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

import logging

from immuneML import Constants
from immuneML.data_model.SequenceSet import ReceptorSequence
from immuneML.encodings.EncoderParams import EncoderParams
from immuneML.encodings.kmer_frequency.sequence_encoding.SequenceEncodingStrategy import SequenceEncodingStrategy
from immuneML.util.KmerHelper import KmerHelper




class VGeneContKmerEncoder(SequenceEncodingStrategy):



    @staticmethod
    def encode_sequence(sequence: ReceptorSequence, params: EncoderParams, encode_locus=False):
        """
        Encodes a receptor sequence into a sequence of k-mers

        Args:
            encode_locus:
            sequence: ReceptorSequence object
            params: EncoderParams object with information on k-mer length

        Returns:

        """
        k = params.model["k"]
        length = len(sequence.get_sequence(params.sequence_type))

        if length < k:
            logging.warning(f'KmerSequenceEncoder: Sequence length {length} is less than {k}. Ignoring sequence...')
            return None

        kmers = KmerHelper.create_kmers_from_sequence(sequence=sequence, k=k, sequence_type=params.sequence_type)
        kmers = [f"{sequence.v_gene}{Constants.FEATURE_DELIMITER}{kmer}" for kmer in kmers]

        if encode_locus:
            kmers = [f"{sequence.locus}{Constants.FEATURE_DELIMITER}{kmer}" for kmer in kmers]

        return kmers




    @staticmethod
    def get_feature_names(params: EncoderParams):
        return ['v_gene', "sequence"]