cellink.resources.get_1000genomes_frq

cellink.resources.get_1000genomes_frq(config_path='./cellink/resources/config/1000genomes.yaml', population='EUR', data_home=None, return_path=False, refresh=False)

Download and extract 1000 Genomes allele frequency files.

Required for ldsc.py --overlap-annot --frqfile-chr. Downloaded from Zenodo record 10515792 (1000G_Phase3_frq.tgz).

Parameters:

• config_path (str or pathlib.Path) – Path to YAML configuration file.

• population (str, default='EUR') – Population code. Currently only 'EUR' is available.

• data_home (str or pathlib.Path, optional) – Root directory where data will be stored.

• return_path (bool, default=False) – If True, returns (DATA, prefix) instead of loading DataFrames. For frq files, return_path=True is the typical usage since these files are passed as a prefix to ldsc.py rather than loaded into memory.

• refresh (bool, default=False) – If True, re-downloads and re-extracts files even if they already exist.

Return type:

tuple[Path, str]

Returns:

tuple If return_path=True: (DATA, prefix) where DATA is a Path to the directory containing the extracted .frq files and prefix is the file name prefix (e.g. "1000G.EUR.QC.").

If return_path=False: (DATA, frq_df) where frq_df is a concatenated pd.DataFrame of all per-chromosome frq files.

Raises:

ValueError – If population is not listed in the configuration.

Examples

>>> frq_dir, frq_prefix = get_1000genomes_frq(population="EUR", return_path=True)
>>> frqfile_chr = str(frq_dir / frq_prefix)  # passed as --frqfile-chr