From 421a9a195daee6ff121efde6dfb5cfc2a787675c Mon Sep 17 00:00:00 2001 From: Evan Morris Date: Fri, 17 Nov 2023 14:15:27 -0500 Subject: [PATCH] converting predicates from bmt get_ancestors to snakified biolink curies --- cli/generate_redundant_kg.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/cli/generate_redundant_kg.py b/cli/generate_redundant_kg.py index 6a10733f..b96fde5a 100644 --- a/cli/generate_redundant_kg.py +++ b/cli/generate_redundant_kg.py @@ -3,7 +3,7 @@ import re import argparse from itertools import product -from Common.utils import quick_jsonl_file_iterator +from Common.utils import quick_jsonl_file_iterator, snakify from Common.kgx_file_writer import KGXFileWriter from bmt import Toolkit @@ -19,7 +19,7 @@ def get_ancestor_predicates_biolink(predicate): cur_predicate = predicate.split(':')[-1] - return set(bmt.get_ancestors(cur_predicate)) + return set([f'biolink:{snakify(curie)}' for curie in bmt.get_ancestors(cur_predicate)]) def check_qualifier(ed): qfs = []