czbenchmarks.datasets.single_cell
=================================

.. py:module:: czbenchmarks.datasets.single_cell


Attributes
----------

.. autoapisummary::

   czbenchmarks.datasets.single_cell.logger


Classes
-------

.. autoapisummary::

   czbenchmarks.datasets.single_cell.SingleCellDataset


Module Contents
---------------

.. py:data:: logger

.. py:class:: SingleCellDataset(dataset_type_name: str, path: pathlib.Path, organism: czbenchmarks.datasets.types.Organism, task_inputs_dir: Optional[pathlib.Path] = None)

   Bases: :py:obj:`czbenchmarks.datasets.dataset.Dataset`


   Abstract base class for single cell datasets containing gene expression data.

   Handles loading and validation of AnnData objects with the following requirements:
   - Must have gene names in `adata.var['ensembl_id']` or `adata.var_names`.
   - Gene names must start with the organism prefix (e.g., "ENSG" for human).
   - Must contain raw counts in `adata.X` (non-negative integers).
   - Should be stored in H5AD format.

   .. attribute:: adata

      Loaded AnnData object containing gene expression data.

      :type: ad.AnnData

   Initialize a SingleCellDataset instance.

   :param dataset_type_name: Name of the dataset type (used for directory naming).
   :type dataset_type_name: str
   :param path: Path to the dataset file.
   :type path: Path
   :param organism: Enum value indicating the organism.
   :type organism: Organism
   :param task_inputs_dir: Directory for storing task-specific inputs.
   :type task_inputs_dir: Optional[Path]


   .. py:attribute:: adata
      :type:  anndata.AnnData


   .. py:method:: load_data(backed: Literal['r', 'r+'] | bool | None = None) -> None

      Load the dataset from the path.

      This method reads the dataset file in H5AD format and loads it into the
      `adata` attribute as an AnnData object.

      :param backed: Whether to load the dataset
                     into memory or use backed mode.
                     Memory: False or None. Default is None.
                     Backed: True, 'r' for read-only, 'r+' for read-write
      :type backed: Literal['r', 'r+'] | bool | None

      Populates:
          adata (ad.AnnData): Loaded AnnData object containing gene expression data.