immuneML.preprocessing package

Submodules

immuneML.preprocessing.Preprocessor module

class immuneML.preprocessing.Preprocessor.Preprocessor[source]

Bases: object

static check_dataset_type(dataset, valid_dataset_types: list, location: str)[source]
abstract static process(dataset: immuneML.data_model.dataset.RepertoireDataset.RepertoireDataset, params: dict) → immuneML.data_model.dataset.RepertoireDataset.RepertoireDataset[source]
abstract process_dataset(dataset: immuneML.data_model.dataset.RepertoireDataset.RepertoireDataset, result_path: pathlib.Path) → immuneML.data_model.dataset.RepertoireDataset.RepertoireDataset[source]

immuneML.preprocessing.SubjectRepertoireCollector module

class immuneML.preprocessing.SubjectRepertoireCollector.SubjectRepertoireCollector(result_path: Optional[pathlib.Path] = None)[source]

Bases: immuneML.preprocessing.Preprocessor.Preprocessor

Merges all the Repertoires in a RepertoireDataset that have the same ‘subject_id’ specified in the metadata. The result is a RepertoireDataset with one Repertoire per subject.

YAML specification:

preprocessing_sequences:
    my_preprocessing:
        - my_filter: SubjectRepertoireCollector
static build_new_metadata(dataset, indices_to_keep, result_path: pathlib.Path)[source]
static process(dataset: immuneML.data_model.dataset.RepertoireDataset.RepertoireDataset, params: dict) → immuneML.data_model.dataset.RepertoireDataset.RepertoireDataset[source]
process_dataset(dataset: immuneML.data_model.dataset.RepertoireDataset.RepertoireDataset, result_path: Optional[pathlib.Path] = None)[source]
static store_repertoire(path, repertoire, sequences)[source]

Module contents