immuneML.IO.dataset_export package

Submodules

immuneML.IO.dataset_export.AIRRExporter module

class immuneML.IO.dataset_export.AIRRExporter.AIRRExporter[source]

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: pandas.DataFrame) pandas.DataFrame[source]
static export(dataset: Dataset, path: Path, number_of_processes: int = 1, omit_columns: list = None)[source]
static process_and_store_data_file(input_filename, output_filename)[source]

immuneML.IO.dataset_export.DataExporter module

class immuneML.IO.dataset_export.DataExporter.DataExporter[source]

Bases: object

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

Module contents