def setUp(self):
self.references, self.configuration = integration_test_tools.load_references()
self.fastafile = integration_test_tools.create_temp_aminoacid_fasta_file()
self.runner = Runner()
self.proteome_blastp_runner = BlastpRunner(
runner=self.runner, configuration=self.configuration,
database=os.path.join(self.references.proteome_db, "homo_sapiens"))
def setUp(self):
references, self.configuration = integration_test_tools.load_references(organism=ORGANISM_MUS_MUSCULUS)
self.runner = Runner()
self.available_alleles = references.get_available_alleles()
self.test_mhc_one = integration_test_tools.get_h2_one_test(references.get_mhc_database())
self.test_mhc_two = integration_test_tools.get_h2_two_test(references.get_mhc_database())
self.mhc_parser = MhcParser.get_mhc_parser(references.get_mhc_database())
self.proteome_blastp_runner = BlastpRunner(
runner=self.runner, configuration=self.configuration,
database=references.get_proteome_database())
def setUp(self):
self.references, self.configuration = integration_test_tools.load_references(
)
self.runner = Runner()
self.prime = Prime(runner=self.runner,
configuration=self.configuration,
mhc_parser=HlaParser(
self.references.get_mhc_database()))
self.hla_database = self.references.get_mhc_database()
self.test_mhc_one = integration_test_tools.get_hla_one_test(
self.hla_database)
self.uniprot = Uniprot(self.references.uniprot_pickle)
def setUp(self):
self.references, self.configuration = integration_test_tools.load_references()
self.runner = Runner()
mhc_parser = MhcParser.get_mhc_parser(self.references.get_mhc_database())
self.mixmhcpred = MixMHCpred(
runner=self.runner, configuration=self.configuration, mhc_parser=mhc_parser
)
self.mixmhc2pred = MixMhc2Pred(
runner=self.runner, configuration=self.configuration, mhc_parser=mhc_parser
)
self.hla_database = self.references.get_mhc_database()
self.test_mhc_one = integration_test_tools.get_hla_one_test(self.hla_database)
self.test_mhc_two = integration_test_tools.get_hla_two_test(self.hla_database)
self.uniprot = Uniprot(self.references.uniprot_pickle)
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 setUp(self):
references, self.configuration = integration_test_tools.load_references(
)
self.runner = Runner()
self.available_alleles_mhc1 = (
references.get_available_alleles().get_available_mhc_i())
self.available_alleles_mhc2 = (
references.get_available_alleles().get_available_mhc_ii())
self.hla_database = references.get_mhc_database()
self.mhc_parser = MhcParser.get_mhc_parser(self.hla_database)
self.test_mhc_one = integration_test_tools.get_hla_one_test(
self.hla_database)
self.test_mhc_two = integration_test_tools.get_hla_two_test(
self.hla_database)
self.uniprot = Uniprot(references.uniprot_pickle)
self.proteome_blastp_runner = BlastpRunner(
runner=self.runner,
configuration=self.configuration,
database=references.get_proteome_database())
def _load_references(self):
references, configuration = integration_test_tools.load_references()
fastafile = integration_test_tools.create_temp_aminoacid_fasta_file()
return references, configuration, fastafile
def setUp(self):
self.references, self.configuration = integration_test_tools.load_references(
)
self.fastafile = integration_test_tools.create_temp_aminoacid_fasta_file(
)
self.runner = Runner()
def setUp(self):
self.references, self.configuration = integration_test_tools.load_references()
self.runner = Runner()
def setUp(self):
self.references, self.configuration = integration_test_tools.load_references()
self.data_generator = DataGenerator(self.references, self.configuration)