diff mothur/lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.py @ 17:57df76d861e4

Modifications for ToolShed proprietary data types

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mothur/lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.py	Tue Jan 17 11:08:15 2012 -0600
@@ -0,0 +1,31 @@
+#!/usr/bin/env python
+"""
+convert a ref.taxonommy file to a seq.taxonomy file
+Usage:
+%python ref_to_seq_taxonomy_converter.py <ref.taxonommy_filename> <seq.taxonomy_filename> 
+"""
+
+import sys, os, re
+from math import *
+
+assert sys.version_info[:2] >= ( 2, 4 )
+
+def stop_err( msg ):
+    sys.stderr.write( "%s" % msg )
+    sys.exit()
+
+def __main__():
+    infile_name = sys.argv[1]
+    outfile = open( sys.argv[2], 'w' )
+    pat = '^([^ \t\n\r\x0c\x0b;]+([(]\\d+[)])?(;[^ \t\n\r\x0c\x0b;]+([(]\\d+[)]))*(;)?)$'
+    for i, line in enumerate( file( infile_name ) ):
+        line = line.rstrip() # eliminate trailing space and new line characters
+        if not line or line.startswith( '#' ):
+            continue
+        fields = line.split('\t')
+        # make sure the 2nd field (taxonomy) ends with a ;
+        outfile.write('%s\t%s;\n' % (fields[0], re.sub(';$','',fields[1])))
+
+    outfile.close()
+
+if __name__ == "__main__": __main__()