diff --git a/tests/test_cds_search.py b/tests/test_cds_search.py index 29949b0..c77c3b2 100644 --- a/tests/test_cds_search.py +++ b/tests/test_cds_search.py @@ -97,19 +97,20 @@ def calcule_important_field_similarity(ref_dict, test_dict): if not type_eq: type_errors.append((k, test_feature["type"], ref_feature["type"])) - name_eq = compare_incorrectly_parsed_list_features( - test_feature["qualifiers"]["Name"], ref_feature["qualifiers"]["Name"] - ) - if not name_eq: - type_errors.append( - ( - k, - convert_incorrectly_parsed_list_to_str(test_feature["qualifiers"]["Name"]), - convert_incorrectly_parsed_list_to_str(ref_feature["qualifiers"]["Name"]), - ) + if "Name" in test_feature["qualifiers"] and "Name" in ref_feature["qualifiers"]: + name_eq = compare_incorrectly_parsed_list_features( + test_feature["qualifiers"]["Name"], ref_feature["qualifiers"]["Name"] ) + if not name_eq: + type_errors.append( + ( + k, + convert_incorrectly_parsed_list_to_str(test_feature["qualifiers"]["Name"]), + convert_incorrectly_parsed_list_to_str(ref_feature["qualifiers"]["Name"]), + ) + ) - if "Dbxref" in test_feature["qualifiers"].keys() and "Dbxref" in ref_feature["qualifiers"].keys(): + if "Dbxref" in test_feature["qualifiers"] and "Dbxref" in ref_feature["qualifiers"]: dbxref_eq = sorted(test_feature["qualifiers"]["Dbxref"]) == sorted(ref_feature["qualifiers"]["Dbxref"]) if not dbxref_eq: dbxref_errors.append( @@ -309,8 +310,8 @@ def process_test_file(self, filename: str, mismatch_n_to_print: int = 5): reference_path = os.path.join(self.REFERENCE_CDS_DIR, filename) test_path = os.path.join(self.TEST_CDS_DIR, filename) - reference_dict = gff3_to_dict(reference_path, limit_info={"gff_type": ["CDS"]}) - test_dict = gff3_to_dict(test_path, limit_info={"gff_type": ["CDS"]}) + reference_dict = gff3_to_dict(reference_path, limit_info=None) + test_dict = gff3_to_dict(test_path, limit_info=None) ref_dict_location_and_contig = use_contig_id_and_location_as_locus_tag(reference_dict) test_dict_location_and_contig = use_contig_id_and_location_as_locus_tag(test_dict)