import logging
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
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class KmerSequenceEncoder(SequenceEncodingStrategy):
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@staticmethod
def encode_sequence(sequence: ReceptorSequence, params: EncoderParams):
"""
Encodes a receptor sequence into a sequence of k-mers
Args:
sequence: ReceptorSequence object
params: EncoderParams object with information on k-mer length
Returns:
"""
k = params.model["k"]
sequence_type = params.model.get('sequence_type', EnvironmentSettings.sequence_type)
length = len(sequence.get_sequence(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=sequence_type)
return kmers
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@staticmethod
def get_feature_names(params: EncoderParams):
return ["sequence"]