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)
