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test_gpad_parser.py
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test_gpad_parser.py
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from ontobio.io.gpadparser import GpadParser, to_association
from ontobio.io import assocparser
from ontobio.model import association
from ontobio.model.association import ConjunctiveSet, ExtensionUnit, Curie
from ontobio.ontol_factory import OntologyFactory
import yaml
POMBASE = "tests/resources/truncated-pombase.gpad"
ALT_ID_ONT = "tests/resources/obsolete.json"
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_obsolete_term_repair_extensions():
vals = ["ZFIN",
"ZFIN:ZDB-GENE-980526-362",
"acts_upstream_of_or_within",
"GO:0007155",
"PMID:15494018",
"ECO:0000305",
"ZFIN:ZDB-MRPHLNO-010101-1,MGI:1232453",
"",
"20041026",
"ZFIN",
"part_of(GO:0005913)|occurs_in(GO:1),has_input(GO:4)|enables(ZFIN:ZDB-MRPHLNO-010101-1),enables(MGI:1232453)",
"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
object_extensions = [association.ConjunctiveSet([association.ExtensionUnit(association.Curie("BFO", "0000050"), association.Curie("GO", "0005912"))]),
# repaired test GO elements
association.ConjunctiveSet([association.ExtensionUnit(association.Curie("BFO", "0000066"), association.Curie(namespace='GO', identity='2')),association.ExtensionUnit(association.Curie("RO", "0002233"), association.Curie(namespace='GO', identity='3'))]),
# non GO elements stay the same, could be obsolete or not
association.ConjunctiveSet([association.ExtensionUnit(association.Curie("RO", "0002327"), association.Curie(namespace='ZFIN', identity='ZDB-MRPHLNO-010101-1')),association.ExtensionUnit(association.Curie("RO", "0002327"), association. Curie(namespace='MGI', identity='1232453'))])
]
assert object_extensions == assoc.object_extensions
def test_skim():
p = GpadParser()
results = p.skim(open(POMBASE,"r"))
print(str(results))
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_parse_1_2():
report = assocparser.Report(group="unknown", dataset="unknown")
vals = [
"MGI",
"MGI:1918911",
"enables",
"GO:0003674",
"MGI:MGI:2156816|GO_REF:0000015",
"ECO:0000307",
"",
"",
"20100209",
"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="1.2")
assert result.skipped == 0
assert len([m for m in result.report.messages if m["level"] == "ERROR"]) == 0
assert len(result.associations) == 1
def test_parse_interacting_taxon():
report = assocparser.Report(group="unknown", dataset="unknown")
vals = [
"MGI",
"MGI:1918911",
"enables",
"GO:0003674",
"MGI:MGI:2156816|GO_REF:0000015",
"ECO:0000307",
"",
"taxon:5678",
"20100209",
"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="1.2")
assert result.associations[0].interacting_taxon == Curie(namespace="NCBITaxon", identity="5678")
def test_duplicate_key_annot_properties():
properties_str = "creation-date=2008-02-07|modification-date=2010-12-01|comment=v-KIND domain binding of Kndc1;MGI:1923734|contributor-id=http://orcid.org/0000-0003-2689-5511|contributor-id=http://orcid.org/0000-0003-3394-9805"
prop_list = association.parse_annotation_properties(properties_str)
contributor_ids = [value for key, value in prop_list if key == "contributor-id"]
assert set(contributor_ids) == {"http://orcid.org/0000-0003-2689-5511", "http://orcid.org/0000-0003-3394-9805"}
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_aspect_fill_for_obsolete_terms():
# Test null aspect on an obsolete term
# GO:4 is obsolete and has no aspect (hasOBONamespace) in obsolete.json ontology
# GO:3 is it's replacement term
# Note that GPAD lines contain no aspect data
vals = [
"MGI",
"MGI:105128",
"involved_in",
"GO:4",
"PMID:25901318",
"ECO:0000314",
"",
"",
"20190517",
"MGI",
"",
"contributor=http://orcid.org/0000-0002-9796-7693|model-state=production|noctua-model-id=gomodel:5c4605cc00004132"
]
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]
assert assoc.object.id == Curie("GO", "3") # GO:4 should be repaired to its replacement term, GO:3
assert assoc.aspect == 'P' # Aspect should not be empty
def test_unmapped_eco_to_gaf_codes():
# By default, ECO codes in GPAD need to be convertible to an ECO GAF code (e.g. IDA, ISO)
vals = [
"MGI",
"MGI:88276",
"is_active_in",
"GO:0098831",
"PMID:8909549",
"ECO:0000164",
"",
"",
"20180711",
"SynGO",
"part_of(UBERON:0000956)",
""
]
parser = GpadParser(config=assocparser.AssocParserConfig())
result = parser.parse_line("\t".join(vals))
assert len(result.associations) == 0
messages = parser.report.messages
assert messages[0]["type"] == parser.report.UNKNOWN_EVIDENCE_CLASS
parser.config.allow_unmapped_eco = True
result = parser.parse_line("\t".join(vals))
assert len(result.associations) == 1
parser.config.allow_unmapped_eco = False
vals[5] = "ECO:0000314" # maps to IDA
result = parser.parse_line("\t".join(vals))
assert len(result.associations) == 1
vals[5] = "ECO:0006003" # indirectly maps to IDA via gaf-eco-mapping-derived.txt
result = parser.parse_line("\t".join(vals))
assert len(result.associations) == 1