Source code for immuneML.data_model.receptor.TCABReceptor

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 TCABReceptor(Receptor): FIELDS = {'alpha': object, 'beta': 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'] == TCABReceptor.version: alpha_record = record[['alpha_' + name for name in ReceptorSequence.get_record_names()]] alpha_record.dtype.names = ReceptorSequence.get_record_names() beta_record = record[['beta_' + name for name in ReceptorSequence.get_record_names()]] beta_record.dtype.names = ReceptorSequence.get_record_names() return TCABReceptor(alpha=ReceptorSequence.create_from_record(alpha_record), beta=ReceptorSequence.create_from_record(beta_record), identifier=record['identifier'], metadata=json.loads(record['metadata'])) else: raise NotImplementedError(f"Supported ({TCABReceptor.version}) and available version differ, but there is no converter available.")
def __init__(self, alpha: ReceptorSequence = None, beta: ReceptorSequence = None, metadata: dict = None, identifier: str = None): self.alpha = alpha self.beta = beta self.metadata = metadata self.identifier = uuid4().hex if identifier is None else identifier
[docs] def get_chains(self): return ["alpha", "beta"]
[docs] @classmethod def get_record_names(cls): return ['alpha_' + name for name in ReceptorSequence.get_record_names()] \ + ['beta_' + name for name in ReceptorSequence.get_record_names()] \ + [name for name in cls.FIELDS if name not in ['alpha', 'beta']]
[docs] def get_attribute(self, name: str): raise NotImplementedError