def test_bad_is_rna_available(self):
ModelValidator.validate_patient(
Patient(identifier="123", is_rna_available=True),
ORGANISM_HOMO_SAPIENS)
ModelValidator.validate_patient(
Patient(identifier="123", is_rna_available=False),
ORGANISM_HOMO_SAPIENS)
self.assertRaises(NeofoxDataValidationException,
ModelValidator.validate_patient,
Patient(identifier="123", is_rna_available="False"),
ORGANISM_HOMO_SAPIENS)
def test_empty_patient_identifier(self):
patient = Patient(identifier=None)
self.assertRaises(NeofoxDataValidationException,
ModelValidator.validate_patient, patient,
ORGANISM_HOMO_SAPIENS)
patient = Patient(identifier="")
self.assertRaises(NeofoxDataValidationException,
ModelValidator.validate_patient, patient,
ORGANISM_HOMO_SAPIENS)
patient = Patient(identifier=" ")
self.assertRaises(NeofoxDataValidationException,
ModelValidator.validate_patient, patient,
ORGANISM_HOMO_SAPIENS)
def test_valid_hla_i_genotype(self):
self._assert_valid_patient(patient=Patient(
identifier="123",
mhc1=[
Mhc1(
name=Mhc1Name.A,
zygosity=Zygosity.HETEROZYGOUS,
alleles=[
self.hla_parser.parse_mhc_allele("HLA-A01:01"),
self.hla_parser.parse_mhc_allele("HLA-A01:02"),
],
),
Mhc1(
name=Mhc1Name.B,
zygosity=Zygosity.HOMOZYGOUS,
alleles=[self.hla_parser.parse_mhc_allele("HLA-B01:01")],
),
Mhc1(
name=Mhc1Name.C,
zygosity=Zygosity.HEMIZYGOUS,
alleles=[self.hla_parser.parse_mhc_allele("HLA-C01:01")],
),
],
),
organism=ORGANISM_HOMO_SAPIENS)
def test_bad_type_raises_exception(self):
self.assertRaises(
NeofoxDataValidationException,
ModelValidator.validate,
Neoantigen(
patient_identifier=
1234, # this should be a string instead of an integer
rna_expression=0.45,
),
)
self.assertRaises(
NeofoxDataValidationException,
ModelValidator.validate,
Neoantigen(patient_identifier="1234", rna_expression="0.45"),
) # this should be a float)
self.assertRaises(
NeofoxDataValidationException,
ModelValidator.validate,
Patient(identifier="1234", is_rna_available="Richtig"),
) # this should be a boolean)
# TODO: make validation capture this data types errors!
ModelValidator.validate(
Neoantigen(
patient_identifier=[
"12345"
], # this should be a string instead of a list of strings
rna_expression=0.45,
))
def validate_patient(patient: Patient, organism=ORGANISM_HOMO_SAPIENS):
# checks format consistency first
ModelValidator.validate(patient)
try:
# checks that patient id is not empty considering white spaces
patient_id = patient.identifier.strip() if patient.identifier else patient.identifier
assert patient_id is not None and patient_id != "", "A patient identifier is missing"
assert patient.identifier == patient.identifier.strip(), \
"Patient identifier contains white spaces at start or end: {}".format(patient.identifier)
# checks MHC I
if patient.mhc1:
for m in patient.mhc1:
ModelValidator._validate_mhc1(m, organism=organism)
# checks MHC II
if patient.mhc2:
for m in patient.mhc2:
ModelValidator._validate_mhc2(m, organism=organism)
except AssertionError as e:
logger.error(patient.to_json(indent=3))
raise NeofoxDataValidationException(e)
def test_valid_h2_i_genotype(self):
self._assert_valid_patient(patient=Patient(
identifier="123",
mhc1=[
Mhc1(
name=Mhc1Name.H2D,
zygosity=Zygosity.HETEROZYGOUS,
alleles=[
self.h2_parser.parse_mhc_allele("H2Dd"),
self.h2_parser.parse_mhc_allele("H2Da"),
],
),
Mhc1(
name=Mhc1Name.H2L,
zygosity=Zygosity.HOMOZYGOUS,
alleles=[self.h2_parser.parse_mhc_allele("H2Ld")],
),
Mhc1(
name=Mhc1Name.H2K,
zygosity=Zygosity.HEMIZYGOUS,
alleles=[self.h2_parser.parse_mhc_allele("H2Kk")],
),
],
),
organism=ORGANISM_MUS_MUSCULUS)
def annotate_neoantigen(neoantigen: Neoantigen,
patient: Patient,
reference_folder: ReferenceFolder,
configuration: DependenciesConfiguration,
tcell_predictor: TcellPrediction,
self_similarity: SelfSimilarityCalculator,
log_file_name: str,
affinity_threshold=AFFINITY_THRESHOLD_DEFAULT):
# the logs need to be initialised inside every dask job
NeoFox._initialise_logs(log_file_name)
logger.info("Starting neoantigen annotation with peptide={}".format(
neoantigen.mutation.mutated_xmer))
start = time.time()
try:
annotated_neoantigen = NeoantigenAnnotator(
reference_folder,
configuration,
tcell_predictor=tcell_predictor,
self_similarity=self_similarity,
affinity_threshold=affinity_threshold).get_annotation(
neoantigen, patient)
except Exception as e:
logger.error("Error processing neoantigen {}".format(
neoantigen.to_dict()))
logger.error("Error processing patient {}".format(
patient.to_dict()))
raise e
end = time.time()
logger.info(
"Elapsed time for annotating neoantigen for peptide={}: {} seconds"
.format(neoantigen.mutation.mutated_xmer, int(end - start)))
return annotated_neoantigen
def test_good_data_does_not_raise_exceptions(self):
neoantigen = Neoantigen(patient_identifier="1234", rna_expression=0.45)
ModelValidator.validate(neoantigen)
patient = Patient(identifier="1234", is_rna_available=True)
ModelValidator.validate(patient)
def test_valid_h2_ii_genotype(self):
patient = Patient(
identifier="123",
mhc2=[
Mhc2(
name=Mhc2Name.H2A_molecule,
genes=[
Mhc2Gene(
name=Mhc2GeneName.H2A,
zygosity=Zygosity.HETEROZYGOUS,
alleles=[
self.h2_parser.parse_mhc_allele("H2Ad"),
self.h2_parser.parse_mhc_allele("H2Ap"),
],
)
],
isoforms=[
self.h2_parser.parse_mhc2_isoform("H2Ad"),
self.h2_parser.parse_mhc2_isoform("H2Ap"),
],
)
],
)
self._assert_valid_patient(patient=patient,
organism=ORGANISM_MUS_MUSCULUS)
patient2 = Patient(
identifier="123",
mhc2=[
Mhc2(name=Mhc2Name.H2E_molecule,
genes=[
Mhc2Gene(
name=Mhc2GeneName.H2E,
zygosity=Zygosity.HOMOZYGOUS,
alleles=[self.h2_parser.parse_mhc_allele("H2Ed")])
],
isoforms=[self.h2_parser.parse_mhc2_isoform("H2Ed")])
])
self._assert_valid_patient(patient=patient2,
organism=ORGANISM_MUS_MUSCULUS)
def build_patient(identifier,
is_rna_available=False,
tumor_type=None,
mhc_alleles: List = [],
mhc2_alleles: List = [],
mhc_database: MhcDatabase = None):
patient = Patient(
identifier=identifier,
is_rna_available=is_rna_available,
tumor_type=tumor_type,
mhc1=MhcFactory.build_mhc1_alleles(mhc_alleles, mhc_database),
mhc2=MhcFactory.build_mhc2_alleles(mhc2_alleles, mhc_database))
ModelValidator.validate_patient(patient=patient,
organism=mhc_database.organism)
return patient
def test_neoantigen_no_wt_failing(self):
patient_identifier = "12345"
neoantigen = Neoantigen(
mutation=Mutation(mutated_xmer="SPSFPLEPDDEVFTAIAKAMEEMVEDS"),
patient_identifier=patient_identifier)
patient = Patient(
identifier=patient_identifier,
mhc1=MhcFactory.build_mhc1_alleles(
[
"HLA-A*02:24", "HLA-A*36:04", "HLA-B*58:25",
"HLA-B*35:102", "HLA-C*02:30", "HLA-C*07:139"
],
mhc_database=self.references.get_mhc_database()),
)
annotations = NeoFox(
neoantigens=[neoantigen],
patients=[patient],
num_cpus=1,
).get_annotations()
# it does not crash even though there are no best 9mers
self.assertIsNotNone(annotations)
def patient(self) -> Patient:
patient = None
found = False
while not found:
dr_isoforms = self.random_elements(self.get_hla_ii_alleles_by_gene(Mhc2Name.DR), unique=True, length=2)
dp_isoforms = self.random_elements(self.get_hla_ii_alleles_by_gene(Mhc2Name.DP), unique=True, length=2)
dq_isoforms = self.random_elements(self.get_hla_ii_alleles_by_gene(Mhc2Name.DQ), unique=True, length=2)
# NOTE: for some reason some DP alleles are malformed and cause a validation error, most do not.
# thus I retry until I get a valid combination of HLA alleles, will clarify in another reincarnation
try:
patient = Patient(
identifier=self.generator.unique.uuid4(),
is_rna_available=True,
tumor_type=self.random_elements(self.available_tumor_types, length=1)[0],
# by setting unique=True we enforce that all patients are heterozygous
mhc1=MhcFactory.build_mhc1_alleles(
self.random_elements(self.get_hla_i_alleles_by_gene(Mhc1Name.A), unique=True, length=2) +
self.random_elements(self.get_hla_i_alleles_by_gene(Mhc1Name.B), unique=True, length=2) +
self.random_elements(self.get_hla_i_alleles_by_gene(Mhc1Name.C), unique=True, length=2),
self.hla_database
),
mhc2=MhcFactory.build_mhc2_alleles(
[i.alpha_chain.name for i in dp_isoforms] +
[i.beta_chain.name for i in dp_isoforms] +
[i.alpha_chain.name for i in dq_isoforms] +
[i.beta_chain.name for i in dq_isoforms] +
[i.beta_chain.name for i in dr_isoforms],
self.hla_database
)
)
ModelValidator.validate_patient(patient)
except NeofoxDataValidationException:
continue
found = True
return patient
def test_neoantigen_failing(self):
patient_identifier = "12345"
neoantigen = Neoantigen(mutation=Mutation(
wild_type_xmer="ARPDMFCLFHGKRYFPGESWHPYLEPQ",
mutated_xmer="ARPDMFCLFHGKRHFPGESWHPYLEPQ"),
patient_identifier=patient_identifier)
patient = Patient(
identifier=patient_identifier,
mhc1=MhcFactory.build_mhc1_alleles(
[
"HLA-A*03:01", "HLA-A*29:02", "HLA-B*07:02", "HLA-B*44:03",
"HLA-C*07:02", "HLA-C*16:01"
],
mhc_database=self.references.get_mhc_database()),
)
annotations = NeoFox(
neoantigens=[neoantigen],
patients=[patient],
num_cpus=1,
).get_annotations()
# it does not crash even though there are no best 9mers
self.assertIsNotNone(annotations)
def test_invalid_hla_i_genotype(self):
# 3 alleles for gene A
self._assert_invalid_patient(patient=Patient(
identifier="123",
mhc1=[
Mhc1(
name=Mhc1Name.A,
zygosity=Zygosity.HOMOZYGOUS,
alleles=[
self.hla_parser.parse_mhc_allele("HLA-A01:01"),
self.hla_parser.parse_mhc_allele("HLA-A01:02"),
self.hla_parser.parse_mhc_allele("HLA-A01:03"),
],
)
],
),
organism=ORGANISM_HOMO_SAPIENS)
# 2 alleles for homozygous gene
self._assert_invalid_patient(patient=Patient(
identifier="123",
mhc1=[
Mhc1(
name=Mhc1Name.A,
zygosity=Zygosity.HOMOZYGOUS,
alleles=[
self.hla_parser.parse_mhc_allele("HLA-A01:01"),
self.hla_parser.parse_mhc_allele("HLA-A01:02"),
],
)
],
),
organism=ORGANISM_HOMO_SAPIENS)
# 1 alleles for heterozygous gene
self._assert_invalid_patient(patient=Patient(
identifier="123",
mhc1=[
Mhc1(
name=Mhc1Name.A,
zygosity=Zygosity.HETEROZYGOUS,
alleles=[self.hla_parser.parse_mhc_allele("HLA-A01:01")],
)
],
),
organism=ORGANISM_HOMO_SAPIENS)
# 1 alleles for hemizygous gene
self._assert_invalid_patient(patient=Patient(
identifier="123",
mhc1=[
Mhc1(
name=Mhc1Name.A,
zygosity=Zygosity.HEMIZYGOUS,
alleles=[
self.hla_parser.parse_mhc_allele("HLA-A01:01"),
self.hla_parser.parse_mhc_allele("HLA-A01:02"),
],
)
],
),
organism=ORGANISM_HOMO_SAPIENS)
# alleles referring to a different gene
self._assert_invalid_patient(patient=Patient(
identifier="123",
mhc1=[
Mhc1(
name=Mhc1Name.A,
zygosity=Zygosity.HETEROZYGOUS,
alleles=[
self.hla_parser.parse_mhc_allele("HLA-B01:01"),
self.hla_parser.parse_mhc_allele("HLA-B01:02"),
],
)
],
),
organism=ORGANISM_HOMO_SAPIENS)
def test_invalid_h2_i_genotype(self):
# 3 alleles for gene A
self._assert_invalid_patient(patient=Patient(
identifier="123",
mhc1=[
Mhc1(
name=Mhc1Name.H2D,
zygosity=Zygosity.HOMOZYGOUS,
alleles=[
self.h2_parser.parse_mhc_allele("H2Dd"),
self.h2_parser.parse_mhc_allele("H2Dk"),
self.h2_parser.parse_mhc_allele("H2Dp"),
],
)
],
),
organism=ORGANISM_MUS_MUSCULUS)
# 2 alleles for homozygous gene
self._assert_invalid_patient(patient=Patient(
identifier="123",
mhc1=[
Mhc1(
name=Mhc1Name.H2D,
zygosity=Zygosity.HOMOZYGOUS,
alleles=[
self.h2_parser.parse_mhc_allele("H2Dd"),
self.h2_parser.parse_mhc_allele("H2Dk"),
],
)
],
),
organism=ORGANISM_MUS_MUSCULUS)
# 1 alleles for heterozygous gene
self._assert_invalid_patient(patient=Patient(
identifier="123",
mhc1=[
Mhc1(
name=Mhc1Name.H2D,
zygosity=Zygosity.HETEROZYGOUS,
alleles=[
self.h2_parser.parse_mhc_allele("H2Dd"),
],
)
],
),
organism=ORGANISM_MUS_MUSCULUS)
# 2 alleles for hemizygous gene
self._assert_invalid_patient(patient=Patient(
identifier="123",
mhc1=[
Mhc1(
name=Mhc1Name.H2D,
zygosity=Zygosity.HEMIZYGOUS,
alleles=[
self.h2_parser.parse_mhc_allele("H2Dd"),
self.h2_parser.parse_mhc_allele("H2Dk"),
],
)
],
),
organism=ORGANISM_MUS_MUSCULUS)
# alleles referring to a different gene
self._assert_invalid_patient(patient=Patient(
identifier="123",
mhc1=[
Mhc1(
name=Mhc1Name.H2D,
zygosity=Zygosity.HETEROZYGOUS,
alleles=[
self.h2_parser.parse_mhc_allele("H2Kd"),
self.h2_parser.parse_mhc_allele("H2Kk"),
],
)
],
),
organism=ORGANISM_MUS_MUSCULUS)
def test_valid_hla_ii_genotype(self):
patient = Patient(
identifier="123",
mhc2=[
Mhc2(
name=Mhc2Name.DQ,
genes=[
Mhc2Gene(
name=Mhc2GeneName.DQA1,
zygosity=Zygosity.HETEROZYGOUS,
alleles=[
self.hla_parser.parse_mhc_allele(
"HLA-DQA1*01:01"),
self.hla_parser.parse_mhc_allele(
"HLA-DQA1*01:02"),
],
),
Mhc2Gene(
name=Mhc2GeneName.DQB1,
zygosity=Zygosity.HOMOZYGOUS,
alleles=[
self.hla_parser.parse_mhc_allele(
"HLA-DQB1*01:01")
],
),
],
isoforms=[
self.hla_parser.parse_mhc2_isoform(
"HLA-DQA1*01:01-DQB1*01:01"),
self.hla_parser.parse_mhc2_isoform(
"HLA-DQA1*01:02-DQB1*01:01"),
],
)
],
)
self._assert_valid_patient(patient=patient,
organism=ORGANISM_HOMO_SAPIENS)
patient2 = Patient(
identifier="123",
mhc2=[
Mhc2(
name=Mhc2Name.DR,
genes=[
Mhc2Gene(
name=Mhc2GeneName.DRB1,
zygosity=Zygosity.HOMOZYGOUS,
alleles=[
self.hla_parser.parse_mhc_allele(
"HLA-DRB1*01:01")
],
)
],
isoforms=[
self.hla_parser.parse_mhc2_isoform("HLA-DRB1*01:01")
],
)
],
)
self._assert_valid_patient(patient=patient2,
organism=ORGANISM_HOMO_SAPIENS)
patient3 = Patient(
identifier="123",
mhc2=[
Mhc2(
name=Mhc2Name.DQ,
genes=[
Mhc2Gene(
name=Mhc2GeneName.DQA1,
zygosity=Zygosity.HETEROZYGOUS,
alleles=[
self.hla_parser.parse_mhc_allele(
"HLA-DQA1*01:01"),
self.hla_parser.parse_mhc_allele(
"HLA-DQA1*01:02"),
],
),
Mhc2Gene(
name=Mhc2GeneName.DQB1,
zygosity=Zygosity.HOMOZYGOUS,
alleles=[
self.hla_parser.parse_mhc_allele(
"HLA-DQB1*01:01")
],
),
],
isoforms=[
self.hla_parser.parse_mhc2_isoform(
"HLA-DQA1*01:01-DQB1*01:01"),
self.hla_parser.parse_mhc2_isoform(
"HLA-DQA1*01:02-DQB1*01:01"),
],
)
],
)
self._assert_valid_patient(patient=patient3,
organism=ORGANISM_HOMO_SAPIENS)
def test_invalid_h2_ii_genotype(self):
# 3 alleles for gene
self._assert_invalid_patient(patient=Patient(
identifier="123",
mhc2=[
Mhc2(
name=Mhc2Name.H2E_molecule,
genes=[
Mhc2Gene(
name=Mhc2GeneName.H2E,
zygosity=Zygosity.HETEROZYGOUS,
alleles=[
self.h2_parser.parse_mhc_allele("H2Ea"),
self.h2_parser.parse_mhc_allele("H2Eb"),
self.h2_parser.parse_mhc_allele("H2Ec"),
],
)
],
)
],
),
organism=ORGANISM_MUS_MUSCULUS)
# 2 alleles for homozygous gene
self._assert_invalid_patient(patient=Patient(
identifier="123",
mhc2=[
Mhc2(
name=Mhc2Name.H2A_molecule,
genes=[
Mhc2Gene(
name=Mhc2GeneName.H2A,
zygosity=Zygosity.HOMOZYGOUS,
alleles=[
self.h2_parser.parse_mhc_allele("H2Aa"),
self.h2_parser.parse_mhc_allele("H2Ab"),
],
),
],
)
],
),
organism=ORGANISM_MUS_MUSCULUS)
# 1 alleles for heterozygous gene
self._assert_invalid_patient(patient=Patient(
identifier="123",
mhc2=[
Mhc2(
name=Mhc2Name.H2A_molecule,
genes=[
Mhc2Gene(
name=Mhc2GeneName.H2A,
zygosity=Zygosity.HETEROZYGOUS,
alleles=[self.h2_parser.parse_mhc_allele("H2Aa")],
)
],
)
],
),
organism=ORGANISM_MUS_MUSCULUS)
# 1 alleles for hemizygous gene
self._assert_invalid_patient(patient=Patient(
identifier="123",
mhc2=[
Mhc2(
name=Mhc2Name.H2A_molecule,
genes=[
Mhc2Gene(
name=Mhc2GeneName.H2A,
zygosity=Zygosity.HETEROZYGOUS,
alleles=[self.h2_parser.parse_mhc_allele("H2Aa")],
)
],
)
],
),
organism=ORGANISM_MUS_MUSCULUS)
# alleles referring to a different gene
self._assert_invalid_patient(patient=Patient(
identifier="123",
mhc2=[
Mhc2(
name=Mhc2Name.H2A_molecule,
genes=[
Mhc2Gene(
name=Mhc2GeneName.H2A,
zygosity=Zygosity.HETEROZYGOUS,
alleles=[self.h2_parser.parse_mhc_allele("H2Ea")],
),
],
)
],
),
organism=ORGANISM_MUS_MUSCULUS)
# MHC and gene referring to different entities
self._assert_invalid_patient(patient=Patient(
identifier="123",
mhc2=[
Mhc2(
name=Mhc2Name.H2A_molecule,
genes=[
Mhc2Gene(
name=Mhc2GeneName.H2E,
zygosity=Zygosity.HETEROZYGOUS,
alleles=[self.h2_parser.parse_mhc_allele("H2Ea")],
),
],
)
],
),
organism=ORGANISM_MUS_MUSCULUS)
def test_invalid_hla_ii_genotype(self):
# 3 alleles for gene
self._assert_invalid_patient(patient=Patient(
identifier="123",
mhc2=[
Mhc2(
name=Mhc2Name.DQ,
genes=[
Mhc2Gene(
name=Mhc2GeneName.DQA1,
zygosity=Zygosity.HETEROZYGOUS,
alleles=[
self.hla_parser.parse_mhc_allele(
"HLA-DQA1*01:01"),
self.hla_parser.parse_mhc_allele(
"HLA-DQA1*01:02"),
self.hla_parser.parse_mhc_allele(
"HLA-DQA1*01:03"),
],
),
Mhc2Gene(
name=Mhc2GeneName.DQB1,
zygosity=Zygosity.HOMOZYGOUS,
alleles=[
self.hla_parser.parse_mhc_allele(
"HLA-DQB1*01:01")
],
),
],
)
],
),
organism=ORGANISM_HOMO_SAPIENS)
# 2 alleles for homozygous gene
self._assert_invalid_patient(patient=Patient(
identifier="123",
mhc2=[
Mhc2(
name=Mhc2Name.DQ,
genes=[
Mhc2Gene(
name=Mhc2GeneName.DQA1,
zygosity=Zygosity.HETEROZYGOUS,
alleles=[
self.hla_parser.parse_mhc_allele(
"HLA-DQA1*01:01"),
self.hla_parser.parse_mhc_allele(
"HLA-DQA1*01:02"),
],
),
Mhc2Gene(
name=Mhc2GeneName.DQB1,
zygosity=Zygosity.HOMOZYGOUS,
alleles=[
self.hla_parser.parse_mhc_allele(
"HLA-DQB1*01:01"),
self.hla_parser.parse_mhc_allele(
"HLA-DQB1*01:02"),
],
),
],
)
],
),
organism=ORGANISM_HOMO_SAPIENS)
# 1 alleles for heterozygous gene
self._assert_invalid_patient(patient=Patient(
identifier="123",
mhc2=[
Mhc2(
name=Mhc2Name.DQ,
genes=[
Mhc2Gene(
name=Mhc2GeneName.DQA1,
zygosity=Zygosity.HETEROZYGOUS,
alleles=[
self.hla_parser.parse_mhc_allele(
"HLA-DQA1*01:01")
],
),
Mhc2Gene(
name=Mhc2GeneName.DQB1,
zygosity=Zygosity.HOMOZYGOUS,
alleles=[
self.hla_parser.parse_mhc_allele(
"HLA-DQB1*01:01")
],
),
],
)
],
),
organism=ORGANISM_HOMO_SAPIENS)
# 1 alleles for hemizygous gene
self._assert_invalid_patient(patient=Patient(
identifier="123",
mhc2=[
Mhc2(
name=Mhc2Name.DQ,
genes=[
Mhc2Gene(
name=Mhc2GeneName.DQA1,
zygosity=Zygosity.HETEROZYGOUS,
alleles=[
self.hla_parser.parse_mhc_allele(
"HLA-DQA1*01:01")
],
),
Mhc2Gene(
name=Mhc2GeneName.DQB1,
zygosity=Zygosity.HEMIZYGOUS,
alleles=[
self.hla_parser.parse_mhc_allele(
"HLA-DQB1*01:01")
],
),
],
)
],
),
organism=ORGANISM_HOMO_SAPIENS)
# alleles referring to a different gene
self._assert_invalid_patient(patient=Patient(
identifier="123",
mhc2=[
Mhc2(
name=Mhc2Name.DQ,
genes=[
Mhc2Gene(
name=Mhc2GeneName.DQA1,
zygosity=Zygosity.HETEROZYGOUS,
alleles=[
self.hla_parser.parse_mhc_allele(
"HLA-DQB1*01:01")
],
),
Mhc2Gene(
name=Mhc2GeneName.DQB1,
zygosity=Zygosity.HEMIZYGOUS,
alleles=[
self.hla_parser.parse_mhc_allele(
"HLA-DQA1*01:01")
],
),
],
)
],
),
organism=ORGANISM_HOMO_SAPIENS)
# MHC and gene referring to different entities
self._assert_invalid_patient(patient=Patient(
identifier="123",
mhc2=[
Mhc2(
name=Mhc2Name.DP,
genes=[
Mhc2Gene(
name=Mhc2GeneName.DQA1,
zygosity=Zygosity.HETEROZYGOUS,
alleles=[
self.hla_parser.parse_mhc_allele(
"HLA-DQA1*01:01")
],
),
Mhc2Gene(
name=Mhc2GeneName.DQB1,
zygosity=Zygosity.HEMIZYGOUS,
alleles=[
self.hla_parser.parse_mhc_allele(
"HLA-DQB1*01:01")
],
),
],
)
],
),
organism=ORGANISM_HOMO_SAPIENS)
# Molecules refer to alleles not in the MHC
self._assert_invalid_patient(patient=Patient(
identifier="123",
mhc2=[
Mhc2(
name=Mhc2Name.DQ,
genes=[
Mhc2Gene(
name=Mhc2GeneName.DQA1,
zygosity=Zygosity.HETEROZYGOUS,
alleles=[
self.hla_parser.parse_mhc_allele(
"HLA-DQA1*01:01"),
self.hla_parser.parse_mhc_allele(
"HLA-DQA1*01:02"),
],
),
Mhc2Gene(
name=Mhc2GeneName.DQB1,
zygosity=Zygosity.HOMOZYGOUS,
alleles=[
self.hla_parser.parse_mhc_allele(
"HLA-DQB1*01:01")
],
),
],
isoforms=[
Mhc2Isoform(name="HLA-DQA1*01:04-DQB1*01:01"),
Mhc2Isoform(name="HLA-DQA1*01:08-DQB1*01:01"),
],
)
],
),
organism=ORGANISM_HOMO_SAPIENS)
def _get_test_patient(self):
return Patient(identifier="12345", is_rna_available=True)