read synonyms table in get_descendant_taxa() if taxid deprecated #436

etetoolkit · Mar 29, 2020 · 1324f66 · 1324f66
1 parent 5e290f5
commit 1324f66
Showing 1 changed file with 5 additions and 0 deletions.
diff --git a/ete3/ncbi_taxonomy/ncbiquery.py b/ete3/ncbi_taxonomy/ncbiquery.py
@@ -342,6 +342,11 @@ def get_descendant_taxa(self, parent, intermediate_nodes=False, rank_limit=None,
             except KeyError:
                 raise ValueError('%s not found!' %parent)
 
+        # checks if taxid is a deprecated one, and converts into the right one. 
+        _, conversion = self._translate_merged([taxid]) #try to find taxid in synonyms table
+        if conversion: 
+            taxid = conversion[taxid]
+
         with open(self.dbfile+".traverse.pkl", "rb") as CACHED_TRAVERSE:
             prepostorder = pickle.load(CACHED_TRAVERSE)
         descendants = {}