omicverse.utils.convert_adata_for_rust

omicverse.utils.convert_adata_for_rust#

omicverse.utils.convert_adata_for_rust(adata, output_file=None, verbose=True, close_file=True)[source]#

Rewrite an AnnData object as an .h5ad file that ov.read(..., backend='rust') can open.

Sorts CSR/CSC minor indices, strips NaN/Inf, coerces problematic obs/var dtypes, and preserves obsm, varm, uns, obsp, varp and layers.

Parameters:

  • adata (anndata.AnnData) – Input AnnData object to convert.

  • output_file (str or None, default=None) – Output .h5ad file path. If None, a temporary file is created.

  • verbose (bool, default=True) – Whether to print conversion progress and diagnostics.

  • close_file (bool, default=True) – Retained for backward compatibility; ignored (there is no persistent handle).

Returns:

Path to the converted Rust-compatible .h5ad file.

Return type:

str

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