def test_upgrade_qualifiers_for_cell_component():
line = [
"SGD", "S000000819", "AFG3", "", "GO:0008372",
"PMID:8681382|SGD_REF:S000055187", "IMP", "", "P",
"Mitochondrial inner membrane m-AAA protease component",
"YER017C|AAA family ATPase AFG3|YTA10", "gene", "taxon:559292",
"20170428", "SGD"
]
ontology = OntologyFactory().create("tests/resources/goslim_generic.json")
p = GafParser(config=assocparser.AssocParserConfig(ontology=ontology))
p.make_internal_cell_component_closure()
parsed = gafparser.to_association(line)
assoc = p.upgrade_empty_qualifier(parsed.associations[0])
assert assoc.qualifiers[0] == association.Curie(namespace="RO",
identity="0002432")
def test_gorule58():
a = ["blah"] * 16
a[0] = "HELLO"
a[1] = "123"
a[3] = ""
a[4] = "GO:0003674"
a[6] = "IBA"
a[5] = "PMID:21873635"
a[8] = "P"
a[9] = "MGI"
a[10] = ""
a[11] = ""
a[14] = "GO_Central"
a[15] = "has_input(GO:0003674),occurs_in(CL:123456)"
with open("tests/resources/extensions-constraints.yaml") as exs_cons:
config = assocparser.AssocParserConfig(
ontology=ontology,
extensions_constraints=yaml.load(exs_cons, Loader=yaml.FullLoader))
assoc = gafparser.to_association(a).associations[0]
test_result = qc.GoRule58().test(assoc, config)
assert test_result.result_type == qc.ResultType.PASS
# Fails because `not_relation` is not an allowed relation
a[15] = "not_relation(GO:987),occurs_in(CL:1234567)|occurs_in(CL:12345)"
assoc = gafparser.to_association(a).associations[0]
test_result = qc.GoRule58().test(assoc, config)
a[15] = "occurs_in(CL:12345)"
expected_repair = gafparser.to_association(a).associations[0]
expected_repair.source_line = assoc.source_line # Make sure original line is the same as test case
assert test_result.result_type == qc.ResultType.WARNING
assert test_result.result == expected_repair
# Fails because `FOO` is not a real namespace for any `has_input` constraint
a[15] = "has_input(FOO:1234566),occurs_in(CL:1234567)"
assoc = gafparser.to_association(a).associations[0]
test_result = qc.GoRule58().test(assoc, config)
assert test_result.result_type == qc.ResultType.WARNING
# Fails because this GO term is not in the constraint term children
a[4] = "GO:0005575"
a[15] = "occurs_in(EMAPA:123),has_input(CL:1234567)"
assoc = gafparser.to_association(a).associations[0]
test_result = qc.GoRule58().test(assoc, config)
assert test_result.result_type == qc.ResultType.WARNING
# Fails because of a cardinality check
a[4] = "GO:0003674"
a[15] = "occurs_in(EMAPA:123),occurs_in(EMAPA:1987654)"
assoc = gafparser.to_association(a).associations[0]
test_result = qc.GoRule58().test(assoc, config)
assert test_result.result_type == qc.ResultType.WARNING
def test_go_rule_17():
# IDA with anything in withfrom
a = ["blah"] * 15
a[3] = ""
a[6] = "IDA"
a[7] = "BLAH:12345"
a[8] = "P"
assoc = gafparser.to_association(a).associations[0]
test_result = qc.GoRule17().test(assoc, assocparser.AssocParserConfig())
assert test_result.result_type == qc.ResultType.WARNING
# Nothing in withfrom, passes
assoc.evidence.with_support_from = []
test_result = qc.GoRule17().test(assoc, assocparser.AssocParserConfig())
assert test_result.result_type == qc.ResultType.PASS
def test_all_rules():
# pass
config = assocparser.AssocParserConfig(ontology=ontology)
a = ["blah"] * 15
a[3] = ""
a[4] = "GO:0006397"
a[6] = "ISS"
a[8] = "P"
a[13] = "20180330"
assoc = gafparser.to_association(a).associations[0]
test_results = qc.test_go_rules(assoc, config).all_results
assert len(test_results.keys()) == 22
assert test_results[
qc.GoRules.GoRule26.value].result_type == qc.ResultType.PASS
assert test_results[
qc.GoRules.GoRule29.value].result_type == qc.ResultType.PASS
def test_gorule42():
a = ["blah"] * 15
a[3] = "NOT"
a[6] = "IKR"
a[8] = "P"
assoc = gafparser.to_association(a).associations[0]
test_result = qc.GoRule42().test(assoc, assocparser.AssocParserConfig())
assert test_result.result_type == qc.ResultType.PASS
assoc.evidence.type = "ECO:0000305" # Not IKR so this rule is fine
test_result = qc.GoRule42().test(assoc, assocparser.AssocParserConfig())
assert test_result.result_type == qc.ResultType.PASS
assoc.evidence.type = "ECO:0000320"
assoc.negated = False # Not negated, so wrong
test_result = qc.GoRule42().test(assoc, assocparser.AssocParserConfig())
assert test_result.result_type == qc.ResultType.ERROR
def test_go_rule02():
a = ["blah"] * 15
a[3] = "NOT"
a[4] = "GO:0005515"
a[8] = "F"
assoc = gafparser.to_association(a).associations[0]
test_result = qc.GoRule02().test(assoc, assocparser.AssocParserConfig())
assert test_result.result_type == qc.ResultType.WARNING
assoc.negated = False
test_result = qc.GoRule02().test(assoc, assocparser.AssocParserConfig())
assert test_result.result_type == qc.ResultType.PASS
assoc.negated = True
assoc.object.id = "GO:0003674"
test_result = qc.GoRule02().test(assoc, assocparser.AssocParserConfig())
assert test_result.result_type == qc.ResultType.PASS
def test_gorule55():
a = ["blah"] * 15
a[0] = "HELLO"
a[1] = "123"
a[3] = ""
a[5] = "GO:0012345|GO:1234567"
a[6] = "ISS"
a[7] = "HELLO:123"
a[8] = "P"
a[13] = "20200303"
assoc = gafparser.to_association(a).associations[0]
test_result = qc.GoRule55().test(assoc, assocparser.AssocParserConfig())
assert test_result.result_type == qc.ResultType.WARNING
assoc.evidence.has_supporting_reference = ["GO:0001234", "PMID:123456"]
test_result = qc.GoRule55().test(assoc, assocparser.AssocParserConfig())
assert test_result.result_type == qc.ResultType.PASS
def test_gorule39():
a = ["blah"] * 15
a[0] = "ComplexPortal"
a[3] = ""
a[4] = "GO:0032991"
a[8] = "C"
assoc = gafparser.to_association(a).associations[0]
test_result = qc.GoRule39().test(assoc, assocparser.AssocParserConfig())
assert test_result.result_type == qc.ResultType.ERROR
assoc.subject.id = "FB:1234"
test_result = qc.GoRule39().test(assoc, assocparser.AssocParserConfig())
assert test_result.result_type == qc.ResultType.PASS
assoc.subject.id = "ComplexPortal:12345"
assoc.object.id = "GO:0000023"
test_result = qc.GoRule39().test(assoc, assocparser.AssocParserConfig())
assert test_result.result_type == qc.ResultType.PASS
def test_all_rules():
# pass
config = all_rules_config(ontology=ontology)
a = ["blah"] * 15
a[3] = ""
a[4] = "GO:0006397"
a[5] = "PMID:21873635"
a[6] = "ISS"
a[7] = "PomBase:SPAC25B8.17"
a[8] = "P"
a[12] = "taxon:123"
a[13] = "20180330"
assoc = gafparser.to_association(a).associations[0]
test_results = qc.test_go_rules(assoc, config).all_results
assert len(test_results.keys()) == 24
assert test_results[
qc.GoRules.GoRule26.value].result_type == qc.ResultType.PASS
assert test_results[
qc.GoRules.GoRule29.value].result_type == qc.ResultType.PASS
def test_go_rule_07():
a = ["blah"] * 15
a[3] = ""
a[4] = "GO:0003824"
a[6] = "IPI"
a[8] = "F"
a[13] = "20200303"
assoc = gafparser.to_association(a).associations[0]
test_result = qc.GoRule07().test(assoc, assocparser.AssocParserConfig(ontology=ontology))
assert test_result.result_type == qc.ResultType.WARNING
assoc.object.id = "GO:1234567"
test_result = qc.GoRule07().test(assoc, assocparser.AssocParserConfig(ontology=ontology))
assert test_result.result_type == qc.ResultType.PASS
assoc.object.id = "GO:0003824"
assoc.evidence.type = "ECO:0000501" # Not IPI
test_result = qc.GoRule07().test(assoc, assocparser.AssocParserConfig(ontology=ontology))
assert test_result.result_type == qc.ResultType.PASS
def test_go_rule_06():
a = ["blah"] * 15
a[3] = ""
a[4] = "GO:0005575" # Cellular component
a[6] = "HEP"
a[8] = "C"
a[13] = "20200303"
assoc = gafparser.to_association(a).associations[0]
test_result = qc.GoRule06().test(assoc, assocparser.AssocParserConfig(ontology=ontology))
assert test_result.result_type == qc.ResultType.ERROR
assoc.aspect = "P"
assoc.object.id = "GO:0008150"
test_result = qc.GoRule06().test(assoc, assocparser.AssocParserConfig(ontology=ontology))
assert test_result.result_type == qc.ResultType.PASS
assoc.evidence.type = "ECO:0000501"
test_result = qc.GoRule06().test(assoc, assocparser.AssocParserConfig(ontology=ontology))
assert test_result.result_type == qc.ResultType.PASS
def test_gorule50():
a = ["blah"] * 15
a[0] = "HELLO"
a[1] = "123"
a[3] = ""
a[6] = "ISS"
a[7] = "HELLO:123"
a[8] = "P"
assoc = gafparser.to_association(a).associations[0]
test_result = qc.GoRule50().test(assoc, assocparser.AssocParserConfig())
assert test_result.result_type == qc.ResultType.WARNING
assoc.subject.id = "BYE:567"
test_result = qc.GoRule50().test(assoc, assocparser.AssocParserConfig())
assert test_result.result_type == qc.ResultType.PASS
a[1] = "HELLO:123"
a[6] = "ECO:0000501"
# Not ISS, so fine to have repeated columns
test_result = qc.GoRule50().test(assoc, assocparser.AssocParserConfig())
assert test_result.result_type == qc.ResultType.PASS
def test_go_rule_16():
# No GO term w/ID
a = ["blah"] * 15
a[3] = ""
a[4] = "GO:1234567"
a[6] = "IC"
a[7] = "BLAH:12345"
a[8] = "P"
a[13] = "20200303"
assoc = gafparser.to_association(a).associations[0]
test_result = qc.GoRule16().test(assoc, assocparser.AssocParserConfig())
assert test_result.result_type == qc.ResultType.ERROR
# withfrom has GO term
assoc.evidence.with_support_from = [association.ConjunctiveSet(["GO:0023456"])]
test_result = qc.GoRule16().test(assoc, assocparser.AssocParserConfig())
assert test_result.result_type == qc.ResultType.PASS
# Pipe
assoc.evidence.with_support_from = [association.ConjunctiveSet(["GO:0012345"]), association.ConjunctiveSet(["BLAH:54321"])]
test_result = qc.GoRule16().test(assoc, assocparser.AssocParserConfig())
assert test_result.result_type == qc.ResultType.PASS
# Empty withfrom
assoc.evidence.with_support_from = []
test_result = qc.GoRule16().test(assoc, assocparser.AssocParserConfig())
assert test_result.result_type == qc.ResultType.ERROR
# Not IC
assoc.evidence.type = "ECO:0000501"
assoc.evidence.with_support_from = [association.ConjunctiveSet(["BLAH:5555555"]), association.ConjunctiveSet(["FOO:999999"])]
test_result = qc.GoRule16().test(assoc, assocparser.AssocParserConfig())
assert test_result.result_type == qc.ResultType.PASS
def test_go_rule29():
a = ["blah"] * 15
a[3] = ""
a[6] = "IEA"
a[8] = "P"
a[13] = "19901111" # Nov 11, 1990, more than a year old
assoc = gafparser.to_association(a).associations[0]
test_result = qc.GoRule29().test(assoc, assocparser.AssocParserConfig())
assert test_result.result_type == qc.ResultType.ERROR
assoc.evidence.type = "ECO:0000305" #Not IEA
test_result = qc.GoRule29().test(assoc, assocparser.AssocParserConfig())
assert test_result.result_type == qc.ResultType.PASS
now = datetime.datetime.now()
six_months_ago = now - datetime.timedelta(days=180)
assoc.date = six_months_ago.strftime("%Y%m%d")
assoc.evidence.type = "ECO:0000501"
test_result = qc.GoRule29().test(assoc, assocparser.AssocParserConfig())
assert test_result.result_type == qc.ResultType.PASS
def test_go_rules_15():
a = ["blah"] * 15
a[3] = ""
a[4] = "GO:0044419"
a[6] = "IEA"
a[8] = "P"
a[12] = "taxon:123|taxon:456"
a[13] = "20200303"
assoc = gafparser.to_association(a).associations[0]
test_result = qc.GoRule15().test(assoc, assocparser.AssocParserConfig(ontology=ontology))
assert test_result.result_type == qc.ResultType.PASS
assoc.object.id = "GO:1234567"
test_result = qc.GoRule15().test(assoc, assocparser.AssocParserConfig(ontology=ontology))
assert test_result.result_type == qc.ResultType.WARNING
assoc.object.id = "GO:0044215"
assoc.object.id = "NCBITaxon:123"
assoc.interacting_taxon = None # This is the important part, no interacting taxon
test_result = qc.GoRule15().test(assoc, assocparser.AssocParserConfig(ontology=ontology))
assert test_result.result_type == qc.ResultType.PASS
def test_go_rules_13():
a = [
"PomBase", "SPBC11B10.09", "cdc2", "", "GO:0007275", "PMID:21873635",
"IBA", "PANTHER:PTN000623979|TAIR:locus:2099478", "P",
"Cyclin-dependent kinase 1", "UniProtKB:P04551|PTN000624043",
"protein", "taxon:284812", "20170228", "GO_Central", "", ""
]
assoc = gafparser.to_association(a).associations[0]
gaferences = gaference.load_gaferencer_inferences_from_file(
"tests/resources/test.inferences.json")
test_result = qc.GoRule13().test(
assoc,
assocparser.AssocParserConfig(annotation_inferences=gaferences,
rule_set=assocparser.RuleSet.ALL))
assert test_result.result_type == qc.ResultType.ERROR
a = [
"PomBase", "SPBC11B10.09", "cdc2", "", "GO:0007275", "PMID:21873635",
"EXP", "PANTHER:PTN000623979|TAIR:locus:2099478", "P",
"Cyclin-dependent kinase 1", "UniProtKB:P04551|PTN000624043",
"protein", "taxon:284812", "20170228", "GO_Central", "", ""
]
assoc = gafparser.to_association(a).associations[0]
gaferences = gaference.load_gaferencer_inferences_from_file(
"tests/resources/test.inferences.json")
test_result = qc.GoRule13().test(
assoc,
assocparser.AssocParserConfig(annotation_inferences=gaferences,
rule_set=assocparser.RuleSet.ALL))
assert test_result.result_type == qc.ResultType.WARNING
a = [
"PomBase", "SPBC11B10.09", "cdc2", "NOT", "GO:0007275",
"PMID:21873635", "EXP", "PANTHER:PTN000623979|TAIR:locus:2099478", "P",
"Cyclin-dependent kinase 1", "UniProtKB:P04551|PTN000624043",
"protein", "taxon:284812", "20170228", "GO_Central", "", ""
]
assoc = gafparser.to_association(a).associations[0]
gaferences = gaference.load_gaferencer_inferences_from_file(
"tests/resources/test.inferences.json")
test_result = qc.GoRule13().test(
assoc,
assocparser.AssocParserConfig(annotation_inferences=gaferences,
rule_set=assocparser.RuleSet.ALL))
assert test_result.result_type == qc.ResultType.PASS
a = [
"AspGD", "ASPL0000059928", "AN0127", "", "GO:0032258",
"AspGD_REF:ASPL0000000005", "IEA", "SGD:S000001917", "P", "",
"AN0127|ANID_00127|ANIA_00127", "gene_product", "taxon:227321",
"20200201", "AspGD", "", ""
]
assoc = gafparser.to_association(a).associations[0]
gaferences = gaference.load_gaferencer_inferences_from_file(
"tests/resources/test.inferences.json")
test_result = qc.GoRule13().test(
assoc,
assocparser.AssocParserConfig(annotation_inferences=gaferences,
rule_set=assocparser.RuleSet.ALL))
assert test_result.result_type == qc.ResultType.ERROR
