def __init__(self, writer=None):
CamRdfTransform.__init__(self, writer)
self.annotons = []
self.classes = []
self.evidences = []
self.ev_ids = []
self.bp_id = None
def test_rdfgen_includes_taxon_in_gp_class():
assoc = association.GoAssociation(
source_line=
"PomBase\tSPAC25B8.17\typf1\t\tGO:1990578\tGO_REF:0000024\tISO\tSGD:S000001583\tC\tintramembrane aspartyl protease of the perinuclear ER membrane Ypf1 (predicted)\tppp81\tprotein\ttaxon:4896\t20150305\tPomBase\t\t",
subject=association.Subject(
id=association.Curie("PomBase", "SPAC25B8.17"),
label="ypf1",
type="protein",
fullname=
"intramembrane aspartyl protease of the perinuclear ER membrane Ypf1 (predicted)",
synonyms=["ppp81"],
taxon=association.Curie("NCBITaxon", "4896")),
object=association.Term(id=association.Curie("GO", "0000006"),
taxon=association.Curie("NCBITaxon", "4896")),
negated=False,
qualifiers=[],
aspect=association.Aspect("C"),
relation=association.Curie("BFO", "0000050"),
interacting_taxon=association.Curie("NCBITaxon", "555"),
evidence=association.Evidence(
type=association.Curie("ECO", "0000266"),
has_supporting_reference=[association.Curie("GO_REF", "0000024")],
with_support_from=[
association.ConjunctiveSet(
elements=[association.Curie("SGD", "S000001583")])
]),
provided_by=association.Provider("PomBase"),
date=association.Date("20150305"),
subject_extensions=[
association.ExtensionUnit(
relation=association.Curie("rdfs", "subClassOf"),
term=association.Curie("UniProtKB", "P12345"))
],
object_extensions=[
association.ConjunctiveSet(elements=[
association.ExtensionUnit(relation=association.Curie(
"BFO", "0000050"),
term=association.Curie("X", "1")),
association.ExtensionUnit(
relation=association.Curie("BFO", "0000066"),
term=association.Curie("GO", "0016020"))
]),
association.ConjunctiveSet(elements=[
association.ExtensionUnit(
relation=association.Curie("RO", "0002233"),
term=association.Curie("PomBase", "12345"))
])
],
properties=dict())
rdfWriter = TurtleRdfWriter(label="pombase_single.ttl")
gaf_transformer = CamRdfTransform(writer=rdfWriter)
gaf_transformer.translate(assoc)
gaf_transformer.provenance()
gp_res = rdfWriter.graph.query(gene_product_class_query())
for row in gp_res:
assert str(row["cls"]) == "http://identifiers.org/pombase/SPAC25B8.17"
assert str(
row["taxon"]) == "http://purl.obolibrary.org/obo/NCBITaxon_4896"
def test_rdfgen_includes_taxon_in_gp_class():
assoc = {
'source_line':
'PomBase\tSPAC25B8.17\typf1\t\tGO:1990578\tGO_REF:0000024\tISO\tSGD:S000001583\tC\tintramembrane aspartyl protease of the perinuclear ER membrane Ypf1 (predicted)\tppp81\tprotein\ttaxon:4896\t20150305\tPomBase\t\t',
'subject': {
'id': 'PomBase:SPAC25B8.17',
'label': 'ypf1',
'type': 'protein',
'fullname':
'intramembrane aspartyl protease of the perinuclear ER membrane Ypf1 (predicted)',
'synonyms': ['ppp81'],
'taxon': {
'id': 'NCBITaxon:4896'
}
},
'object': {
'id': 'GO:1990578',
'taxon': 'NCBITaxon:4896'
},
'negated': False,
'qualifiers': [],
'aspect': 'C',
'relation': {
'id': 'part_of'
},
'interacting_taxon': None,
'evidence': {
'type': 'ISO',
'has_supporting_reference': ['GO_REF:0000024'],
'with_support_from': ['SGD:S000001583']
},
'provided_by': 'PomBase',
'date': '20150305',
"subject_extensions": [],
"object_extensions": {}
}
rdfWriter = TurtleRdfWriter(label="pombase_single.ttl")
gaf_transformer = CamRdfTransform(writer=rdfWriter)
gaf_transformer.translate(assoc)
gaf_transformer.provenance()
gp_res = rdfWriter.graph.query(gene_product_class_query())
for row in gp_res:
assert str(row["cls"]) == "http://identifiers.org/pombase/SPAC25B8.17"
assert str(
row["taxon"]) == "http://purl.obolibrary.org/obo/NCBITaxon_4896"
def test_parse():
ont = OntologyFactory().create(ONT)
p = GafParser()
assocs = p.parse(open(POMBASE, "r"))
#gen(assocs,SimpleAssocRdfTransform(),'simple')
gen(assocs, CamRdfTransform(), 'cam')