From 0a57dd4e5652620bb90037e54e116e6262a183e2 Mon Sep 17 00:00:00 2001
From: Robert Bossy <Robert.Bossy@inra.fr>
Date: Fri, 12 Apr 2024 16:52:20 +0200
Subject: [PATCH] workaround NCBI Taxonomy bug
nodes.dmp has empty rank for taxa of rank "subclass"
the workaround attributes the rank "subclass" when the rank is empty
---
taxutils.py | 2 ++
1 file changed, 2 insertions(+)
diff --git a/taxutils.py b/taxutils.py
index 7a98dee..7238636 100644
--- a/taxutils.py
+++ b/taxutils.py
@@ -612,6 +612,8 @@ class NCBIParser:
@staticmethod
def _get_rank(name):
attr = name.replace(' ', '')
+ if attr == '': # as of 2024-04-12 the NCBI taxonomy nodes.dmp has empty rank for subclasses
+ return Rank.subclass # TODO: remove fix when NCBI has fixed nodes.dmp
if attr == 'class':
return Rank.class_
if attr == 'forma' or attr == 'formaspecialis':
--
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