terra.tokenize_adata

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terra.tokenize_adata#

terra.tokenize_adata(adata, model_folder_path, cache_directory_path, nproc=4, processing_mode='parallel', add_neigh_cell_ids=False, use_generator=True, keep_in_memory=False, include_special_tokens=False)#

Harmonize and tokenize an AnnData object based on the parameters in the model config and return the tokenized Hugging Face dataset and harmonized AnnData object.

Parameters:

  • adata (AnnData) – AnnData object to be tokenized.

  • model_folder_path (str) – Path to the folder containing the model config, token dictionary, and normalization factors.

  • cache_directory_path (str) – Path where the cache is stored during dataset creation.

  • n_proc – Number of processes used.

  • processing_mode (Literal['sequential', 'parallel'] (default: 'parallel')) – Mode of processing.

  • add_neigh_cell_ids (bool (default: False)) – Whether neighbor cell IDs should be stored in tokenized data (used for perturbations).

  • use_generator (bool (default: True)) – Whether to use generator for dataset creation.

  • keep_in_memory (bool (default: False)) – Whether to keep dataset in memory.

Return type:

Dataset

Returns:

dataset: The tokenized data stored in a Hugging Face dataset.

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