--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/maf/maf_by_block_number.py	Fri Mar 09 19:37:19 2012 -0500
@@ -0,0 +1,46 @@
+#!/usr/bin/env python
+#Dan Blankenberg
+"""
+Reads a list of block numbers and a maf. Produces a new maf containing the
+blocks specified by number.
+"""
+
+import sys
+from galaxy import eggs
+import pkg_resources; pkg_resources.require( "bx-python" )
+from galaxy.tools.util import maf_utilities
+import bx.align.maf
+
+assert sys.version_info[:2] >= ( 2, 4 )
+
+def __main__():
+    input_block_filename = sys.argv[1].strip()
+    input_maf_filename = sys.argv[2].strip()
+    output_filename1 = sys.argv[3].strip()
+    block_col = int( sys.argv[4].strip() ) - 1
+    if block_col < 0:
+        print >> sys.stderr, "Invalid column specified"
+        sys.exit(0)
+    species = maf_utilities.parse_species_option( sys.argv[5].strip() )
+    
+    maf_writer = bx.align.maf.Writer( open( output_filename1, 'w' ) )
+    #we want to maintain order of block file and write blocks as many times as they are listed
+    failed_lines = []
+    for ctr, line in enumerate( open( input_block_filename, 'r' ) ):
+        try:
+            block_wanted = int( line.split( "\t" )[block_col].strip() )
+        except:
+            failed_lines.append( str( ctr ) )
+            continue
+        try:
+            for count, block in enumerate( bx.align.maf.Reader( open( input_maf_filename, 'r' ) ) ):
+                if count == block_wanted:
+                    if species:
+                        block = block.limit_to_species( species )
+                    maf_writer.write( block )
+                    break
+        except:
+            print >>sys.stderr, "Your MAF file appears to be malformed."
+            sys.exit()
+    if len( failed_lines ) > 0: print "Failed to extract from %i lines (%s)." % ( len( failed_lines ), ",".join( failed_lines ) )
+if __name__ == "__main__": __main__()