def test_obsolete_term_repair_withfrom():
vals = ["ZFIN",
"ZFIN:ZDB-GENE-980526-362",
"acts_upstream_of_or_within",
"GO:0007155",
"PMID:15494018",
"ECO:0000305",
"GO:0005913|GO:1,GO:4|ZFIN:ZDB-MRPHLNO-010101-1,MGI:1232453",
"",
"20041026",
"ZFIN",
"",
"contributor=GOC:zfin_curators|model-state=production|noctua-model-id=gomodel:ZFIN_ZDB-GENE-980526-362"
]
ont = OntologyFactory().create(ALT_ID_ONT)
config = assocparser.AssocParserConfig(ontology=ont, rule_set=assocparser.RuleSet.ALL)
parser = GpadParser(config=config)
result = parser.parse_line("\t".join(vals))
assoc = result.associations[0]
# GO:0005913 should be repaired to its replacement term, GO:00005912
assert [ConjunctiveSet(elements=[Curie(namespace='GO', identity='0005912')]),
# repaired test GO elements
ConjunctiveSet(elements=[Curie(namespace='GO', identity='2'), Curie(namespace='GO', identity='3')]),
# non GO elements stay the same, could be obsolete or not
ConjunctiveSet(elements=[Curie(namespace='ZFIN', identity='ZDB-MRPHLNO-010101-1'),
Curie(namespace='MGI', identity='1232453')])] == assoc.evidence.with_support_from
def test_parse_2_0():
version = "2.0"
report = assocparser.Report(group="unknown", dataset="unknown")
vals = [
"MGI:MGI:1918911",
"",
"RO:0002327",
"GO:0003674",
"MGI:MGI:2156816|GO_REF:0000015",
"ECO:0000307",
"",
"",
"2020-09-17",
"MGI",
"",
"creation-date=2020-09-17|modification-date=2020-09-17|contributor-id=http://orcid.org/0000-0003-2689-5511"
]
result = to_association(list(vals), report=report, version=version)
assert result.skipped == 0
assert len([m for m in result.report.messages if m["level"] == "ERROR"]) == 0
assert len(result.associations) == 1
# Annotation_Extensions
vals[10] = "BFO:0000066(CL:0000010),GOREL:0001004(CL:0000010)"
result = to_association(list(vals), report=report, version=version)
assert result.associations[0].object_extensions == [ConjunctiveSet([
ExtensionUnit(Curie("BFO", "0000066"), Curie("CL", "0000010")),
ExtensionUnit(Curie("GOREL", "0001004"), Curie("CL", "0000010"))
])]
# With_or_From
vals[6] = "PR:Q505B8|PR:Q8CHK4"
result = to_association(list(vals), report=report, version=version)
assert result.associations[0].evidence.with_support_from == [
ConjunctiveSet([Curie("PR", "Q505B8")]),
ConjunctiveSet([Curie("PR", "Q8CHK4")])
]
# Interacting taxon - this example should fail
vals[7] = "Staphylococcus aureus ; NCBITaxon:1280"
result = to_association(list(vals), report=report, version=version)
assert len([m for m in result.report.messages if m["level"] == "ERROR"]) > 0
assert len(result.associations) == 0
# Now test valid interacting taxon value
vals[7] = "NCBITaxon:1280"
result = to_association(list(vals), report=report, version=version)
assert result.associations[0].interacting_taxon == Curie("NCBITaxon", "1280")
# Confirm non-"MGI:MGI:" IDs will parse
vals[0] = "WB:WBGene00001189"
result = to_association(list(vals), report=report, version=version)
assert result.associations[0].subject.id == Curie("WB", "WBGene00001189")
# Test annotation property retrieval
contributors = result.associations[0].annotation_property_values(property_key="contributor-id")
assert set(contributors) == {"http://orcid.org/0000-0003-2689-5511"}
def test_gaf_writer():
association = GoAssociation(
source_line="",
subject=Subject(
id=Curie("PomBase", "SPAC25B8.17"),
label="ypf1",
type=["protein"],
fullname=[
"intramembrane aspartyl protease of the perinuclear ER membrane Ypf1 (predicted)"
],
synonyms=["ppp81"],
taxon=Curie("NCBITaxon", "4896")),
object=Term(id=Curie("GO", "0000006"),
taxon=Curie("NCBITaxon", "4896")),
negated=False,
qualifiers=[],
aspect=Aspect("C"),
relation=Curie("BFO", "0000050"),
interacting_taxon=Curie("NCBITaxon", "555"),
evidence=Evidence(
type=Curie("ECO", "0000266"),
has_supporting_reference=[Curie("GO_REF", "0000024")],
with_support_from=[
ConjunctiveSet(elements=[Curie("SGD", "S000001583")])
]),
provided_by=Provider("PomBase"),
date=Date(year="2015", month="03", day="05", time=""),
subject_extensions=[
ExtensionUnit(relation=Curie("rdfs", "subClassOf"),
term=Curie("UniProtKB", "P12345"))
],
object_extensions=[
ConjunctiveSet(elements=[
ExtensionUnit(relation=Curie("BFO", "0000050"),
term=Curie("X", "1"))
])
],
properties=dict())
out = io.StringIO()
writer = assocwriter.GafWriter(file=out)
# `out` will get written with gaf lines from the above assocation object
expected = "PomBase\tSPAC25B8.17\typf1\t\tGO:0000006\tGO_REF:0000024\tISO\tSGD:S000001583\tC\tintramembrane aspartyl protease of the perinuclear ER membrane Ypf1 (predicted)\tppp81\tprotein\ttaxon:4896|taxon:555\t20150305\tPomBase\tpart_of(X:1)\tUniProtKB:P12345"
writer.write_assoc(association)
print(out.getvalue())
gaf = [
line.strip("\n") for line in out.getvalue().split("\n")
if not line.startswith("!")
][0]
assert expected == gaf
def test_obsolete_replair_of_withfrom():
p = GafParser(config=assocparser.AssocParserConfig(
ontology=OntologyFactory().create(OBSOLETE_ONT)))
assocs = p.parse(open(ZFIN_GAF, "r"), skipheader=True)
assert assocs[0].evidence.with_support_from == [
ConjunctiveSet(elements=[Curie(namespace='GO', identity='0005912')])
]
# Reset parser report
p = GafParser(config=assocparser.AssocParserConfig(
ontology=OntologyFactory().create(OBSOLETE_ONT)))
p.version = "2.2"
obsolete_no_replacement_line = "FB\tFBgn0003334\tScm\tlocated_in\tGO:0005634\tFB:FBrf0179383|PMID:15280237\tIC\tGO:0016458\tC\tSex comb on midleg\tCG9495|SCM|Sex Comb on Midleg|Sex Comb on the Midleg|Sex combs on midleg|Sex combs on midlegs|Su(z)302|l(3)85Ef|scm|sex comb on midleg\tprotein\ttaxon:7227\t20050203\tUniProt\t\t"
assoc_result = p.parse_line(obsolete_no_replacement_line)
assert assoc_result.associations == []
assert p.report.to_report_json(
)["messages"]["gorule-0000020"][0]["obj"] == "GO:0016458"