omicverse.io.read

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omicverse.io.read#

omicverse.io.read(path, backend='python', **kwargs)[source]#

Read common omics file formats into AnnData or pandas DataFrame.

Parameters:

  • path (str or pathlib.Path) – Input file path.

  • backend ({'python', 'rust'}, default='python') – Backend used for .h5ad reading. 'rust' loads out-of-memory via anndataoom / anndata-rs. When the file’s sparse X has unsorted minor indices the call is aborted with a clear ValueError (rather than an anndata-rs panic) pointing at ov.utils.convert_adata_for_rust() for recovery.

  • **kwargs – Additional keyword arguments forwarded to backend readers.

Returns:

Loaded AnnData object (for .h5ad) or DataFrame (for table files).

Return type:

anndata.AnnData or pandas.DataFrame

Raises:

  • ImportError – If backend='rust' is requested but anndataoom is not installed.

  • ValueError – If backend is invalid for .h5ad reading, the file suffix is unsupported, or the .h5ad has an unsorted sparse X.

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