Source code for immuneML.encodings.kmer_frequency.sequence_encoding.GappedKmerSequenceEncoder

import warnings

from immuneML.data_model.receptor.receptor_sequence.ReceptorSequence import ReceptorSequence
from immuneML.encodings.EncoderParams import EncoderParams
from immuneML.encodings.kmer_frequency.sequence_encoding.SequenceEncodingStrategy import SequenceEncodingStrategy
from immuneML.environment.EnvironmentSettings import EnvironmentSettings
from immuneML.util.KmerHelper import KmerHelper

[docs] class GappedKmerSequenceEncoder(SequenceEncodingStrategy):
[docs] @staticmethod def encode_sequence(sequence: ReceptorSequence, params: EncoderParams): """ creates all overlapping gapped k-mers from a sequence as features for use in KmerFrequencyEncoder. this gap length goes from min_gap to max_gap inclusive, and there is a k-mer of length k_left on the left side of the gap and a k-mer of length k_right on the right side of the gap. :param sequence: ReceptorSequence :param params: EncoderParams (within the "model", the following keys are used: "k_left", "k_right", "max_gap", "min_gap") :return: SequenceEncodingResult """ k_left = params.model.get('k_left') k_right = params.model.get('k_right', k_left) max_gap = params.model.get('max_gap') min_gap = params.model.get('min_gap', 0) sequence_type = params.model.get('sequence_type', EnvironmentSettings.sequence_type) length = len(sequence.get_sequence(sequence_type)) if length < k_left + k_right + max_gap: warnings.warn('Sequence length is less than k_left + k_right + max_gap. Ignoring sequence') return None gapped_kmers = KmerHelper.create_gapped_kmers_from_sequence(sequence, k_left=k_left, max_gap=max_gap, min_gap=min_gap, k_right=k_right, sequence_type=sequence_type) return gapped_kmers
[docs] @staticmethod def get_feature_names(params: EncoderParams): return ["sequence"]