--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/maf/maf_to_fasta_multiple_sets.py	Fri Mar 09 19:37:19 2012 -0500
@@ -0,0 +1,58 @@
+#!/usr/bin/env python
+
+"""
+Read a maf and output a multiple block fasta 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:
+        maf_reader = maf.Reader( open( sys.argv[1] ) )
+    except Exception, e:
+        maf_utilities.tool_fail( "Error opening input MAF: %s" % e )
+    try:
+        file_out = open( sys.argv[2], 'w' )
+    except Exception, e:
+        maf_utilities.tool_fail( "Error opening file for output: %s" % e )
+    try:
+        species = maf_utilities.parse_species_option( sys.argv[3] )
+        if species:
+            num_species = len( species )
+        else:
+            num_species = 0
+    except Exception, e:
+        maf_utilities.tool_fail( "Error determining species value: %s" % e )
+    try:
+        partial = sys.argv[4]
+    except Exception, e:
+        maf_utilities.tool_fail( "Error determining keep partial value: %s" % e )
+    
+    if species:
+        print "Restricted to species: %s" % ', '.join( species )
+    else:
+        print "Not restricted to species."
+    
+    for block_num, block in enumerate( maf_reader ):
+        if species:
+            block = block.limit_to_species( species )
+            if len( maf_utilities.get_species_in_block( block ) ) < num_species and partial == "partial_disallowed": continue
+        spec_counts = {}
+        for component in block.components:
+            spec, chrom = maf_utilities.src_split( component.src )
+            if spec not in spec_counts:
+                spec_counts[ spec ] = 0
+            else:
+                spec_counts[ spec ] += 1
+            file_out.write( "%s\n" % maf_utilities.get_fasta_header( component, { 'block_index' : block_num, 'species' : spec, 'sequence_index' : spec_counts[ spec ] }, suffix = "%s_%i_%i" % ( spec, block_num, spec_counts[ spec ] ) ) )
+            file_out.write( "%s\n" % component.text )
+        file_out.write( "\n" )
+    file_out.close()
+
+if __name__ == "__main__": __main__()