--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/maf/maf_split_by_species.py	Fri Mar 09 19:37:19 2012 -0500
@@ -0,0 +1,44 @@
+#!/usr/bin/env python
+
+"""
+Read a maf and split blocks by unique species combinations 
+"""
+import sys
+from galaxy import eggs
+import pkg_resources; pkg_resources.require( "bx-python" )
+from bx.align import maf
+from galaxy.tools.util import maf_utilities
+from galaxy.util import string_as_bool
+
+assert sys.version_info[:2] >= ( 2, 4 )
+
+def __main__():    
+    try:
+        maf_reader = maf.Reader( open( sys.argv[1] ) )
+    except Exception, e:
+        maf_utilities.tool_fail( "Error opening MAF: %s" % e )
+    try:
+        out = maf.Writer( open( sys.argv[2], "w") )
+    except Exception, e:
+        maf_utilities.tool_fail( "Error opening file for output: %s" % e )
+    try:
+        collapse_columns = string_as_bool( sys.argv[3] )
+    except Exception, e:
+        maf_utilities.tool_fail( "Error determining collapse columns value: %s" % e )
+    
+    start_count = 0
+    end_count = 0
+    for start_count, start_block in enumerate( maf_reader ):
+        for block in maf_utilities.iter_blocks_split_by_species( start_block ):
+            if collapse_columns:
+                block.remove_all_gap_columns()
+            out.write( block )
+            end_count += 1
+    out.close()
+    
+    if end_count:
+        print "%i alignment blocks created from %i original blocks." % ( end_count, start_count + 1 )
+    else:
+        print "No alignment blocks were created."
+
+if __name__ == "__main__": __main__()