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test_gafparser.py
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test_gafparser.py
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from ontobio.io import assocparser
from ontobio.io.gpadparser import GpadParser
from ontobio.io import gafparser, gafgpibridge
from ontobio.io.gafparser import GafParser
from ontobio.io import GafWriter
from ontobio.io.assocwriter import GpadWriter
from ontobio.assoc_factory import AssociationSetFactory
from ontobio.ontol_factory import OntologyFactory
from ontobio.model import association
from ontobio.rdfgen import relations
from ontobio.model.association import ConjunctiveSet, ExtensionUnit, Curie
from ontobio.ecomap import EcoMap
import tempfile
import logging
import pytest
import io
import json
ecomap = EcoMap()
ecomap.mappings()
POMBASE = "tests/resources/truncated-pombase.gaf"
POMBASE_GPAD = "tests/resources/truncated-pombase.gpad"
ONT = "tests/resources/go-truncated-pombase.json"
QGAF = "tests/resources/test-qualifiers.gaf"
ALT_ID_ONT = "tests/resources/obsolete.json"
ZFIN_GAF = "tests/resources/zfin_test_gaf.gaf"
OBSOLETE_ONT = "tests/resources/obsolete.json"
def test_skim_gaf():
p = GafParser()
p.config.ecomap = EcoMap()
results = p.skim(open(POMBASE, "r"))
assert len(results) == 370
for r in results:
print(str(r))
(s, sn, o) = r
assert o.startswith('GO:')
assert s.startswith('PomBase:')
def test_skim_gaf_qualifiers():
p = GafParser()
p.config.ecomap = EcoMap()
p.config.remove_double_prefixes = True
results = p.skim(open(QGAF, "r"))
for r in results:
print(str(r))
(s, sn, o) = r
assert o.startswith('GO:')
assert s.startswith('MGI:') or s.startswith('PomBase')
assert len(results) == 5 # ensure NOTs are skipped
p.config.exclude_relations = ['contributes_to', 'colocalizes_with']
results = p.skim(open(QGAF, "r"))
for r in results:
(s, sn, o) = r
assert o.startswith('GO:')
assert s.startswith('MGI:') or s.startswith('PomBase')
assert len(results) == 3 # ensure NOTs and excludes relations skipped
def test_one_line():
p = GafParser(config=assocparser.AssocParserConfig(
ontology=OntologyFactory().create("tests/resources/goslim_generic.json")))
parsed = p.parse_line("PomBase SPBC16D10.09 pcn1 GO:0009536 PMID:8663159 IDA C PCNA pcn protein taxon:4896 20150326 PomBase")
def test_skim_gpad():
p = GpadParser()
p.config.ecomap = EcoMap()
results = p.skim(open(POMBASE_GPAD, "r"))
assert len(results) == 1984
for r in results:
print(str(r))
(s, sn, o) = r
assert o.startswith('GO:')
assert s.startswith('PomBase:') or s.startswith('PR:')
def test_parse_gaf():
parse_with(POMBASE, GafParser())
def test_parse_gpad():
parse_with(POMBASE_GPAD, GpadParser())
def parse_with(f, p):
p.config.ecomap = EcoMap()
is_gaf = f == POMBASE
ont = OntologyFactory().create(ONT)
if is_gaf:
# only do ontology checking on GAF parse;
# this is because ontology is made from GAF
p.config.ontology = ont
else:
p.config.ontology = None
results = p.parse(open(f, "r"), skipheader=True)
print(p.report.to_markdown())
r1 = results[0]
# TODO: test datafile does not have ECOs yet!!
assert ecomap.ecoclass_to_coderef(str(r1.evidence.type))[0] == 'ISO' or str(r1.evidence.type) == 'ECO:0000201'
assert r1.evidence.with_support_from == [association.ConjunctiveSet([association.Curie.from_str('SGD:S000001583')])]
assert r1.evidence.has_supporting_reference == [association.Curie.from_str('GO_REF:0000024')]
if is_gaf:
assert r1.subject.label == 'ypf1'
assert association.ymd_str(r1.date, "") == '20150305'
for r in results:
#print(str(r))
sid = r.subject.id
prov = r.provided_by
assert prov == 'PomBase' or prov == 'UniProt'
assert r.object.id.namespace == "GO"
assert sid.namespace == 'PomBase' or (not is_gaf and sid.namespace == 'PR')
if is_gaf:
assert str(r.subject.taxon) =='NCBITaxon:4896'
# for m in p.report.messages:
# print("MESSAGE: {}".format(m))
print("MESSAGES (sample): {}".format(p.report.messages[0:5]))
# Messages that aren't about upgrading qualifiers in rule 59 should be 0
assert len([msg for msg in p.report.messages if msg["rule"] != 59 and msg["rule"] != 27]) == 0
# print(p.report.to_markdown())
def test_flag_invalid_id():
ont = OntologyFactory().create(ONT)
p = GafParser()
p.config.ontology = ont
p._validate_ontology_class_id("FAKE:1", assocparser.SplitLine("fake", [""]*17, taxon="foo"))
assert len(p.report.messages) == 1
def test_no_flag_valid_id():
ont = OntologyFactory().create(ONT)
p = GafParser()
p.config.ontology = ont
p._validate_ontology_class_id("GO:0000785", assocparser.SplitLine("fake", [""]*17, taxon="foo"))
assert len(p.report.messages) == 0
def test_convert_gaf_to_gpad():
p = GafParser()
p.config.ecomap = EcoMap()
w = GpadWriter()
p2 = GpadParser()
convert(POMBASE, p, w, p2)
def convert(file, p, w, p2):
assocs = p.parse(file, skipheader=True)
outfile = tempfile.NamedTemporaryFile(mode='w', delete=False)
w.file = outfile
for a in assocs:
w.write_assoc(a)
outfile.close()
assocs2 = p2.parse(outfile.name)
for a in assocs2:
print("REPARSED: {}".format(a))
assert len(assocs) == len(assocs2)
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_validate_go_idspaces():
ont = OntologyFactory().create(ONT)
p = GafParser()
p.config.class_idspaces = ['FOOZ']
assocs = p.parse(open(POMBASE, "r"), skipheader=True)
for m in p.report.messages:
print("MESSAGE: {}".format(m))
assert len(assocs) == 0
assert len(p.report.messages) > 1
summary = p.report.to_report_json()
assert summary['associations'] == 0
assert summary['lines'] > 300
print(p.report.to_markdown())
# ensure config is not preserved
p = GafParser()
assert p.config.class_idspaces is None
def test_qualifiers_gaf():
p = GafParser()
assocs = p.parse(open(QGAF, "r"), skipheader=True)
neg_assocs = [a for a in assocs if a.negated == True]
assert len(neg_assocs) == 3
for a in assocs:
print('REL: {}'.format(str(a.relation)))
assert len([a for a in assocs if str(a.relation) == 'RO:0002326']) == 1
# For the space in `colocalizes with`
assert len(list(filter(lambda e: e["obj"] == "colocalizes with", p.report.to_report_json()["messages"]["gorule-0000001"]))) == 1
assert len(list(filter(lambda e: e["obj"] == "involved_in", p.report.to_report_json()["messages"]["gorule-0000001"]))) == 1
def test_gaf_2_1_unknown_qualifier():
line = ["UniProtKB", "P0AFI2", "parC", "Contributes_to", "GO:0003916", "PMID:1334483", "IDA", "", "F", "", "", "gene", "taxon:83333", "20081208", "EcoliWiki"]
parsed = gafparser.to_association(line)
assert parsed.skipped is True
assert parsed.report.to_report_json()["messages"]["gorule-0000001"][0]["type"] == parsed.report.INVALID_QUALIFIER
def test_qualifiers_gaf_2_2():
p = GafParser()
assocs = p.parse(open("tests/resources/test-qualifiers-2.2.gaf"), skipheader=True)
# NOT by itself is not allowed
assert len(list(filter(lambda e: e["obj"] == "NOT", p.report.to_report_json()["messages"]["gorule-0000001"]))) == 1
assert len(list(filter(lambda e: e["obj"] == "contributes_to|enables", p.report.to_report_json()["messages"]["gorule-0000001"]))) == 1
assert len([a for a in assocs if association.Curie.from_str("RO:0004035") in a.qualifiers]) == 1
def test_gaf_2_1_creates_cell_component_closure():
ontology = OntologyFactory().create("tests/resources/goslim_generic.json")
closure = gafparser.protein_complex_sublcass_closure(ontology)
# "GO:1902494" as an example that should be in the set
assert "GO:0005840" in closure
p = GafParser(config=assocparser.AssocParserConfig(ontology=ontology))
with open("tests/resources/pombase_single.gaf") as gaf:
# First line will be version declaration, triggering closure computation
p.parse_line(gaf.readline())
assert "GO:0005840" in p.cell_component_descendants_closure
def test_gaf_2_1_qualifiers_upconvert():
line = ["SGD", "S000000819", "AFG3", "", "GO:0005840", "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"]
parsed = gafparser.to_association(line)
assoc = parsed.associations[0]
ontology = OntologyFactory().create("tests/resources/goslim_generic.json")
p = GafParser(config=assocparser.AssocParserConfig(ontology=ontology))
p.make_internal_cell_component_closure()
assoc = p.upgrade_empty_qualifier(assoc)
assert assoc.qualifiers[0] == association.Curie(namespace="BFO", identity="0000050")
def test_gaf_2_1_upconvert_in_parse():
gaf = io.StringIO("!gaf-version: 2.1\nSGD\tS000000819\tAFG3\t\tGO:0005840\tPMID:8681382|SGD_REF:S000055187\tIMP\t\tP\tMitochondrial inner membrane m-AAA protease component\tYER017C|AAA family ATPase AFG3|YTA10\tgene\ttaxon:559292\t20170428\tSGD")
ontology = OntologyFactory().create("tests/resources/goslim_generic.json")
p = GafParser(config=assocparser.AssocParserConfig(ontology=ontology))
# We're 2.1, qualifier blank, cell component term from above, ontology defined: should upgrade
assocs = p.parse(gaf, skipheader=True)
assert assocs[0].relation == association.Curie(namespace="BFO", identity="0000050")
def test_gaf_2_1_simple_terms():
line = ["SGD", "S000000819", "AFG3", "", "GO:0006259", "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="0002264")
line = ["SGD", "S000000819", "AFG3", "", "GO:0042393", "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="0002327")
line = ["SGD", "S000000819", "AFG3", "", "GO:0005773", "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="0001025")
def test_upgrade_qualifiers_for_biological_process():
line = ["SGD", "S000000819", "AFG3", "", "GO:0008150", "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="0002331")
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_default_gaf_version():
p = GafParser()
assocs = p.parse(open("tests/resources/test-qualifiers-no-version.gaf"), skipheader=True)
assert p.version == "2.1"
def parse_with2(f, p):
ont = OntologyFactory().create(ONT)
p.config.ontology = ont
assocs = p.parse(open(f, "r"), skipheader=True)
neg_assocs = [a for a in assocs if a.negated == True]
assert len(neg_assocs) == 3
for a in assocs:
print('REL: {}'.format(a.relation))
assert len([a for a in assocs if str(a.relation) == relations.lookup_label('involved_in')]) == 1
assert len([a for a in assocs if str(a.relation) == relations.lookup_label('contributes_to')]) == 1
def test_errors_gaf():
config = assocparser.AssocParserConfig(
ecomap=EcoMap()
)
p = GafParser(config=config)
assocs = p.parse(open("tests/resources/errors.gaf", "r"), skipheader=True)
msgs = p.report.messages
print(json.dumps(p.report.to_report_json(), indent=4))
# print("MESSAGES: {}".format(len(msgs)))
n_invalid_idspace = 0
for m in msgs:
print("MESSAGE: {}".format(m))
if m['type'] == assocparser.Report.INVALID_IDSPACE:
n_invalid_idspace += 1
assert len(msgs) == 13
assert n_invalid_idspace == 1
assert len(assocs) == 1
w = GafWriter()
w.write(assocs)
for a in assocs:
if a.object_extensions != []:
# our test file has no ORs, so in DNF this is always the first
xs = a.object_extensions[0].elements
print(xs)
for x in xs:
print('X: {}'.format(x))
# ensure that invalid expressions have been eliminated
assert x.relation == association.Curie("BFO", "0000050")
assert x.term == association.Curie.from_str('X:1')
assert len(xs) == 1
def test_alt_id_repair():
p = GafParser()
ont = OntologyFactory().create(ALT_ID_ONT)
p.config.ecomap = EcoMap()
p.config.ontology = ont
gaf = io.StringIO("SGD\tS000000819\tAFG3\t\tGO:1\tPMID:8681382|SGD_REF:S000055187\tIMP\t\tP\tMitochondrial inner membrane m-AAA protease component\tYER017C|AAA family ATPase AFG3|YTA10\tgene\ttaxon:559292\t20170428\tSGD")
assocs = p.parse(gaf, skipheader=True)
# GO:1 is obsolete, and has replaced by GO:0034622, so we should see that class ID.
assert assocs[0].object.id == association.Curie.from_str("GO:2")
gaf = io.StringIO("SGD\tS000000819\tAFG3\t\tGO:4\tPMID:8681382|SGD_REF:S000055187\tIMP\t\tP\tMitochondrial inner membrane m-AAA protease component\tYER017C|AAA family ATPase AFG3|YTA10\tgene\ttaxon:559292\t20170428\tSGD")
assocs = p.parse(gaf, skipheader=True)
# GO:4 is obsolete due to it being merged into GO:3
assert assocs[0].object.id == association.Curie.from_str("GO:3")
def test_gorule_repair():
config = assocparser.AssocParserConfig(
ontology=OntologyFactory().create("tests/resources/goslim_generic.json"),
rule_set=assocparser.RuleSet.ALL
)
p = GafParser(config=config)
# Here this gaf line has the wrong aspect, and should be picked up by gorule 28
gaf = io.StringIO("PomBase\tSPCC962.06c\tbpb1\t\tGO:0005634\tPMID:20970342\tIPI\t\tP\tKH and CC/hC domain splicing factor Bpb1\tsf1|ods3\tprotein\ttaxon:4896\t20110804\tPomBase\tpart_of(GO:0007137)")
assocs = p.parse(gaf, skipheader=True)
assert assocs[0].aspect == "C"
assert len(p.report.to_report_json()["messages"]["gorule-0000028"]) == 1
assert p.report.to_report_json()["messages"]["gorule-0000028"][0]["type"] == assocparser.Report.VIOLATES_GO_RULE
def test_bad_date():
p = GafParser()
assoc_result = p.parse_line("PomBase\tSPAC25B8.17\typf1\t\tGO:0000007\tGO_REF:0000024\tISO\tSGD:S000001583\tC\tintramembrane aspartyl protease of the perinuclear ER membrane Ypf1 (predicted)\tppp81\tprotein\ttaxon:4896\tTODAY\tPomBase\tfoo(X:1)")
assert assoc_result.skipped == True
assert assoc_result.associations == []
def test_bad_gene_symbol():
p = GafParser()
assoc_result = p.parse_line("PomBase\tSPAC25B8.17\ta|pipeisnotallowed\t\tGO:0000007\tGO_REF:0000024\tISO\tSGD:S000001583\tC\tintramembrane aspartyl protease of the perinuclear ER membrane Ypf1 (predicted)\tppp81\tprotein\ttaxon:4896\t20231110\tPomBase\tfoo(X:1)")
assert assoc_result.skipped == True
assert assoc_result.associations == []
def test_bad_go_id():
p = GafParser()
assoc_result = p.parse_line("PomBase\tSPAC25B8.17\typf1\t\tINVALID:0000007\tGO_REF:0000024\tISO\tSGD:S000001583\tC\tintramembrane aspartyl protease of the perinuclear ER membrane Ypf1 (predicted)\tppp81\tprotein\ttaxon:4896\t20231110\tPomBase\tfoo(X:1)")
assert assoc_result.skipped == True
assert assoc_result.associations == []
def test_bad_taxon():
p = GafParser()
assoc_result = p.parse_line("PomBase\tSPAC25B8.17\typf1\t\tGO:0000007\tGO_REF:0000024\tISO\tSGD:S000001583\tC\tintramembrane aspartyl protease of the perinuclear ER membrane Ypf1 (predicted)\tppp81\tprotein\ttaxon:1abc\t20231003\tPomBase\tfoo(X:1)")
assert assoc_result.skipped == True
assert assoc_result.associations == []
def test_subject_extensions():
p = GafParser()
assoc_result = p.parse_line("PomBase\tSPAC25B8.17\typf1\t\tGO:0000007\tGO_REF:0000024\tISO\tSGD:S000001583\tC\tintramembrane aspartyl protease of the perinuclear ER membrane Ypf1 (predicted)\tppp81\tprotein\ttaxon:4896\t20181024\tPomBase\tpart_of(X:1)\tUniProtKB:P12345")
assert len(assoc_result.associations[0].subject_extensions) == 1
subject_extensions = assoc_result.associations[0].subject_extensions
gene_product_form_id = subject_extensions[0].term
assert gene_product_form_id == association.Curie.from_str("UniProtKB:P12345")
def test_bad_withfrom():
p = GafParser()
# With/from has no identity portion after the namespace
assoc_result = p.parse_line("PomBase\tSPAC25B8.17\typf1\t\tGO:0000007\tGO_REF:0000024\tISO\tSGD:\tC\tintramembrane aspartyl protease of the perinuclear ER membrane Ypf1 (predicted)\tppp81\tprotein\ttaxon:4896\t20181024\tPomBase")
assert assoc_result.associations == []
assert p.report.to_report_json()["messages"]["gorule-0000001"][0]["obj"] == "SGD:"
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"
def test_subject_extensions_bad_curie():
"""
Offending field is `GDP_bound`
"""
p = GafParser()
assoc_result = p.parse_line("PomBase\tSPBC1289.03c\tspi1\t\tGO:0005515\tPMID:18422602\tIPI\tPomBase:SPAC25A8.01c\tF\tRan GTPase Spi1\t\tprotein\ttaxon:4896\t20080718\tPomBase\t\tGDP_bound")
assert assoc_result.associations == []
assert assoc_result.skipped == True
assert len(p.report.to_report_json()["messages"]["gorule-0000001"]) == 1
assert p.report.to_report_json()["messages"]["gorule-0000001"][0]["type"] == p.report.INVALID_ID
assert p.report.to_report_json()["messages"]["gorule-0000001"][0]["obj"] == "GDP_bound"
print(json.dumps(p.report.to_report_json(), indent=4))
def test_object_extensions():
p = GafParser()
assoc_result = p.parse_line("PomBase\tSPAC25B8.17\typf1\t\tGO:0000007\tGO_REF:0000024\tISO\tSGD:S000001583\tC\tintramembrane aspartyl protease of the perinuclear ER membrane Ypf1 (predicted)\tppp81\tprotein\ttaxon:4896\t20181024\tPomBase\tpart_of(X:1)\tUniProtKB:P12345")
print(p.report.to_markdown())
assert len(assoc_result.associations[0].object_extensions) > 0
object_extensions = [
association.ConjunctiveSet([
association.ExtensionUnit(association.Curie("BFO", "0000050"), association.Curie("X", "1"))
])
]
assert assoc_result.associations[0].object_extensions == object_extensions
def test_object_extensions_error():
p = GafParser()
assoc_result = p.parse_line("PomBase\tSPAC25B8.17\typf1\t\tGO:0000007\tGO_REF:0000024\tISO\tSGD:S000001583\tC\tintramembrane aspartyl protease of the perinuclear ER membrane Ypf1 (predicted)\tppp81\tprotein\ttaxon:4896\t20181024\tPomBase\tpart_of(X)\tUniProtKB:P12345")
assert len(p.report.to_report_json()["messages"]["gorule-0000001"]) == 1
def test_obsolete_replair_of_extensions():
p = GafParser(config=assocparser.AssocParserConfig(
ontology=OntologyFactory().create(OBSOLETE_ONT)))
assoc_result = p.parse_line("ZFIN\tZDB-GENE-980526-362\tctnnb1\t\tGO:0007155\tPMID:15494018\tIC\tGO:0005913\tP\tcatenin (cadherin-associated protein), beta 1\tctnnb|id:ibd2058|wu:fb73e10|wu:fi81c06|wu:fk25h01\tprotein_coding_gene\ttaxon:7955\t20041026\tZFIN\tpart_of(GO:0005913)\tUniProtKB:P12345")
print(p.report.to_markdown())
assert len(assoc_result.associations[0].object_extensions) > 0
object_extensions = [
association.ConjunctiveSet([
association.ExtensionUnit(association.Curie("BFO", "0000050"), association.Curie("GO", "0005912"))
])
]
assert assoc_result.associations[0].object_extensions == object_extensions
#Reset the report
p = GafParser(config=assocparser.AssocParserConfig(
ontology=OntologyFactory().create(OBSOLETE_ONT)))
assoc_result = p.parse_line("ZFIN\tZDB-GENE-980526-362\tctnnb1\t\tGO:0007155\tPMID:15494018\tIC\tGO:0005912\tP\tcatenin (cadherin-associated protein), beta 1\tctnnb|id:ibd2058|wu:fb73e10|wu:fi81c06|wu:fk25h01\tprotein_coding_gene\ttaxon:7955\t20041026\tZFIN\tpart_of(GO:0005913)|part_of(GO:0016458)\tUniProtKB:P12345")
print(p.report.to_markdown())
assert assoc_result.associations == []
assert p.report.to_report_json()["messages"]["gorule-0000020"][0]["obj"] == "GO:0016458"
assert p.report.to_report_json()["messages"]["gorule-0000020"][1]["obj"] == "GO:0005913"
#Reset the report
p = GafParser(config=assocparser.AssocParserConfig(
ontology=OntologyFactory().create(OBSOLETE_ONT)))
assoc_result = p.parse_line("ZFIN\tZDB-GENE-980526-362\tctnnb1\t\tGO:0007155\tPMID:15494018\tIC\tGO:0005912\tP\tcatenin (cadherin-associated protein), beta 1\tctnnb|id:ibd2058|wu:fb73e10|wu:fi81c06|wu:fk25h01\tprotein_coding_gene\ttaxon:7955\t20041026\tZFIN\tpart_of(GO:0005913)|part_of(GO:0007155),occurs_in(Y:1)\tUniProtKB:P12345")
print(p.report.to_markdown())
assert len(assoc_result.associations[0].object_extensions) > 0
object_extensions = [
association.ConjunctiveSet([association.ExtensionUnit(association.Curie("BFO", "0000050"), association.Curie("GO", "0005912"))]),
association.ConjunctiveSet([association.ExtensionUnit(association.Curie("BFO", "0000050"), association.Curie("GO", "0007155")),association.ExtensionUnit(association.Curie("BFO", "0000066"), association.Curie("Y", "1"))])
]
assert assoc_result.associations[0].object_extensions == object_extensions
#Reset the report
p = GafParser(config=assocparser.AssocParserConfig(
ontology=OntologyFactory().create(OBSOLETE_ONT)))
assoc_result = p.parse_line("ZFIN\tZDB-GENE-980526-362\tctnnb1\t\tGO:0007155\tPMID:15494018\tIC\tGO:0005912\tP\tcatenin (cadherin-associated protein), beta 1\tctnnb|id:ibd2058|wu:fb73e10|wu:fi81c06|wu:fk25h01\tprotein_coding_gene\ttaxon:7955\t20041026\tZFIN\tpart_of(GO:0016458)\tUniProtKB:P12345")
print(p.report.to_markdown())
assert assoc_result.associations == []
assert p.report.to_report_json()["messages"]["gorule-0000020"][0]["obj"] == "GO:0016458"
def test_factory():
afa = AssociationSetFactory()
ont = OntologyFactory().create(ONT)
aset = afa.create_from_file(POMBASE, ontology=ont, skim=False)
found = 0
for s in aset.subjects:
print('{} {}'.format(s, aset.label(s)))
for c in aset.annotations(s):
print(' {} {}'.format(c, ont.label(c)))
for a in aset.associations(s, c):
e = a['evidence']
print(' {} {} {}'.format(e['type'], e['with_support_from'], e['has_supporting_reference']))
if s == 'PomBase:SPBC2D10.10c' and c == 'GO:0005730':
if e['type'] == 'ISO':
if e['with_support_from'] == ['SGD:S000002172'] and e['has_supporting_reference'] == ['GO_REF:0000024']:
found +=1
logging.info('** FOUND: {}'.format(a))
if e['type'] == 'IDA':
if e['has_supporting_reference'] == ['PMID:16823372']:
found +=1
logging.info('** FOUND: {}'.format(a))
assert len(aset.associations_by_subj) > 0
assert found == 2
def test_gaf_gpi_bridge():
gaf = ["MGI", "MGI:1923503", "0610006L08Rik", "enables", "GO:0003674", "MGI:MGI:2156816|GO_REF:0000015", "ND", "",
"F", "RIKEN cDNA 0610006L08 gene", "", "gene", "taxon:10090", "20120430", "MGI", "", ""]
association = gafparser.to_association(gaf, qualifier_parser=assocparser.Qualifier2_2()).associations[0]
bridge = gafgpibridge.GafGpiBridge()
entity = bridge.convert_association(association)
assert entity.get("type") == ["gene"]
if __name__ == "__main__":
pytest.main(args=["tests/test_gafparser.py::test_parse_gaf"])