def test_parse(): p = GpadParser(config=assocparser.AssocParserConfig( group_metadata=yaml.load(open("tests/resources/mgi.dataset.yaml"), Loader=yaml.FullLoader))) test_gpad_file = "tests/resources/mgi.test.gpad" results = p.parse(open(test_gpad_file, "r")) print(p.report.to_markdown())
def test_invalid_goid_in_gpad(): # Note: this ontology is a subset of GO extracted using the GAF, not GPAD p = GpadParser() p.config.ontology = OntologyFactory().create(ONT) results = p.parse(open(POMBASE_GPAD, "r"), skipheader=True) # we expect errors since ONT is not tuned for the GPAD file # for m in p.report.messages: # print("MESSAGE: {}".format(m)) assert len(p.report.messages) > 500 print(p.report.to_markdown())
def test_parse(): p = GpadParser() results = p.parse(open(POMBASE, "r")) for r in results: print(str(r))
if sorted(r.upper() for r in source['evidence']['has_supporting_reference']) == \ sorted(r.upper() for r in target['evidence']['has_supporting_reference']): match_score = 5 return match_score if __name__ == '__main__': f = open("compare.txt", "w") print("Starting comparison ") parser = argparse.ArgumentParser() parser.add_argument('-g1', '--gpad_file1', help="Filepath of GPAD file 1", required=True) parser.add_argument('-g2', '--gpad_file2', help="Filepath of GPAD file 2", required=True) args = parser.parse_args() gpad_parser = GpadParser() assocs1 = gpad_parser.parse(args.gpad_file1, skipheader=True) assocs2 = gpad_parser.parse(args.gpad_file2, skipheader=True) for a in assocs1: #gene_id_a = a["subject"]["id"] #ont_id_a = a["object"]["id"] #print("a" + gene_id_a + " "+ont_id_a) match = is_assoc_in_list(a, assocs2) if match.__eq__("exact match"): exact_matches = exact_matches + 1 elif match.__eq__("close match"): close_matches = close_matches + 1 elif match.__eq__("no match"): no_matches = no_matches + 1 f.write(match + "\t" + a["source_line"]) input_lines = input_lines + 1 f.close()
def __init__(self, gpad_file, filter_rule: FilterRule): gpad_parser = GpadParser() assocs = gpad_parser.parse(gpad_file, skipheader=True) self.assocs = extract_properties_from_assocs(assocs) self.assoc_filter = AssocFilter(filter_rule)