Source code for immuneML.encodings.onehot.OneHotReceptorEncoder

import numpy as np

from immuneML.data_model.dataset.ReceptorDataset import ReceptorDataset
from immuneML.data_model.encoded_data.EncodedData import EncodedData
from immuneML.encodings.EncoderParams import EncoderParams
from immuneML.encodings.onehot.OneHotEncoder import OneHotEncoder

[docs] class OneHotReceptorEncoder(OneHotEncoder): """ One-hot encoded repertoire data is represented in a matrix with dimensions: [receptors, chains, sequence_lengths, one_hot_characters] when use_positional_info is true, the last 3 indices in one_hot_characters represents the positional information: - start position (high when close to start) - middle position (high in the middle of the sequence) - end position (high when close to end) """ def _encode_new_dataset(self, dataset, params: EncoderParams): encoded_data = self._encode_data(dataset, params) encoded_dataset = dataset.clone() encoded_dataset.encoded_data = encoded_data return encoded_dataset def _encode_data(self, dataset: ReceptorDataset, params: EncoderParams): receptor_objs = [receptor for receptor in dataset.get_data()] sequences = [[getattr(obj, chain).get_sequence(self.sequence_type) for chain in obj.get_chains()] for obj in receptor_objs] first_chain_seqs, second_chain_seqs = zip(*sequences) if any(seq is None for seq in first_chain_seqs) or any(seq is None for seq in second_chain_seqs): raise ValueError(f"{OneHotEncoder.__name__}: receptor dataset {} (id: {dataset.identifier}) contains empty sequences for the " f"specified sequence type {}. Please check that the dataset is imported correctly.") max_seq_len = max(max([len(seq) for seq in first_chain_seqs]), max([len(seq) for seq in second_chain_seqs])) example_ids = dataset.get_example_ids() labels = self._get_labels(receptor_objs, params) if params.encode_labels else None examples_first_chain = self._encode_sequence_list(first_chain_seqs, pad_n_sequences=len(receptor_objs), pad_sequence_len=max_seq_len) examples_second_chain = self._encode_sequence_list(second_chain_seqs, pad_n_sequences=len(receptor_objs), pad_sequence_len=max_seq_len) examples = np.stack((examples_first_chain, examples_second_chain), axis=1) feature_names = self._get_feature_names(max_seq_len, receptor_objs[0].get_chains()) if self.flatten: examples = examples.reshape((len(receptor_objs), 2*max_seq_len*len(self.onehot_dimensions))) feature_names = [item for sublist in feature_names for subsublist in sublist for item in subsublist] encoded_data = EncodedData(examples=examples, labels=labels, example_ids=example_ids, feature_names=feature_names, encoding=OneHotEncoder.__name__, info={"chain_names": receptor_objs[0].get_chains() if all(receptor_obj.get_chains() == receptor_objs[0].get_chains() for receptor_obj in receptor_objs) else None}) return encoded_data def _get_feature_names(self, max_seq_len, chains): return [[[f"{chain}_{pos}_{dim}" for dim in self.onehot_dimensions] for pos in range(max_seq_len)] for chain in chains] def _get_labels(self, receptor_objs, params: EncoderParams): label_names = params.label_config.get_labels_by_name() labels = {name: [None] * len(receptor_objs) for name in label_names} for idx, receptor in enumerate(receptor_objs): for name in label_names: labels[name][idx] = receptor.metadata[name] return labels