cellink.tl.run_favor

cellink.tl.run_favor(config_file='../configs/favor.yaml', database_dir=None, version='essential', G=None, output=None, return_annos=True)

Annotates variants using the FAVOR database from within Python

Requires access to FAVOR CSV databases either locally or via automatic download.

Parameters:

• G (anndata.AnnData) – AnnData object with a .var DataFrame containing variant information, including ‘chrom’, ‘pos’, ‘a0’, and ‘a1’ columns. Required for chromosome-wise annotation.

• return_annos (bool) – Whether to return the annotations as a Pandas DataFrame after writing them to disk. Defaults to False.

Returns:

None or pandas.DataFrame Returns None if return_annos is False. If True, returns a DataFrame of annotations loaded from the output file.