cellink.resources.get_1000genomes_plink_files

cellink.resources.get_1000genomes_plink_files(config_path='./cellink/resources/config/1000genomes.yaml', population='EUR', data_home=None, refresh=False)

Download and extract 1000 Genomes PLINK files (BED/BIM/FAM format).

This function downloads population-specific PLINK files from the 1000 Genomes project, extracts them to a local directory, and returns the path to the extracted files.

Parameters:

• config_path (str or pathlib.Path, default='./cellink/resources/config/1000genomes.yaml') – Path to YAML configuration file specifying URLs and file names for PLINK files.

• population (str, default='EUR') – Population code for PLINK files. Currently only ‘EUR’ is supported.

• data_home (str or pathlib.Path, optional) – Root directory where data will be stored. Defaults to user-specific cache directory.

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

Return type:

Path

Returns:

• pathlib.Path

  Path to the directory containing extracted PLINK files (.bed, .bim, .fam). Files are named as: {prefix}{chrom}.bed/bim/fam where chrom ranges from 1-22.

• prefixstr

  File name prefix used in the extracted data.

Raises:

ValueError – If population is not supported in the configuration.

Examples

>>> plink_dir = get_1000genomes_plink_files(population="EUR")
>>> # Access chromosome 1 files at:
>>> # plink_dir / "1000G.EUR.QC.1.bed"
>>> # plink_dir / "1000G.EUR.QC.1.bim"
>>> # plink_dir / "1000G.EUR.QC.1.fam"