def _prepare_parameters(reference: dict,
max_edit_distances: dict,
name: str = None):
location = "MatchedReceptorsEncoder"
legal_chains = [
chain
for receptor in (TCABReceptor(), TCGDReceptor(), BCReceptor())
for chain in receptor.get_chains()
]
if type(max_edit_distances) is int:
max_edit_distances = {
chain: max_edit_distances
for chain in legal_chains
}
elif type(max_edit_distances) is dict:
ParameterValidator.assert_keys(max_edit_distances.keys(),
legal_chains,
location,
"max_edit_distances",
exclusive=False)
else:
ParameterValidator.assert_type_and_value(max_edit_distances, dict,
location,
'max_edit_distances')
reference_receptors = MatchedReferenceUtil.prepare_reference(
reference, location=location, paired=True)
return {
"reference_receptors": reference_receptors,
"max_edit_distances": max_edit_distances,
"name": name
}
def build_receptor_from_rows(first_row, second_row, identifier, chain_pair, metadata_columns):
first_sequence = ImportHelper.import_sequence(first_row, metadata_columns=metadata_columns)
second_sequence = ImportHelper.import_sequence(second_row, metadata_columns=metadata_columns)
if chain_pair == ChainPair.TRA_TRB:
receptor = TCABReceptor(alpha=first_sequence,
beta=second_sequence,
identifier=identifier,
metadata={**second_sequence.metadata.custom_params})
elif chain_pair == ChainPair.TRG_TRD:
receptor = TCGDReceptor(gamma=first_sequence,
delta=second_sequence,
identifier=identifier,
metadata={**second_sequence.metadata.custom_params})
elif chain_pair == ChainPair.IGH_IGL:
receptor = BCReceptor(heavy=first_sequence,
light=second_sequence,
identifier=identifier,
metadata={**first_sequence.metadata.custom_params})
elif chain_pair == ChainPair.IGH_IGK:
receptor = BCKReceptor(heavy=first_sequence,
kappa=second_sequence,
identifier=identifier,
metadata={**first_sequence.metadata.custom_params})
else:
raise NotImplementedError(f"ImportHelper: {chain_pair} chain pair is not supported.")
return receptor
def build_object(cls,
sequences: dict,
identifier: str = None,
metadata: dict = None) -> Receptor:
if all(chain in ChainPair.TRA_TRB.value for chain in sequences.keys()):
return TCABReceptor(alpha=sequences[Chain.ALPHA.value],
beta=sequences[Chain.BETA.value],
identifier=identifier,
metadata=metadata)
elif all(chain in ChainPair.TRG_TRD.value
for chain in sequences.keys()):
return TCGDReceptor(gamma=sequences[Chain.GAMMA.value],
delta=sequences[Chain.DELTA.value],
identifier=identifier,
metadata=metadata)
elif all(chain in ChainPair.IGH_IGL.value
for chain in sequences.keys()):
return BCReceptor(heavy=sequences[Chain.HEAVY.value],
light=sequences[Chain.LIGHT.value],
identifier=identifier,
metadata=metadata)
elif all(chain in ChainPair.IGH_IGK.value
for chain in sequences.keys()):
return BCKReceptor(heavy=sequences[Chain.HEAVY.value],
kappa=sequences[Chain.KAPPA.value],
identifier=identifier,
metadata=metadata)
else:
warnings.warn(
f"ReceptorBuilder: attempt to build_from_objects receptor with chains {sequences.keys()}, returning None..."
)
return None