import itertools
import warnings
from typing import List
from immuneML.data_model.receptor.BCKReceptor import BCKReceptor
from immuneML.data_model.receptor.BCReceptor import BCReceptor
from immuneML.data_model.receptor.ChainPair import ChainPair
from immuneML.data_model.receptor.Receptor import Receptor
from immuneML.data_model.receptor.TCABReceptor import TCABReceptor
from immuneML.data_model.receptor.TCGDReceptor import TCGDReceptor
from immuneML.data_model.receptor.receptor_sequence.Chain import Chain
from immuneML.data_model.receptor.receptor_sequence.ReceptorSequenceList import ReceptorSequenceList
[docs]class ReceptorBuilder:
[docs] @classmethod
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
[docs] @classmethod
def build_objects(cls, sequences: ReceptorSequenceList) -> List[Receptor]:
receptors = []
sequences_per_chain = {chain.value: [sequence for sequence in sequences if sequence.metadata.chain.value == chain.value]
for chain in Chain}
for chain_pair in ChainPair:
all_chain_1 = sequences_per_chain[chain_pair.value[0]]
all_chain_2 = sequences_per_chain[chain_pair.value[1]]
combinations = list(itertools.product(all_chain_1, all_chain_2))
receptors.extend([ReceptorBuilder.build_object({sequence.metadata.chain.value: sequence for sequence in combination})
for combination in combinations])
return receptors