--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/alignment/fasta_concatenate_by_species.py	Tue Mar 11 12:19:13 2014 -0700
@@ -0,0 +1,40 @@
+#!/usr/bin/env python
+#Dan Blankenberg
+"""
+Takes a Multiple Alignment FASTA file and concatenates 
+sequences for each species, resulting in one sequence 
+alignment per species.
+"""
+
+import sys, tempfile
+from galaxy import eggs
+from galaxy.tools.util.maf_utilities import iter_fasta_alignment
+from galaxy.util.odict import odict
+
+def __main__():
+    input_filename = sys.argv[1]
+    output_filename = sys.argv[2]
+    species = odict()
+    cur_size = 0
+    for components in iter_fasta_alignment( input_filename ):
+        species_not_written = species.keys()
+        for component in components:
+            if component.species not in species:
+                species[component.species] = tempfile.TemporaryFile()
+                species[component.species].write( "-" * cur_size )
+            species[component.species].write( component.text )
+            try:
+                species_not_written.remove( component.species )
+            except ValueError:
+                #this is a new species
+                pass
+        for spec in species_not_written:
+            species[spec].write( "-" * len( components[0].text ) )
+        cur_size += len( components[0].text )
+    out = open( output_filename, 'wb' )
+    for spec, f in species.iteritems():
+        f.seek( 0 )
+        out.write( ">%s\n%s\n" % ( spec, f.read() ) )
+    out.close()
+
+if __name__ == "__main__" : __main__()