Source code for immuneML.data_model.receptor.TCGDReceptor

import json
from uuid import uuid4

import numpy as np

from immuneML.data_model.receptor.Receptor import Receptor
from immuneML.data_model.receptor.receptor_sequence.ReceptorSequence import ReceptorSequence

[docs]class TCGDReceptor(Receptor): FIELDS = {'gamma': object, 'delta': object, 'identifier': str, 'metadata': dict, 'version': str} version = "1"
[docs] @classmethod def create_from_record(cls, record: np.void): if 'version' in record.dtype.names and record['version'] == TCGDReceptor.version: gamma_record = record[['gamma_' + name for name in ReceptorSequence.get_record_names()]] gamma_record.dtype.names = ReceptorSequence.get_record_names() delta_record = record[['delta_' + name for name in ReceptorSequence.get_record_names()]] delta_record.dtype.names = ReceptorSequence.get_record_names() return TCGDReceptor(gamma=ReceptorSequence.create_from_record(gamma_record), delta=ReceptorSequence.create_from_record(delta_record), identifier=record['identifier'], metadata=json.loads(record['metadata'])) else: raise NotImplementedError(f"Supported ({TCGDReceptor.version}) and available version differ, but there is no converter available.")
[docs] @classmethod def get_record_names(cls): return ['gamma_' + name for name in ReceptorSequence.get_record_names()] \ + ['delta_' + name for name in ReceptorSequence.get_record_names()] \ + [name for name in cls.FIELDS if name not in ['gamma', 'delta']]
def __init__(self, gamma: ReceptorSequence = None, delta: ReceptorSequence = None, metadata: dict = None, identifier: str = None): self.gamma = gamma = delta self.metadata = metadata self.identifier = identifier if identifier is not None else uuid4().hex
[docs] def get_chains(self): return ["gamma", "delta"]
[docs] def get_attribute(self, name: str): raise NotImplementedError