--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/maf/maf_reverse_complement.py	Fri Mar 09 19:37:19 2012 -0500
@@ -0,0 +1,42 @@
+#!/usr/bin/env python
+
+"""
+Reads a MAF file. Produces a MAF file containing
+the reverse complement for each block in the source file.
+
+usage: %prog input_maf_file output_maf_file
+"""
+#Dan Blankenberg
+from galaxy import eggs
+import pkg_resources; pkg_resources.require( "bx-python" )
+import bx.align.maf
+from galaxy.tools.util import maf_utilities
+import sys
+
+assert sys.version_info[:2] >= ( 2, 4 )
+
+def __main__():
+    #Parse Command Line
+    input_file = sys.argv.pop( 1 )
+    output_file = sys.argv.pop( 1 )
+    species = maf_utilities.parse_species_option( sys.argv.pop( 1 ) )
+    
+    try:
+        maf_writer = bx.align.maf.Writer( open( output_file, 'w' ) )
+    except:
+        print sys.stderr, "Unable to open output file"
+        sys.exit()
+    try:
+        count = 0
+        for count, maf in enumerate( bx.align.maf.Reader( open( input_file ) ) ):
+            maf = maf.reverse_complement()
+            if species:
+                maf = maf.limit_to_species( species )
+            maf_writer.write( maf )
+    except:
+        print >>sys.stderr, "Your MAF file appears to be malformed."
+        sys.exit()
+    print "%i regions were reverse complemented." % count
+    maf_writer.close()
+
+if __name__ == "__main__": __main__()