immuneML.api package

Subpackages

• immuneML.api.aggregated_runs package
  • Submodules
  • immuneML.api.aggregated_runs.MultiDatasetBenchmarkTool module
    • MultiDatasetBenchmarkTool
      • MultiDatasetBenchmarkTool.run()
  • Module contents
• immuneML.api.galaxy package
  • Submodules
  • immuneML.api.galaxy.DataSimulationTool module
    • DataSimulationTool
      • DataSimulationTool.prepare_specs()
  • immuneML.api.galaxy.DatasetGenerationTool module
    • DatasetGenerationTool
  • immuneML.api.galaxy.GalaxyMLApplicationTool module
    • GalaxyMLApplicationTool
  • immuneML.api.galaxy.GalaxySimulationTool module
    • GalaxySimulationTool
      • GalaxySimulationTool.prepare_specs()
  • immuneML.api.galaxy.GalaxyTool module
    • GalaxyTool
      • GalaxyTool.run()
  • immuneML.api.galaxy.GalaxyTrainMLModel module
    • GalaxyTrainMLModel
  • immuneML.api.galaxy.GalaxyYamlTool module
    • GalaxyYamlTool
      • GalaxyYamlTool.update_specs()
  • immuneML.api.galaxy.RepertoireClassificationTool module
    • RepertoireClassificationTool
  • immuneML.api.galaxy.Util module
    • Util
      • Util.check_export_format()
      • Util.check_instruction_type()
      • Util.check_parameters()
      • Util.check_paths()
      • Util.run_tool()
      • Util.update_dataset_key()
      • Util.update_result_paths()
  • immuneML.api.galaxy.build_dataset_yaml module
    • build_metadata_column_mapping()
    • build_specs()
    • main()
    • parse_commandline_arguments()
  • immuneML.api.galaxy.build_yaml_from_arguments module
    • build_encodings_specs()
    • build_labels()
    • build_ml_methods_specs()
    • build_settings_specs()
    • build_specs()
    • check_arguments()
    • discover_dataset_params()
    • get_ml_method_spec()
    • get_sequence_enc_type()
    • main()
    • parse_commandline_arguments()
  • Module contents

Submodules

immuneML.api.api_encoding module

immuneML.api.api_encoding.encode_dataset_by_kmer_freq(path_to_dataset_directory: str, result_path: str, metadata_path: str = None)

encodes the repertoire dataset using KmerFrequencyEncoder

Parameters:

• path_to_dataset_directory (str) – path to directory containing all repertoire files with .tsv extension in MiXCR format

• result_path (str) – where to store the results

• metadata_path (str) – csv file with columns “filename”, “subject_id”, “disease” which is filled by default if value of argument is None, otherwise any metadata csv file passed to the function, must include filename and subject_id columns, and an arbitrary disease column

Returns:

encoded dataset with encoded data in encoded_dataset.encoded_data.examples

immuneML.api.api_encoding.generate_random_metadata(path_to_dataset_directory: Path, result_path: Path)

Module contents