anndict.utils.uce_adata

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anndict.utils.uce_adata#

anndict.utils.uce_adata(adata_paths)[source]#

Runs the eval_single_anndata.py script for each specified AnnData path. This function is included largely for instructional purposes and will be restrictivley slow without a gpu.

Parameters:
adata_paths list[str]

A list of paths to the .h5ad files to be processed.

Return type:

None

Returns:

None

Notes

Writes the output to the ./uce_wd/ directory.

This function constructs the command to run the eval_single_anndata.py script with specified arguments and then executes the command using subprocess.run().

The function assumes that a uce-compatible conda environment is already activated and the working directory is correctly set to UCE (i.e. as in snap-stanford/UCE)

Examples

uce_adata(["../dat/liver.h5ad", "../dat/kidney.h5ad"])
> # Output is written to the ./uce_wd/ directory
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