cellink.io.read_dd

cellink.io.read_dd(path, fmt=None)

Read a DonorData object from disk in either HDF5 or Zarr format.

This function automatically detects the file format from the file extension unless explicitly specified, and reconstructs a DonorData object containing donor-level genotype data (G), cell-level expression data (C), and associated metadata.

Parameters:

• path (str) – Path to the DonorData file (.h5, .dd.h5, .zarr, or .dd.zarr).

• fmt ({'h5', 'zarr'}, optional) – File format to use. If None (default), inferred from the file extension.

Return type:

DonorData

Returns:

DonorData A DonorData object with: - G: Genotype data as AnnData or MuData. - C: Cell-level expression data as AnnData or MuData. - donor_id: Donor identifier string. - var_dims_to_sync: List of variable dimensions synchronized across G and C. - uns: Unstructured metadata dictionary.

Raises:

ValueError – If the file extension cannot be mapped to a known format or if fmt is not one of {‘h5’, ‘zarr’}.

Examples

>>> dd = read_dd("donor_data.dd.h5")
>>> dd = read_dd("donor_data.dd.zarr")
>>> dd = read_dd("custom_data.h5", fmt="h5")