lib/qiime/assign_taxonomy.py.patch

patch to enhance output of assign taxonomy and use multiple CPUs

--- lib/qiime/assign_taxonomy.py        2011-09-11 20:53:06.000000000 +0100
+++ ../16s/Qiime-1.2.1/build/lib/qiime/assign_taxonomy.py       2011-02-22 21:00:06.000000000 +0000
@@ -89,7 +89,7 @@
         """ Initialize the object
         """
         _params = {
-            'Min percent identity': 90,
+            'Min percent identity': 0.90,
             'Max E value': 1e-30,
             'Application': 'blastn/megablast'
             }
@@ -174,12 +174,9 @@
             # if the user provided a result_path, write the
             # results to file
             of = open(result_path,'w')
-            for seq_id, stuff in result.items():
-                import sys
-                print >>sys.stderr, stuff
-                lineage, confidence, blast_hit_id, identity, aln_length = stuff
-                of.write('%s\t%s\t%s\t%s\t%s\t%s\n' %
-                 (seq_id, lineage, confidence, blast_hit_id, identity, aln_length))
+            for seq_id, (lineage, confidence, blast_hit_id) in result.items():
+                of.write('%s\t%s\t%s\t%s\n' %
+                 (seq_id, lineage, confidence, blast_hit_id))
             of.close()
             result = None
             logger.info('Result path: %s' % result_path)
@@ -232,11 +229,11 @@
         for query_id, hit in hits.items():
             query_id=query_id.split()[0]
             try:
-                hit_id, e_value, idy, aln_length = hit
+                hit_id, e_value = hit
                 hits[query_id] = \
-                  (id_to_taxonomy_map.get(hit_id, None),e_value,hit_id,idy, aln_length)
+                  (id_to_taxonomy_map.get(hit_id, None),e_value,hit_id)
             except TypeError:
-                hits[query_id] = ('No blast hit', None, None, None, None)
+                hits[query_id] = ('No blast hit', None, None)

         return hits

@@ -250,7 +247,7 @@

         blast_result = blast_seqs(\
          seqs,Blastall,blast_db=blast_db,\
-         params={'-p':'blastn','-n':'T','-a':'8'},\
+         params={'-p':'blastn','-n':'T'},\
          add_seq_names=False)

         if blast_result['StdOut']:
@@ -262,7 +259,7 @@
         for seq_id in seq_ids:
             blast_result_id = seq_id.split()[0]
             try:
-                result[seq_id] = [(e['SUBJECT ID'],float(e['E-VALUE']),e['% IDENTITY'],e['ALIGNMENT LENGTH']) \
+                result[seq_id] = [(e['SUBJECT ID'],float(e['E-VALUE'])) \
                  for e in blast_result[blast_result_id][0]
                  if (float(e['E-VALUE']) <= max_evalue and \
                   float(e['% IDENTITY']) >= min_percent_identity)]