Source code for immuneML.encodings.kmer_frequency.KmerFreqReceptorEncoder

from collections import Counter

from immuneML.data_model.dataset.ReceptorDataset import ReceptorDataset
from immuneML.encodings.EncoderParams import EncoderParams
from immuneML.encodings.kmer_frequency.KmerFrequencyEncoder import KmerFrequencyEncoder


[docs] class KmerFreqReceptorEncoder(KmerFrequencyEncoder): 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_examples(self, dataset: ReceptorDataset, params: EncoderParams): encoded_receptors_counts, encoded_receptors = [], [] receptor_ids = [] label_config = params.label_config labels = {label: [] for label in label_config.get_labels_by_name()} if params.encode_labels else None chains = [] sequence_encoder = self._prepare_sequence_encoder() feature_names = sequence_encoder.get_feature_names(params) for receptor in dataset.get_data(params.pool_size): counts = {chain: Counter() for chain in receptor.get_chains()} chains = receptor.get_chains() for chain in receptor.get_chains(): counts[chain] = self._encode_sequence(receptor.get_chain(chain), params, sequence_encoder, counts[chain]) encoded_receptors_counts.append(counts) receptor_ids.append(receptor.identifier) if params.encode_labels: for label_name in label_config.get_labels_by_name(): label = receptor.metadata[label_name] labels[label_name].append(label) for encoded_receptor_count in encoded_receptors_counts: counts = [self._add_chain_to_name(encoded_receptor_count[chain], chain) for chain in chains] encoded_receptors.append(counts[0] + counts[1]) return encoded_receptors, receptor_ids, labels, feature_names def _add_chain_to_name(self, count: Counter, chain: str) -> Counter: new_counter = Counter() for key in count.keys(): new_counter[f"{chain}_{key}"] = count[key] return new_counter