def test_exists(self):
hla_database = FakeHlaDatabase()
self.assertTrue(
hla_database.exists(
MhcAllele(gene="DPB1", group="104", protein="01")))
self.assertFalse(
hla_database.exists(
MhcAllele(gene="DPB1", group="10", protein="401")))
self.assertTrue(
hla_database.exists(MhcAllele(gene="B", group="15",
protein="228")))
self.assertFalse(
hla_database.exists(MhcAllele(gene="B", group="152",
protein="28")))
# badly formed HLA alleles
self.assertFalse(
hla_database.exists(MhcAllele(gene="B", group="15", protein=None)))
self.assertFalse(
hla_database.exists(MhcAllele(gene="B", group=None,
protein="228")))
self.assertFalse(
hla_database.exists(MhcAllele(gene=None, group="15",
protein="228")))
self.assertFalse(
hla_database.exists(MhcAllele(gene="Z", group="15",
protein="228")))
def test_hla_database(self):
hla_database = FakeHlaDatabase()
self.assertIsNotNone(hla_database)
self.assertIsNotNone(hla_database.alleles)
self.assertTrue(len(hla_database.alleles) > 1000)
self.assertTrue("DPB1*104:01" in hla_database.alleles)
self.assertFalse("DPB1*10:401" in hla_database.alleles)
self.assertTrue("B*15:228" in hla_database.alleles)
self.assertFalse("B*152:28" in hla_database.alleles)
def setUp(self) -> None:
faker = Faker()
self.patient_provider = PatientProvider(faker, [
"HLA-A*01:01", "HLA-A*01:02", "HLA-A*01:03", "HLA-B*01:01",
"HLA-B*01:02", "HLA-B*01:03", "HLA-C*01:01", "HLA-C*01:02",
"HLA-C*01:03"
], [
"DRB10101", "DRB10102", "DRB10103", "DRB10104",
"HLA-DPA10101-DPB10101", "HLA-DPA10102-DPB10102",
"HLA-DPA10103-DPB10103", "HLA-DPA10104-DPB10104"
"HLA-DQA10101-DQB10101", "HLA-DQA10102-DQB10102",
"HLA-DQA10103-DQB10103", "HLA-DQA10104-DQB10104"
], FakeHlaDatabase())
self.neoantigen_provider = NeoantigenProvider(
faker,
proteome_fasta=pkg_resources.resource_filename(
neofox.tests.__name__, "resources/proteome_test.fa"))
def setUp(self) -> None:
self.hla_database = FakeHlaDatabase()
def setUp(self) -> None:
self.mhc_parser = MhcParser.get_mhc_parser(FakeHlaDatabase())