+import optparse
+import subprocess
+import sys
+
+def __main__():
+    # load arguments
+    print 'Parsing Anomaly input options...'
+    parser = optparse.OptionParser()
+    parser.add_option('--anSequence', dest='sequence', help='')
+    parser.add_option('--anCoords', dest='coords', help='')
+    parser.add_option('--anCheckFirstCodon', action='store_true', dest='check_first_codon', help='')
+    parser.add_option('--anCheckStopCodon', action='store_true', dest='check_stop_codon', help='')
+    parser.add_option('--anStartCodons', dest='start_codons', help='')
+    parser.add_option('--anStopCodons', dest='stop_codons', help='')
+    parser.add_option('--anOutput', 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 Anomaly command to be executed
+    # sequence file
+    sequence = options.sequence
+    coords = options.coords
+    if options.start_codons:
+        start_codons = '-A %s' % (options.start_codons)
+    else:
+        start_codons = ''
+    if options.stop_codons:
+        stop_codons = '-Z %s' % (options.stop_codons)
+    else:
+        stop_codons = ''
+    if options.check_first_codon:
+        check_first_codon = '-s'
+    else:
+        check_first_codon = ''
+    if options.check_stop_codon:
+        check_stop_codon = '-t'
+    else:
+        check_stop_codon = ''
+    output = options.output
+    logfile = options.logfile
+    
+    # Build Anomaly command
+    cmd = 'anomaly %s %s %s %s %s %s > %s' % (start_codons, check_first_codon, check_stop_codon, stop_codons, sequence, coords, output)
+    print '\nAnomaly command to be executed: \n %s' % (cmd)
+    
+    print 'Executing Anomaly...'
+    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 'Anomaly executed!'
+
+
+if __name__ == "__main__":
+    __main__()