immuneML.data_model.receptor.receptor_sequence package

Submodules

immuneML.data_model.receptor.receptor_sequence.Chain module

class immuneML.data_model.receptor.receptor_sequence.Chain.Chain(value)

Bases: enum.Enum

An enumeration.

ALPHA = 'TRA'

BETA = 'TRB'

DELTA = 'TRD'

GAMMA = 'TRG'

HEAVY = 'IGH'

KAPPA = 'IGK'

LIGHT = 'IGL'

static get_chain(item: str)

immuneML.data_model.receptor.receptor_sequence.ReceptorSequence module

class immuneML.data_model.receptor.receptor_sequence.ReceptorSequence.ReceptorSequence(amino_acid_sequence: Optional[str] = None, nucleotide_sequence: Optional[str] = None, identifier: Optional[str] = None, annotation: Optional[immuneML.data_model.receptor.receptor_sequence.SequenceAnnotation.SequenceAnnotation] = None, metadata: immuneML.data_model.receptor.receptor_sequence.SequenceMetadata.SequenceMetadata = <immuneML.data_model.receptor.receptor_sequence.SequenceMetadata.SequenceMetadata object>)

Bases: immuneML.data_model.DatasetItem.DatasetItem

FIELDS = {'amino_acid_sequence': <class 'str'>, 'annotation': <class 'dict'>, 'identifier': <class 'str'>, 'metadata': <class 'dict'>, 'nucleotide_sequence': <class 'str'>, 'version': <class 'str'>}

classmethod create_from_record(record: numpy.void)

get_attribute(name: str)

get_record()

exports the sequence object as a numpy record

classmethod get_record_names()

get_sequence(sequence_type: Optional[immuneML.environment.SequenceType.SequenceType] = None)

Returns receptor_sequence (nucleotide/amino acid) that corresponds to provided sequence type or preset receptor_sequence type from EnvironmentSettings class if no type is provided

set_annotation(annotation: immuneML.data_model.receptor.receptor_sequence.SequenceAnnotation.SequenceAnnotation)

set_metadata(metadata: immuneML.data_model.receptor.receptor_sequence.SequenceMetadata.SequenceMetadata)

set_sequence(sequence: str, sequence_type: immuneML.environment.SequenceType.SequenceType)

version = '1'

immuneML.data_model.receptor.receptor_sequence.ReceptorSequenceList module

class immuneML.data_model.receptor.receptor_sequence.ReceptorSequenceList.ReceptorSequenceList

Bases: collections.abc.MutableSequence

check(v)

insert(i, v)

S.insert(index, value) – insert value before index

immuneML.data_model.receptor.receptor_sequence.SequenceAnnotation module

class immuneML.data_model.receptor.receptor_sequence.SequenceAnnotation.SequenceAnnotation(implants: Optional[list] = None, other: Optional[dict] = None)

Bases: object

Sequence Annotation class includes antigen-specific data (in experimental scenario) and implanted signals (in simulated scenario)

add_implant(implant)

immuneML.data_model.receptor.receptor_sequence.SequenceFrameType module

class immuneML.data_model.receptor.receptor_sequence.SequenceFrameType.SequenceFrameType(value)

Bases: enum.Enum

An enumeration.

IN = 'IN'

OUT = 'OUT'

STOP = 'STOP'

immuneML.data_model.receptor.receptor_sequence.SequenceMetadata module

class immuneML.data_model.receptor.receptor_sequence.SequenceMetadata.SequenceMetadata(v_subgroup: Optional[str] = None, v_gene: Optional[str] = None, v_allele: Optional[str] = None, j_subgroup: Optional[str] = None, j_gene: Optional[str] = None, j_allele: Optional[str] = None, chain=None, count: Optional[int] = None, frame_type: str = 'IN', region_type: Optional[str] = None, cell_id: Optional[str] = None, custom_params: Optional[dict] = None)

Bases: object

class modeling the existing knowledge about a receptor_sequence, should be stored according to IMGT gene nomenclature (human can be found here):

• v subgroup

• v gene

• v allele

• j subgroup

• j gene

• j allele

• chain

• count

• region_type (e.g. IMGT_CDR3, IMGT_CDR1, FULL_SEQUENCE)

• frame_type (e.g. IN, OUT, STOP)

• sample

• custom params (dictionary with custom sequence information)

get_attribute(name: str)

Returns the attribute value if attribute is present either directly or in custom_params, otherwise returns None

Module contents