--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mugsy.py	Fri Sep 06 05:58:59 2013 -0400
@@ -0,0 +1,48 @@
+# -*- coding: utf-8 -*-
+"""
+Mugsy wrapper
+
+For draft genomes a single multi-FASTA file containig all contigs should be provided.
+"""
+
+import optparse
+import os
+import shutil
+import subprocess
+import sys
+import tempfile
+
+def __main__():
+    """ main function """
+    parser = optparse.OptionParser()
+    parser.add_option('-r', dest='reference', help='reference FASTA file')
+    parser.add_option('-c', dest='contigs', help='contigs FASTA file')
+    parser.add_option('-p', dest='prefix', default='prefix', help='prefix ')
+    parser.add_option('-l', dest='logfile', help='logfile')
+    parser.add_option('--ml', dest='mugsylog', help='mugsylog file')
+    parser.add_option('--maf', dest='maf', help='ouput MAF alignment file ')
+    (options, args) = parser.parse_args()
+    if len(args) > 0:
+        parser.error('Wrong number of arguments')
+    
+    logfile = options.logfile
+    wd = tempfile.mkdtemp()
+    try:
+        command = "mugsy --directory %s --prefix %s --log %s %s %s" % (wd, options.prefix, options.mugsylog, options.reference, options.contigs)
+        print 'Mugsy command to be executed:\n ' + command
+        
+        log = open(logfile, 'w') if logfile else sys.stdout
+        try:
+            subprocess.check_call(command, stderr=log, shell=True) # need to redirect stderr because mugsy writes its logging info there
+        finally:
+            if log != sys.stdout:
+                log.close()
+        print 'Mugsy executed!'
+        
+        shutil.move(os.path.join(wd, options.prefix + '.maf'), options.maf)
+    finally:
+        shutil.rmtree(wd)
+
+
+if __name__ == "__main__":
+    __main__()