Get ontology ID only from list file

ncbo · Sep 5, 2024 · 98f3ad2 · 98f3ad2
1 parent 414d0cf
commit 98f3ad2
Showing 1 changed file with 2 additions and 2 deletions.
diff --git a/src/kg_bioportal/cli.py b/src/kg_bioportal/cli.py
@@ -136,7 +136,7 @@ def download(
             with open(f"{output_dir}/{ONTOLOGY_LIST_NAME}", "r") as f:
                 f.readline()  # Skip the header
                 for line in f:
-                    onto_list.append(line.strip())
+                    onto_list.append(line.strip().split("\t")[0])
         except FileNotFoundError:
             logging.error(
                 f"Ontology list file not found. Please run the 'get_ontology_list' command first."
@@ -153,7 +153,7 @@ def download(
         with open(ontology_file, "r") as f:
             f.readline()  # Skip the header
             for line in f:
-                onto_list.append(line.strip())
+                onto_list.append(line.strip().split("\t")[0])
 
     logging.info(f"{len(onto_list)} ontologies to retrieve.")