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"]
def make_annotation(db="blah",
db_id="blah12345",
db_obj_symb="blah",
qualifier="",
negated=False,
goid="GO:1234567",
references="BLAH:54321",
evidence="IDA",
withfrom="BLAH:12345",
aspect="C",
db_obj_name="",
db_obj_syn="",
db_obj_type="blah",
taxon="taxon:12345",
date="20200330",
assigned_by="blah",
extension="",
gene_form_id="",
properties="",
version=None,
from_gaf=True):
if from_gaf:
qual_parse = assocparser.Qualifier2_1()
if version == "2.2":
qual_parse = assocparser.Qualifier2_2()
annotation = [
db, db_id, db_obj_symb, qualifier, goid, references, evidence,
withfrom, aspect, db_obj_name, db_obj_syn, db_obj_type, taxon,
date, assigned_by, extension, gene_form_id
]
return gafparser.to_association(annotation,
qualifier_parser=qual_parse)
else:
if version != "2.0":
# Default to 1.2 if we're anything but 2.0
annotation = [
db, db_id, qualifier, goid, references, evidence, withfrom,
taxon, date, assigned_by, extension, properties
]
return gpadparser.to_association(annotation, version="1.2")
else:
annotation = [
"{}:{}".format(db, db_id), "NOT" if negated else "", qualifier,
goid, references, evidence, withfrom, taxon, date, assigned_by,
extension, properties
]
return gpadparser.to_association(annotation, version="2.0")
def qualifier_parser(self) -> assocparser.ColumnValidator:
if self.gaf_version() == "2.2":
return assocparser.Qualifier2_2()
return assocparser.Qualifier2_1()
from ontobio.ontol import Ontology
import dateutil.parser
import functools
import click
logger = logging.getLogger(__name__)
gaf_line_validators = {
"default": assocparser.ColumnValidator(),
"qualifier2_1": assocparser.Qualifier2_1(),
"qualifier2_2": assocparser.Qualifier2_2(),
"curie": assocparser.CurieValidator(),
"taxon": assocparser.TaxonValidator()
}
def protein_complex_sublcass_closure(ontology: Ontology) -> Set[str]:
protein_containing_complex = association.Curie(namespace="GO", identity="0032991")
children_of_complexes = set(ontology.descendants(str(protein_containing_complex), relations=["subClassOf"], reflexive=True))
return children_of_complexes
class GafParser(assocparser.AssocParser):
"""
Parser for GO GAF format
"""