def test_produce_inference_produces_many_inferences():
with open("tests/resources/test.inferences.json") as inference_file:
gaferences = json.load(inference_file)
inferences = gaference.build_annotation_inferences(gaferences)
gaf_line = "MGI\tMGI:1345162\tAdam23\t\tGO:0099056\tMGI:MGI:4431144|PMID:20133599\tIDA\t\tC\ta disintegrin and metallopeptidase domain 23\tMDC3\tprotein\ttaxon:10090\t20180711\tSynGO\tpart_of(GO:0098978),part_of(UBERON:0000061),part_of(EMAPA:35405)|part_of(GO:0098978),part_of(UBERON:0000061),part_of(EMAPA:16894)\t"
gaf = gaf_line.split("\t")
results = gaference.produce_inferences(gaf, inferences)
expected_lines = [
[
"MGI", "MGI:1345162", "Adam23", "", "GO:0098978",
"MGI:MGI:4431144|PMID:20133599", "IDA", "", "C",
"a disintegrin and metallopeptidase domain 23", "MDC3", "protein",
"taxon:10090", "20180711", "SynGO", "", ""
],
[
"MGI", "MGI:1345162", "Adam23", "", "GO:0098978",
"MGI:MGI:4431144|PMID:20133599", "IDA", "", "C",
"a disintegrin and metallopeptidase domain 23", "MDC3", "protein",
"taxon:10090", "20180711", "SynGO", "", ""
],
]
assert len(results) == 2
assert results[0].inferred_gafs[0] == expected_lines[0]
assert results[1].inferred_gafs[0] == expected_lines[1]
def test(self,
annotation: association.GoAssociation,
config: assocparser.AssocParserConfig,
group=None) -> TestResult:
if config.annotation_inferences is None:
# Auto pass if we don't have inferences
return self._result(True)
if annotation.negated:
# The rule is passed if the annotation is negated
return self._result(True)
inference_results = gaference.produce_inferences(
annotation, config.annotation_inferences
) # type: List[gaference.InferenceResult]
taxon_passing = True
for result in inference_results:
if result.problem == gaference.ProblemType.TAXON:
taxon_passing = False
break
if taxon_passing:
return self._result(True)
else:
# Filter non experimental evidence
if str(annotation.evidence.type) in self.non_experimental_evidence:
return self._result(False)
else:
# Only submit a warning/report if we are an experimental evidence
return TestResult(ResultType.WARNING, self.title, False)
def test_pombase_taxon_failure():
with open("tests/resources/test.inferences.json") as inference_file:
gaferences = json.load(inference_file)
inferences = gaference.build_annotation_inferences(gaferences)
gaf_line = "PomBase\tSPBC11B10.09\tcdc2\t\tGO:0007275\tPMID:21873635\tIBA\tPANTHER:PTN000623979|TAIR:locus:2099478\tP\tCyclin-dependent kinase 1\tUniProtKB:P04551|PTN000624043\tprotein\ttaxon:284812\t20170228\tGO_Central"
gaf = gaf_line.split("\t")
results = gaference.produce_inferences(gaf, inferences)
assert len(results) == 1
assert results[0].problem == gaference.ProblemType.TAXON
def test_taxon_check_failure():
with open("tests/resources/test.inferences.json") as inference_file:
gaferences = json.load(inference_file)
inferences = gaference.build_annotation_inferences(gaferences)
gaf_line = "MGI\tMGI:1924956\tAbcb5\t\tGO:0048058\tMGI:MGI:5585659|PMID:25030174\tIMP\t\tP\tATP-binding cassette, sub-family B (MDR/TAP), member 5\t9230106F14Rik\tprotein\ttaxon:10090\t20140729\tUniProt\t\t"
gaf = gaf_line.split("\t")
results = gaference.produce_inferences(gaf, inferences)
assert len(results) == 1
assert results[0].problem == gaference.ProblemType.TAXON
def test_extension_check_failure():
with open("tests/resources/test.inferences.json") as inference_file:
gaferences = json.load(inference_file)
inferences = gaference.build_annotation_inferences(gaferences)
gaf_line = "MGI\tMGI:109192\tActn2\t\tGO:0072659\tMGI:MGI:4366185|PMID:19815520\tIMP\t\tP\tactinin alpha 2\t1110008F24Rik\tprotein\ttaxon:10090\t20150506\tUniProt\tpart_of(CL:0002495),has_direct_input(UniProtKB:P58390)\t"
gaf = gaf_line.split("\t")
results = gaference.produce_inferences(gaf, inferences)
assert len(results) == 1
assert results[0].problem == gaference.ProblemType.EXTENSION
def test(self, annotation: association.GoAssociation,
config: assocparser.AssocParserConfig) -> TestResult:
if config.annotation_inferences is None:
# Auto pass if we don't have inferences
return self._result(True)
inference_results = gaference.produce_inferences(
annotation, config.annotation_inferences
) #type: List[gaference.InferenceResult]
taxon_passing = True
for result in inference_results:
if result.problem == gaference.ProblemType.TAXON:
taxon_passing = False
break
return self._result(taxon_passing)
def test_produce_inference_produces_inferences():
with open("tests/resources/test.inferences.json") as inference_file:
gaferences = json.load(inference_file)
inferences = gaference.build_annotation_inferences(gaferences)
gaf_line = "MGI\tMGI:2178217\tAkap9\t\tGO:0036064\tMGI:MGI:5303017|PMID:22031837\tIDA\t\tC\tA kinase (PRKA) anchor protein (yotiao) 9\t5730481H23Rik|AKAP450|G1-448-15|mei2-5|repro12\tprotein\ttaxon:10090\t20131226\tMGI\tpart_of(EMAPA:17168),part_of(CL:0010009)\t"
gaf = gaf_line.split("\t")
results = gaference.produce_inferences(gaf, inferences)
expected_line = [
"MGI", "MGI:2178217", "Akap9", "", "GO:0097458",
"MGI:MGI:5303017|PMID:22031837", "IDA", "", "C",
"A kinase (PRKA) anchor protein (yotiao) 9",
"5730481H23Rik|AKAP450|G1-448-15|mei2-5|repro12", "protein",
"taxon:10090", "20131226", "MGI", "", ""
]
assert len(results) == 1
assert len(results[0].inferred_gafs) == 1
assert results[0].inferred_gafs[0] == expected_line