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 export(dataset: <module 'immuneML.data_model.dataset.Dataset' from '/Users/milenpa/PycharmProjects/BMIimmuneML/immuneML/data_model/dataset/Dataset.py'>, path: ~pathlib.Path, number_of_processes: int = 1)[source]

static export_repertoire(repertoire: Repertoire, repertoire_path: Path)[source]

static export_updated_metadata(dataset: RepertoireDataset, result_path: Path, repertoire_folder: str)[source]

static get_sequence_aa_field(region_type)[source]

static get_sequence_field(region_type)[source]

static update_gene_columns(df, allele_name, gene_name)[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]

immuneML.IO.dataset_export.ImmuneMLExporter module

class immuneML.IO.dataset_export.ImmuneMLExporter.ImmuneMLExporter[source]