def _read_data(
candidate_file, json_file, patients_data, patient_id,
mhc_database: MhcDatabase) -> Tuple[List[Neoantigen], List[Patient]]:
# parse patient data
patients = ModelConverter.parse_patients_file(patients_data, mhc_database)
# parse the neoantigen candidate data
if candidate_file is not None:
neoantigens = ModelConverter.parse_candidate_file(
candidate_file, patient_id)
else:
neoantigens = ModelConverter.parse_neoantigens_json_file(json_file)
return neoantigens, patients
def setUp(self):
self.references, self.configuration = integration_test_tools.load_references(
)
self.references_mouse, self.configuration_mouse = integration_test_tools.load_references(
organism=ORGANISM_MUS_MUSCULUS)
# self.fastafile = integration_test_tools.create_temp_aminoacid_fasta_file()
# self.runner = Runner()
self.patient_id = "Pt29"
input_file = pkg_resources.resource_filename(
neofox.tests.__name__, "resources/test_candidate_file.txt")
patients_file = pkg_resources.resource_filename(
neofox.tests.__name__, "resources/test_patient_file.txt")
patients_file_mouse = pkg_resources.resource_filename(
neofox.tests.__name__, "resources/test_patient_file_mouse.txt")
self.hla_database = self.references.get_mhc_database()
self.h2_database = self.references_mouse.get_mhc_database()
self.patients = ModelConverter.parse_patients_file(
patients_file, self.hla_database)
self.patients_mouse = ModelConverter.parse_patients_file(
patients_file_mouse, self.h2_database)
self.neoantigens = ModelConverter.parse_candidate_file(input_file)
self.neoantigens_mouse = ModelConverter.parse_candidate_file(
input_file)
def test_neofox_only_one_neoantigen(self):
""""""
input_file = pkg_resources.resource_filename(
neofox.tests.__name__, "resources/test_data_only_one.txt")
neoantigens = ModelConverter.parse_candidate_file(input_file)
annotations = NeoFox(
neoantigens=neoantigens,
patient_id=self.patient_id,
patients=self.patients,
num_cpus=4,
).get_annotations()
self.assertEqual(1, len(annotations))
self.assertIsInstance(annotations[0], Neoantigen)
self.assertTrue(
len(annotations[0].neofox_annotations.annotations) > 10)
def test_neofox_performance_single_neoantigen(self):
input_file = pkg_resources.resource_filename(
neofox.tests.__name__, "resources/test_data_only_one.txt")
neoantigens, _ = ModelConverter.parse_candidate_file(input_file)
def compute_annotations():
return NeoFox(
neoantigens=neoantigens,
patient_id=self.patient_id,
patients=self.patients,
num_cpus=4,
).get_annotations()
print("Average time: {}".format(
timeit.timeit(compute_annotations, number=10)))
def test_no_expression_imputation(self):
input_file = pkg_resources.resource_filename(
neofox.tests.__name__, "resources/test_candidate_file.txt"
)
patients_file = pkg_resources.resource_filename(
neofox.tests.__name__, "resources/test_patient_file.txt"
)
patients = ModelConverter.parse_patients_file(patients_file, self.hla_database)
neoantigens = ModelConverter.parse_candidate_file(input_file)
neofox_runner = NeoFox(
neoantigens=neoantigens,
patients=patients,
reference_folder=FakeReferenceFolder(),
configuration=FakeDependenciesConfiguration(),
)
for neoantigen in neoantigens:
for neoantigen_imputed in neofox_runner.neoantigens:
if neoantigen.mutation.mutated_xmer == neoantigen_imputed.mutation.mutated_xmer:
self.assertEqual(
neoantigen.rna_expression, neoantigen_imputed.rna_expression
)
def test_with_expression_imputation(self):
input_file = pkg_resources.resource_filename(
neofox.tests.__name__, "resources/test_candidate_file_Pty.txt"
)
neoantigens= ModelConverter.parse_candidate_file(input_file)
import copy
original_neoantigens = copy.deepcopy(neoantigens)
patients_file = pkg_resources.resource_filename(
neofox.tests.__name__, "resources/test_patient_file.txt"
)
patients = ModelConverter.parse_patients_file(patients_file, self.hla_database)
neofox_runner = NeoFox(
neoantigens=neoantigens,
patients=patients,
reference_folder=FakeReferenceFolder(),
configuration=FakeDependenciesConfiguration(),
)
for neoantigen in original_neoantigens:
for neoantigen_imputed in neofox_runner.neoantigens:
self.assertFalse(
neoantigen.rna_expression == neoantigen_imputed.rna_expression
)