def test_get_attributes(self):
"""Tests - get attributes."""
test_db = Db.objects.create(name="SO")
test_dbxref = Dbxref.objects.create(accession="12345", db=test_db)
test_cv = Cv.objects.create(name="sequence")
Cvterm.objects.create(
name="polypeptide",
cv=test_cv,
dbxref=test_dbxref,
is_obsolete=0,
is_relationshiptype=0,
)
test_dbxref = Dbxref.objects.create(accession="123455", db=test_db)
Cvterm.objects.create(
name="protein_match",
cv=test_cv,
dbxref=test_dbxref,
is_obsolete=0,
is_relationshiptype=0,
)
test_db = Db.objects.create(name="RO")
test_dbxref = Dbxref.objects.create(accession="00002", db=test_db)
test_cv = Cv.objects.create(name="relationship")
Cvterm.objects.create(
name="contained in",
cv=test_cv,
dbxref=test_dbxref,
is_obsolete=0,
is_relationshiptype=0,
)
Organism.objects.create(genus="Mus", species="musculus")
test_feature_file = FeatureLoader(filename="file.name",
source="GFF_loader")
test_attrs = test_feature_file.get_attributes("ID=1;name=feat1")
self.assertEqual("1", test_attrs.get("id"))
self.assertEqual("feat1", test_attrs.get("name"))
def test_process_attributes(self):
"""Tests - get attributes."""
test_organism = Organism.objects.create(genus="Mus",
species="musculus")
# creating test GO term
test_db = Db.objects.create(name="GO")
test_dbxref = Dbxref.objects.create(accession="12345", db=test_db)
test_cv = Cv.objects.create(name="biological_process")
Cvterm.objects.create(
name="go test term",
cv=test_cv,
dbxref=test_dbxref,
is_obsolete=0,
is_relationshiptype=0,
)
# creating test SO term
test_db = Db.objects.create(name="SO")
test_dbxref = Dbxref.objects.create(accession="12345", db=test_db)
test_cv = Cv.objects.create(name="sequence")
test_so_term = Cvterm.objects.create(
name="gene",
cv=test_cv,
dbxref=test_dbxref,
is_obsolete=0,
is_relationshiptype=0,
)
test_dbxref = Dbxref.objects.create(accession="123455", db=test_db)
test_so_term = Cvterm.objects.create(
name="polypeptide",
cv=test_cv,
dbxref=test_dbxref,
is_obsolete=0,
is_relationshiptype=0,
)
test_dbxref = Dbxref.objects.create(accession="1234555", db=test_db)
Cvterm.objects.create(
name="protein_match",
cv=test_cv,
dbxref=test_dbxref,
is_obsolete=0,
is_relationshiptype=0,
)
# creating test feature
test_feature = Feature.objects.create(
organism=test_organism,
uniquename="feat1",
is_analysis=False,
type_id=test_so_term.cvterm_id,
is_obsolete=False,
timeaccessioned=datetime.now(timezone.utc),
timelastmodified=datetime.now(timezone.utc),
)
# creating exact term
test_db_global = Db.objects.create(name="_global")
test_dbxref = Dbxref.objects.create(accession="exact",
db=test_db_global)
test_cv = Cv.objects.create(name="synonym_type")
test_so_term = Cvterm.objects.create(
name="exact",
cv=test_cv,
dbxref=test_dbxref,
is_obsolete=0,
is_relationshiptype=0,
)
test_db = Db.objects.create(name="RO")
test_dbxref = Dbxref.objects.create(accession="00002", db=test_db)
test_cv = Cv.objects.create(name="relationship")
Cvterm.objects.create(
name="contained in",
cv=test_cv,
dbxref=test_dbxref,
is_obsolete=0,
is_relationshiptype=0,
)
# new FeatureLoader
test_feature_file = FeatureLoader(filename="file.name",
source="GFF_source")
# running get_attributes
test_attrs = test_feature_file.get_attributes(
"ID=1;name=feat1;note=Test feature;display=feat1;gene=gene1;"
"orf_classification=1;ontology_term=GO:12345,GO:54321;parent=2;"
"alias=Feature1;dbxref=GI:12345,NC:12345;noecziste=True")
# running process_attributes
test_feature_file.process_attributes(
feature_id=test_feature.feature_id, attrs=test_attrs)
# creating feature_property cvterm
cv_feature_property = Cv.objects.get(name="feature_property")
# asserting note
test_prop_cvterm = Cvterm.objects.get(name="note",
cv=cv_feature_property)
test_prop = Featureprop.objects.get(feature=test_feature,
type_id=test_prop_cvterm.cvterm_id,
rank=0)
self.assertEqual("Test feature", test_prop.value)
# asserting ontology_term
test_feat_cvterm = FeatureCvterm.objects.get(feature=test_feature)
test_cvterm = Cvterm.objects.get(cvterm_id=test_feat_cvterm.cvterm_id)
self.assertEqual("go test term", test_cvterm.name)
# asserting dbxref
test_dbxref_ids = FeatureDbxref.objects.filter(
feature=test_feature).values_list("dbxref_id", flat=True)
test_db = Db.objects.get(name="GI")
test_dbxref = Dbxref.objects.get(dbxref_id__in=test_dbxref_ids,
db=test_db)
self.assertEqual("12345", test_dbxref.accession)
# asserting alias
test_synonym = FeatureSynonym.objects.select_related("synonym").get(
feature=test_feature)
self.assertEqual("Feature1", test_synonym.synonym.name)
# asserting ignored goterms
self.assertEqual("GO:54321", test_feature_file.ignored_goterms.pop())