From 55d4f98d60a1c51ba9ded99a46214fbb017f4ef7 Mon Sep 17 00:00:00 2001
From: Celine Mercier <celine.mercier@metabarcoding.org>
Date: Wed, 29 Apr 2020 14:24:40 +0200
Subject: [PATCH] obi annotate: fixed annotation at ranks

---
 python/obitools3/commands/annotate.pyx | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/python/obitools3/commands/annotate.pyx b/python/obitools3/commands/annotate.pyx
index 640be94..4bc613e 100755
--- a/python/obitools3/commands/annotate.pyx
+++ b/python/obitools3/commands/annotate.pyx
@@ -13,7 +13,8 @@ from obitools3.dms.capi.obiview cimport NUC_SEQUENCE_COLUMN, \
                                         ID_COLUMN, \
                                         DEFINITION_COLUMN, \
                                         QUALITY_COLUMN, \
-                                        COUNT_COLUMN
+                                        COUNT_COLUMN, \
+                                        TAXID_COLUMN
 
 import time
 import math 
@@ -175,8 +176,8 @@ def sequenceTaggerGenerator(config, taxo=None):
             counter[0]+=1
                             
         for rank in annoteRank:
-            if 'taxid' in seq:
-                taxid = seq['taxid']
+            if TAXID_COLUMN in seq:
+                taxid = seq[TAXID_COLUMN]
                 if taxid is not None:
                     rtaxid = taxo.get_taxon_at_rank(taxid, rank)
                     if rtaxid is not None: