immuneML.api package

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: Optional[str] = None)[source]

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: pathlib.Path, result_path: pathlib.Path)[source]

Module contents