Merge pull request #1 from shenwei356/speedup

accelerate rank query
nick-youngblut · Feb 9, 2020 · a3ec9f8 · a3ec9f8
2 parents 6b86cef + 22eb954
commit a3ec9f8
Showing 1 changed file with 1 addition and 4 deletions.
diff --git a/gtdb_to_taxdump.py b/gtdb_to_taxdump.py
@@ -125,10 +125,7 @@ def __str__(self):
 
     def get_rank(self, vertex):
         """ Getting rank based on GTDB prefixes """
-        for r in self.__ranks:
-            if vertex.startswith(r):
-                return self.__ranks[r]
-        return 'subspecies'
+        return self.__ranks.get(vertex[0:3], 'subspecies')
 
     def iter_graph(self, vertex):
         """ General iteration of all nodes in the graph """