immuneML.encodings.kmer_frequency.sequence_encoding package

Submodules

immuneML.encodings.kmer_frequency.sequence_encoding.GappedKmerSequenceEncoder module

class immuneML.encodings.kmer_frequency.sequence_encoding.GappedKmerSequenceEncoder.GappedKmerSequenceEncoder

Bases: SequenceEncodingStrategy

static encode_sequence(sequence: ReceptorSequence, params: EncoderParams, encode_locus=False)

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”)

Returns:

SequenceEncodingResult

Parameters:

encode_locus

static get_feature_names(params: EncoderParams)

immuneML.encodings.kmer_frequency.sequence_encoding.IMGTGappedKmerEncoder module

class immuneML.encodings.kmer_frequency.sequence_encoding.IMGTGappedKmerEncoder.IMGTGappedKmerEncoder

Bases: SequenceEncodingStrategy

static encode_sequence(sequence: ReceptorSequence, params: EncoderParams, encode_locus=False)

creates all overlapping gapped k-mers and IMGT position pairs 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”)

Returns:

SequenceEncodingResult

Parameters:

encode_locus

static get_feature_names(params: EncoderParams)

immuneML.encodings.kmer_frequency.sequence_encoding.IMGTKmerSequenceEncoder module

class immuneML.encodings.kmer_frequency.sequence_encoding.IMGTKmerSequenceEncoder.IMGTKmerSequenceEncoder

Bases: SequenceEncodingStrategy

static encode_sequence(sequence: ReceptorSequence, params: EncoderParams, encode_locus=False)

creates overlapping continuous k-mers from a sequence as features for use in KmerFrequencyEncoder object of type EncoderParams, same object as passed into KmerFrequencyEncoder :param sequence: ReceptorSequence :param params: EncoderParams (where params[“model”][“k”] is used) :return: SequenceEncodingResult consisting of features and feature information names

Parameters:

encode_locus

static get_feature_names(params: EncoderParams)

immuneML.encodings.kmer_frequency.sequence_encoding.KmerSequenceEncoder module

class immuneML.encodings.kmer_frequency.sequence_encoding.KmerSequenceEncoder.KmerSequenceEncoder

Bases: SequenceEncodingStrategy

static encode_sequence(sequence: ReceptorSequence, params: EncoderParams, encode_locus=False)

Encodes a receptor sequence into a sequence of k-mers

Parameters:

• encode_locus

• sequence – ReceptorSequence object

• params – EncoderParams object with information on k-mer length

Returns:

static get_feature_names(params: EncoderParams)

immuneML.encodings.kmer_frequency.sequence_encoding.SequenceEncodingStrategy module

class immuneML.encodings.kmer_frequency.sequence_encoding.SequenceEncodingStrategy.SequenceEncodingStrategy

Bases: object

abstract static encode_sequence(sequence: ReceptorSequence, params: EncoderParams, encode_locus=False)

abstract static get_feature_names(params: EncoderParams)

immuneML.encodings.kmer_frequency.sequence_encoding.SequenceEncodingType module

class immuneML.encodings.kmer_frequency.sequence_encoding.SequenceEncodingType.SequenceEncodingType(value, names=None, *, module=None, qualname=None, type=None, start=1, boundary=None)

Bases: Enum

CONTINUOUS_KMER = 'KmerSequenceEncoder'

GAPPED_KMER = 'GappedKmerSequenceEncoder'

IMGT_CONTINUOUS_KMER = 'IMGTKmerSequenceEncoder'

IMGT_GAPPED_KMER = 'IMGTGappedKmerEncoder'

V_GENE_CONT_KMER = 'VGeneContKmerEncoder'

V_GENE_IMGT_KMER = 'VGeneIMGTKmerEncoder'

immuneML.encodings.kmer_frequency.sequence_encoding.VGeneContKmerEncoder module

class immuneML.encodings.kmer_frequency.sequence_encoding.VGeneContKmerEncoder.VGeneContKmerEncoder

Bases: SequenceEncodingStrategy

static encode_sequence(sequence: ReceptorSequence, params: EncoderParams, encode_locus=False)

Encodes a receptor sequence into a sequence of k-mers

Parameters:

• encode_locus

• sequence – ReceptorSequence object

• params – EncoderParams object with information on k-mer length

Returns:

static get_feature_names(params: EncoderParams)

immuneML.encodings.kmer_frequency.sequence_encoding.VGeneIMGTKmerEncoder module

class immuneML.encodings.kmer_frequency.sequence_encoding.VGeneIMGTKmerEncoder.VGeneIMGTKmerEncoder

Bases: SequenceEncodingStrategy

static encode_sequence(sequence: ReceptorSequence, params: EncoderParams, encode_locus=False)

Encodes a receptor sequence into a sequence of k-mers

Parameters:

• encode_locus

• sequence – ReceptorSequence object

• params – EncoderParams object with information on k-mer length

Returns:

static get_feature_names(params: EncoderParams)

Module contents