add annotation about rank during rank filtering

src/obitools/options/taxonomyfilter.py

@@ -62,14 +62,23 @@ def taxonomyFilterGenerator(options):
     loadTaxonomyDatabase(options)
     if options.taxonomy is not None:
         taxonomy=options.taxonomy
-        def taxonomyFilter(seq):
+        def taxonomyFilter(seq,rank):
+            def annotateAtRank(seq):
+                if 'taxid' in seq:
+                    taxid = seq['taxid']
+                    rtaxid= taxonomy.getTaxonAtRank(taxid,rank)
+                    if rtaxid is not None:
+                        seq["%s_taxid" % rank]=rtaxid
+                        seq[rank]=taxonomy.getScientificName(rtaxid)
+                    return rtaxid
+                return None
             good = True
             if 'taxid' in seq:
                 taxid = seq['taxid']
 #                print taxid,
                 if options.requiredRank:
                     taxonatrank = reduce(lambda x,y: x and y,
-                                         (taxonomy.getTaxonAtRank(taxid,rank) is not None
+                                         (annotateAtRank(seq,rank) is not None
                                             for rank in options.requiredRank),True)
                     good = good and taxonatrank 
 #                    print >>sys.stderr, " Has rank : ",good,