gretapy.ds.read_db

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gretapy.ds.read_db#

gretapy.ds.read_db(organism, db_name, verbose=False)#

Read a database file for a given organism.

Downloads the database if not already cached locally, then reads it based on its file format (bed, tsv, csv, or h5ad).

Parameters:

  • organism (str) – The organism identifier (e.g., ‘hg38’ for human).

  • db_name (str) – The name of the database to read (e.g., ‘Promoters’, ‘CollecTRI’).

  • verbose (bool (default: False)) – Whether to print progress messages. Default is False.

Return type:

DataFrame

Returns:

pd.DataFrame | pr.PyRanges | ad.AnnData The loaded database. The return type depends on the file format: - bed files return PyRanges objects - tsv/csv files return pandas DataFrames - h5ad files return AnnData objects

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