def test_csv_neoantigens2model(self):
neoantigens_file = pkg_resources.resource_filename(
neofox.tests.__name__, "resources/test_data_model.txt"
)
data = pd.read_csv(neoantigens_file, sep="\t")
neoantigens = ModelConverter._neoantigens_csv2objects(data)
self.assertEqual(5, len(neoantigens))
for n in neoantigens:
self.assertTrue(isinstance(n, Neoantigen))
self.assertNotEmpty(n.mutation)
self.assertNotEmpty(n.patient_identifier)
self.assertNotEmpty(n.gene)
self.assertTrue(isinstance(n.mutation, Mutation))
self.assertNotEmpty(n.mutation.mutated_xmer)
self.assertNotEmpty(n.mutation.wild_type_xmer)
self.assertIsNotNone(n.mutation.position)
# test external annotations
self._assert_external_annotations(
expected_external_annotations=["external_annotation_1", "external_annotation_2"],
neoantigen_annotations=n.external_annotations,
non_nullable_annotations=["external_annotation_1", "external_annotation_2"]
)
for a in n.external_annotations:
if a.name == "external_annotation_1":
self.assertEqual(a.value, "blah1")
elif a.name == "external_annotation_2":
self.assertEqual(a.value, "blah2")
def _get_test_data(self):
input_file = pkg_resources.resource_filename(
neofox.tests.__name__, "resources/test_model_file.txt")
data = pd.read_csv(input_file, sep="\t")
data = data.replace({np.nan: None})
neoantigens = ModelConverter._neoantigens_csv2objects(data)
patients_file = pkg_resources.resource_filename(
neofox.tests.__name__, "resources/test_patient_file.txt")
patients = ModelConverter.parse_patients_file(patients_file,
self.hla_database)
patient_id = "Pt29"
return neoantigens, patients, patient_id
def test_neofox_synthetic_data(self):
"""
this test just ensures that NeoFox does not crash with the synthetic data
"""
data = [
("resources/synthetic_data/neoantigens_1patients_10neoantigens.2.txt",
"resources/synthetic_data/patients_1patients_10neoantigens.2.txt"
),
("resources/synthetic_data/neoantigens_10patients_10neoantigens.0.txt",
"resources/synthetic_data/patients_10patients_10neoantigens.0.txt"
),
#("resources/synthetic_data/neoantigens_100patients_10neoantigens.2.txt",
# "resources/synthetic_data/patients_100patients_10neoantigens.2.txt"),
#("resources/synthetic_data/neoantigens_no_wt_1patients_10neoantigens.3.txt",
# "resources/synthetic_data/patients_no_wt_1patients_10neoantigens.3.txt"),
#("resources/synthetic_data/poltergeist_neoantigens.txt",
# "resources/synthetic_data/poltergeist_patients.txt")
("resources/synthetic_data/neoantigens_no_wt_10patients_10neoantigens.4.txt",
"resources/synthetic_data/patients_no_wt_10patients_10neoantigens.4.txt"
),
#("resources/synthetic_data/neoantigens_100patients_10neoantigens.4.txt",
# "resources/synthetic_data/patients_100patients_10neoantigens.4.txt"),
]
for n, p, in data:
input_file = pkg_resources.resource_filename(
neofox.tests.__name__, n)
data = pd.read_csv(input_file, sep="\t")
data = data.replace({np.nan: None})
neoantigens = ModelConverter._neoantigens_csv2objects(data)
patients_file = pkg_resources.resource_filename(
neofox.tests.__name__, p)
patients = ModelConverter.parse_patients_file(
patients_file, self.hla_database)
annotations = NeoFox(
neoantigens=neoantigens,
patients=patients,
num_cpus=4,
).get_annotations()
self.assertIsNotNone(annotations)
def test_model2csv2model(self):
neoantigen = get_random_neoantigen()
csv_data = ModelConverter._objects2dataframe([neoantigen])
neoantigen2 = ModelConverter._neoantigens_csv2objects(csv_data)[0]
self.assertEqual(neoantigen, neoantigen2)