ncbi_query get_topoly does not break when some taxids are not found.

etetoolkit · Aug 29, 2020 · 7597af3 · 7597af3
1 parent 7914155
commit 7597af3
Showing 1 changed file with 2 additions and 2 deletions.
diff --git a/ete3/ncbi_taxonomy/ncbiquery.py b/ete3/ncbi_taxonomy/ncbiquery.py
@@ -542,9 +542,9 @@ def annotate_tree(self, t, taxid_attr="name", tax2name=None, tax2track=None, tax
                     node_taxid = merged_conversion[node_taxid]
                 n.add_features(sci_name = tax2name.get(node_taxid, getattr(n, taxid_attr, '')),
                                common_name = tax2common_name.get(node_taxid, ''),
-                               lineage = tax2track[node_taxid],
+                               lineage = tax2track.get(node_taxid, []),
                                rank = tax2rank.get(node_taxid, 'Unknown'),                               
-                               named_lineage = [tax2name.get(tax, str(tax)) for tax in tax2track[node_taxid]])
+                               named_lineage = [tax2name.get(tax, str(tax)) for tax in tax2track.get(node_taxid, [])])
             elif n.is_leaf():
                 n.add_features(sci_name = getattr(n, taxid_attr, 'NA'),
                                common_name = '',