immuneML.data_model.receptor package

Subpackages

• immuneML.data_model.receptor.receptor_sequence package
  • Submodules
  • immuneML.data_model.receptor.receptor_sequence.Chain module
    • Chain
      • Chain.ALPHA
      • Chain.BETA
      • Chain.DELTA
      • Chain.GAMMA
      • Chain.HEAVY
      • Chain.KAPPA
      • Chain.LIGHT
      • Chain.get_chain()
  • immuneML.data_model.receptor.receptor_sequence.ReceptorSequence module
    • ReceptorSequence
      • ReceptorSequence.FIELDS
      • ReceptorSequence.create_from_record()
      • ReceptorSequence.get_attribute()
      • ReceptorSequence.get_record()
      • ReceptorSequence.get_record_names()
      • ReceptorSequence.get_sequence()
      • ReceptorSequence.set_annotation()
      • ReceptorSequence.set_metadata()
      • ReceptorSequence.set_sequence()
      • ReceptorSequence.version
  • immuneML.data_model.receptor.receptor_sequence.SequenceAnnotation module
    • SequenceAnnotation
      • SequenceAnnotation.add_implant()
  • immuneML.data_model.receptor.receptor_sequence.SequenceFrameType module
    • SequenceFrameType
      • SequenceFrameType.IN
      • SequenceFrameType.OUT
      • SequenceFrameType.STOP
  • immuneML.data_model.receptor.receptor_sequence.SequenceMetadata module
    • SequenceMetadata
      • SequenceMetadata.get_attribute()
  • Module contents

Submodules

immuneML.data_model.receptor.BCKReceptor module

class immuneML.data_model.receptor.BCKReceptor.BCKReceptor(heavy: ReceptorSequence = None, kappa: ReceptorSequence = None, metadata: dict = None, identifier: str = None)

Bases: Receptor

FIELDS = {'heavy': <class 'object'>, 'identifier': <class 'str'>, 'kappa': <class 'object'>, 'metadata': <class 'dict'>, 'version': <class 'str'>}

classmethod create_from_record(record)

get_chains()

classmethod get_record_names()

version = '1'

immuneML.data_model.receptor.BCReceptor module

class immuneML.data_model.receptor.BCReceptor.BCReceptor(heavy: ReceptorSequence = None, light: ReceptorSequence = None, metadata: dict = None, identifier: str = None)

Bases: Receptor

FIELDS = {'heavy': <class 'object'>, 'identifier': <class 'str'>, 'light': <class 'object'>, 'metadata': <class 'dict'>, 'version': <class 'str'>}

classmethod create_from_record(record)

get_chains()

classmethod get_record_names()

version = '1'

immuneML.data_model.receptor.ChainPair module

class immuneML.data_model.receptor.ChainPair.ChainPair(value, names=None, *, module=None, qualname=None, type=None, start=1, boundary=None)

Bases: Enum

IGH_IGK = ('IGH', 'IGK')

IGH_IGL = ('IGH', 'IGL')

TRA_TRB = ('TRA', 'TRB')

TRG_TRD = ('TRG', 'TRD')

static get_chain_pair(chains: List[Chain])

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 = '')

Bases: object

build_batch_generator()

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()

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

get_element_count()

make_subset(example_indices: list, path: Path, dataset_type: str, dataset_identifier: str)

immuneML.data_model.receptor.Receptor module

class immuneML.data_model.receptor.Receptor.Receptor(metadata: dict = None, identifier: str = None)

Bases: DatasetItem

FIELDS = {}

clone()

abstract classmethod create_from_record(record)

get_attribute(name: str)

get_chain(chain: str)

abstract get_chains()

get_record()

abstract classmethod get_record_names()

immuneML.data_model.receptor.ReceptorBuilder module

class immuneML.data_model.receptor.ReceptorBuilder.ReceptorBuilder

Bases: object

classmethod build_object(sequences: dict, identifier: str = None, metadata: dict = None) → Receptor

classmethod build_objects(sequences: List[ReceptorSequence]) → List[Receptor]

immuneML.data_model.receptor.RegionType module

class immuneML.data_model.receptor.RegionType.RegionType(value, names=None, *, module=None, qualname=None, type=None, start=1, boundary=None)

Bases: Enum

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: ReceptorSequence = None, beta: ReceptorSequence = None, metadata: dict = None, identifier: str = None)

Bases: Receptor

FIELDS = {'alpha': <class 'object'>, 'beta': <class 'object'>, 'identifier': <class 'str'>, 'metadata': <class 'dict'>, 'version': <class 'str'>}

classmethod create_from_record(record: void)

get_chains()

classmethod get_record_names()

version = '1'

immuneML.data_model.receptor.TCGDReceptor module

class immuneML.data_model.receptor.TCGDReceptor.TCGDReceptor(gamma: ReceptorSequence = None, delta: ReceptorSequence = None, metadata: dict = None, identifier: str = None)

Bases: Receptor

FIELDS = {'delta': <class 'object'>, 'gamma': <class 'object'>, 'identifier': <class 'str'>, 'metadata': <class 'dict'>, 'version': <class 'str'>}

classmethod create_from_record(record: void)

get_chains()

classmethod get_record_names()

version = '1'

Module contents