immuneML.IO.dataset_export package

Submodules

immuneML.IO.dataset_export.AIRRExporter module

class immuneML.IO.dataset_export.AIRRExporter.AIRRExporter

Bases: DataExporter

Exports a RepertoireDataset of Repertoires in AIRR format.

Things to note:

• one filename_prefix is given, which is combined with the Repertoire identifiers for the filenames, to create one file per Repertoire

• ‘counts’ is written into the field ‘duplicate_counts’

• ‘sequence_identifiers’ is written both into the fields ‘sequence_id’ and ‘rearrangement_id’

static add_cdr3_from_junction(df: DataFrame) → DataFrame

static export(dataset: Dataset, path: Path, number_of_processes: int = 1, omit_columns: list = None)

static export_repertoire_dataset(dataset: RepertoireDataset, path: Path, omit_columns: list = None)

static export_repertoire_files(dataset: RepertoireDataset, repertoire_path: Path)

static process_and_store_data_file(input_filename, output_filename)

static process_and_store_dataset_file(input_filename, output_filename)

immuneML.IO.dataset_export.DataExporter module

class immuneML.IO.dataset_export.DataExporter.DataExporter

Bases: object

abstract static export(dataset: Dataset, path: Path, number_of_processes: int = 1)

Module contents