add get_ordered_ancestor method to TaxonomyDb

metagenomics.py

@@ -154,6 +154,13 @@ def load_nodes(self, nodes_db):
                 ranks[taxid] = rank
         return ranks, parents
 
+    def get_ordered_ancestors(self, taxid):
+        ''' returns all ancestors of a taxid in proximity order: [parent, grandparent, greatgrandparent, etc] '''
+        if taxid in self.parents and taxid != self.parents[taxid]:
+            return [self.parents[taxid]] + self.get_ordered_ancestors(self.parents[taxid])
+        else:
+            return []
+
     def process_blast_hits(self, hits, top_percent):
         '''Filter groups of blast hits and perform lca.
 

test/unit/test_metagenomics.py

@@ -231,6 +231,10 @@ def test_translate_gi_to_tax_id(taxa_db_simple):
     assert taxa_db_simple.translate_gi_to_tax_id(blast1) == expected
 
 
+def test_ancestor_lookup(taxa_db_simple):
+    assert taxa_db_simple.get_ordered_ancestors(4) == [3, 2, 1]
+
+
 def test_kraken_dfs_report(taxa_db):
     hits = Counter({1: 101, 3: 103, 10: 105, 12: 107})