--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/maf/maf_to_fasta_concat.py	Fri Mar 09 19:37:19 2012 -0500
@@ -0,0 +1,59 @@
+#!/usr/bin/env python
+
+"""
+Read a maf and output a single block fasta file, concatenating blocks
+
+usage %prog species1,species2 maf_file out_file
+"""
+#Dan Blankenberg
+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
+
+assert sys.version_info[:2] >= ( 2, 4 )
+
+def __main__():
+    try:
+        species = maf_utilities.parse_species_option( sys.argv[1] )
+    except Exception, e:
+        maf_utilities.tool_fail( "Error determining species value: %s" % e )
+    try:
+        input_filename = sys.argv[2]
+    except Exception, e:
+        maf_utilities.tool_fail( "Error reading MAF filename: %s" % e )
+    try:
+        file_out = open( sys.argv[3], 'w' )
+    except Exception, e:
+        maf_utilities.tool_fail( "Error opening file for output: %s" % e )
+    
+    if species:
+        print "Restricted to species: %s" % ', '.join( species )
+    else:
+        print "Not restricted to species."
+    
+    if not species:
+        try:
+            species = maf_utilities.get_species_in_maf( input_filename )
+        except Exception, e:
+            maf_utilities.tool_fail( "Error determining species in input MAF: %s" % e )
+    
+    for spec in species:
+        file_out.write( ">" + spec + "\n" )
+        try:
+            for start_block in maf.Reader( open( input_filename, 'r' ) ):
+                for block in maf_utilities.iter_blocks_split_by_species( start_block ):
+                    block.remove_all_gap_columns() #remove extra gaps
+                    component = block.get_component_by_src_start( spec ) #blocks only have one occurrence of a particular species, so this is safe
+                    if component:
+                        file_out.write( component.text )
+                    else:
+                        file_out.write( "-" * block.text_size )
+        except Exception, e:
+            maf_utilities.tool_fail( "Your MAF file appears to be malformed: %s" % e )
+        file_out.write( "\n" )
+    file_out.close()
+
+
+if __name__ == "__main__": __main__()