immuneML.data_model.receptor package

Submodules

immuneML.data_model.receptor.BCKReceptor module

class immuneML.data_model.receptor.BCKReceptor.BCKReceptor(heavy: Optional[immuneML.data_model.receptor.receptor_sequence.ReceptorSequence.ReceptorSequence] = None, kappa: Optional[immuneML.data_model.receptor.receptor_sequence.ReceptorSequence.ReceptorSequence] = None, metadata: Optional[dict] = None, identifier: Optional[str] = None)[source]

Bases: immuneML.data_model.receptor.Receptor.Receptor

FIELDS = {'heavy': <class 'object'>, 'identifier': <class 'str'>, 'kappa': <class 'object'>, 'metadata': <class 'dict'>, 'version': <class 'str'>}
classmethod create_from_record(record)[source]
get_attribute(name: str)[source]
get_chains()[source]
classmethod get_record_names()[source]
version = '1'

immuneML.data_model.receptor.BCReceptor module

class immuneML.data_model.receptor.BCReceptor.BCReceptor(heavy: Optional[immuneML.data_model.receptor.receptor_sequence.ReceptorSequence.ReceptorSequence] = None, light: Optional[immuneML.data_model.receptor.receptor_sequence.ReceptorSequence.ReceptorSequence] = None, metadata: Optional[dict] = None, identifier: Optional[str] = None)[source]

Bases: immuneML.data_model.receptor.Receptor.Receptor

FIELDS = {'heavy': <class 'object'>, 'identifier': <class 'str'>, 'light': <class 'object'>, 'metadata': <class 'dict'>, 'version': <class 'str'>}
classmethod create_from_record(record)[source]
get_attribute(name: str)[source]
get_chains()[source]
classmethod get_record_names()[source]
version = '1'

immuneML.data_model.receptor.ChainPair module

class immuneML.data_model.receptor.ChainPair.ChainPair(value)[source]

Bases: enum.Enum

An enumeration.

IGH_IGK = ('IGH', 'IGK')
IGH_IGL = ('IGH', 'IGL')
TRA_TRB = ('TRA', 'TRB')
TRG_TRD = ('TRG', 'TRD')
static get_chain_pair(chains: List[immuneML.data_model.receptor.receptor_sequence.Chain.Chain])[source]

Given a list of 2 chain objects, returns the relevant ChainPair

immuneML.data_model.receptor.ElementGenerator module

class immuneML.data_model.receptor.ElementGenerator.ElementGenerator(file_list: list, file_size: int = 1000, element_class_name: str = '')[source]

Bases: object

build_batch_generator()[source]

creates a generator which will return one batch of elements at the time

Parameters

batch_size – how many elements should be returned at once (default 1)

Returns

element generator

build_element_generator()[source]

creates a generator which will return one element at the time :return: element generator

get_element_count()[source]
make_subset(example_indices: list, path: pathlib.Path, dataset_type: str, dataset_identifier: str)[source]

immuneML.data_model.receptor.Receptor module

class immuneML.data_model.receptor.Receptor.Receptor[source]

Bases: immuneML.data_model.DatasetItem.DatasetItem

FIELDS = {}
clone()[source]
abstract classmethod create_from_record(record)[source]
get_chain(chain: str)[source]
abstract get_chains()[source]
get_record()[source]
abstract classmethod get_record_names()[source]

immuneML.data_model.receptor.ReceptorBuilder module

class immuneML.data_model.receptor.ReceptorBuilder.ReceptorBuilder[source]

Bases: object

classmethod build_object(sequences: dict, identifier: Optional[str] = None, metadata: Optional[dict] = None) → immuneML.data_model.receptor.Receptor.Receptor[source]
classmethod build_objects(sequences: immuneML.data_model.receptor.receptor_sequence.ReceptorSequenceList.ReceptorSequenceList) → List[immuneML.data_model.receptor.Receptor.Receptor][source]

immuneML.data_model.receptor.RegionType module

class immuneML.data_model.receptor.RegionType.RegionType(value)[source]

Bases: enum.Enum

An enumeration.

FULL_SEQUENCE = 'FULL_SEQUENCE'
IMGT_CDR1 = 'IMGT_CDR1'
IMGT_CDR2 = 'IMGT_CDR2'
IMGT_CDR3 = 'IMGT_CDR3'
IMGT_FR1 = 'IMGT_FR1'
IMGT_FR2 = 'IMGT_FR2'
IMGT_FR3 = 'IMGT_FR3'
IMGT_FR4 = 'IMGT_FR4'
IMGT_JUNCTION = 'IMGT_JUNCTION'

immuneML.data_model.receptor.TCABReceptor module

class immuneML.data_model.receptor.TCABReceptor.TCABReceptor(alpha: Optional[immuneML.data_model.receptor.receptor_sequence.ReceptorSequence.ReceptorSequence] = None, beta: Optional[immuneML.data_model.receptor.receptor_sequence.ReceptorSequence.ReceptorSequence] = None, metadata: Optional[dict] = None, identifier: Optional[str] = None)[source]

Bases: immuneML.data_model.receptor.Receptor.Receptor

FIELDS = {'alpha': <class 'object'>, 'beta': <class 'object'>, 'identifier': <class 'str'>, 'metadata': <class 'dict'>, 'version': <class 'str'>}
classmethod create_from_record(record: numpy.void)[source]
get_attribute(name: str)[source]
get_chains()[source]
classmethod get_record_names()[source]
version = '1'

immuneML.data_model.receptor.TCGDReceptor module

class immuneML.data_model.receptor.TCGDReceptor.TCGDReceptor(gamma: Optional[immuneML.data_model.receptor.receptor_sequence.ReceptorSequence.ReceptorSequence] = None, delta: Optional[immuneML.data_model.receptor.receptor_sequence.ReceptorSequence.ReceptorSequence] = None, metadata: Optional[dict] = None, identifier: Optional[str] = None)[source]

Bases: immuneML.data_model.receptor.Receptor.Receptor

FIELDS = {'delta': <class 'object'>, 'gamma': <class 'object'>, 'identifier': <class 'str'>, 'metadata': <class 'dict'>, 'version': <class 'str'>}
classmethod create_from_record(record: numpy.void)[source]
get_attribute(name: str)[source]
get_chains()[source]
classmethod get_record_names()[source]
version = '1'

Module contents