immuneML.IO.ml_method package

Submodules

immuneML.IO.ml_method.ClusteringExporter module

class immuneML.IO.ml_method.ClusteringExporter.ClusteringExporter[source]

Bases: object

static export(cl_item: ClusteringItem, path: Path) → Path[source]

Export a clustering item’s components to disk.

Parameters:

  • cl_item – The ClusteringItem to export

  • path – The directory where files will be stored

Returns:

Path to the export directory

static export_zip(cl_item: ClusteringItem, path: Path, setting_key: str) → Path[source]

Export a clustering setting (encoder, dim reduction if any, clustering method) as a zip file.

Parameters:

  • cl_item – The ClusteringItem containing the fitted encoder and clustering method

  • path – The directory where the export will be stored

  • setting_key – A key identifying this setting (used for naming)

Returns:

Path to the created zip file

immuneML.IO.ml_method.ClusteringImporter module

class immuneML.IO.ml_method.ClusteringImporter.ClusteringImporter[source]

Bases: object

Import clustering settings and items from exported zip files.

static import_clustering_item(config_dir: Path) → Tuple[ClusteringItem, dict][source]

Import a ClusteringItem from an exported directory.

Parameters:

config_dir – Path to the directory containing the exported clustering files

Returns:

Tuple of (ClusteringItem, config dict)

immuneML.IO.ml_method.MLExporter module

class immuneML.IO.ml_method.MLExporter.MLExporter[source]

Bases: object

static export(hp_item: HPItem, path: Path) → Path[source]
static export_zip(hp_item: HPItem, path: Path, label_name: str) → str[source]
static store_ml_method(method: MLMethod, path: Path, preproc_filename, encoder_filename, encoder_name, encoder_params, encoder_class_name, train_dataset, preproc_sequence_name, preproc_sequence)[source]

immuneML.IO.ml_method.MLImport module

class immuneML.IO.ml_method.MLImport.MLImport[source]

Bases: object

static import_encoder(config: MLMethodConfiguration, config_dir: Path)[source]
static import_hp_setting(config_dir: Path) → Tuple[HPSetting, Label][source]
static import_label(config: MLMethodConfiguration) → Label[source]
static import_preprocessing_sequence(config: MLMethodConfiguration, config_dir) → List[Preprocessor][source]

immuneML.IO.ml_method.MLMethodConfiguration module

class immuneML.IO.ml_method.MLMethodConfiguration.MLMethodConfiguration(label_name: str = None, label_values: list = None, label_positive_class: str = None, encoding_name: str = None, encoding_class: str = None, encoding_parameters: dict = None, encoding_file: str = None, preprocessing_sequence_name: str = None, preprocessing_parameters: dict = None, preprocessing_file: str = None, ml_method: str = None, ml_method_name: str = None, train_dataset_id: str = None, train_dataset_name: str = None, software_used: str = None)[source]

Bases: object

encoding_class: str = None
encoding_file: str = None
encoding_name: str = None
encoding_parameters: dict = None
label_name: str = None
label_positive_class: str = None
label_values: list = None
load(path: Path)[source]
ml_method: str = None
ml_method_name: str = None
preprocessing_file: str = None
preprocessing_parameters: dict = None
preprocessing_sequence_name: str = None
software_used: str = None
store(path: Path)[source]
train_dataset_id: str = None
train_dataset_name: str = None

immuneML.IO.ml_method.UtilIO module

class immuneML.IO.ml_method.UtilIO.UtilIO[source]

Bases: object

static export_comparison_data(comp_data: ComparisonData, path: Path)[source]
static export_pairwise_comparison(pairwise_comparison: PairwiseRepertoireComparison, path: Path) → Path[source]
static import_comparison_data(path: Path) → ComparisonData[source]
static import_pairwise_comparison(path: Path) → PairwiseRepertoireComparison[source]

Module contents