cellink.tl.external.get_magma_gene_loc

cellink.tl.external.get_magma_gene_loc(genome_build='GRCh38', data_home=None, overwrite=False)

Download and cache a MAGMA-compatible gene location file from Ensembl BioMart.

The file is in the headless four-column format expected by MAGMA’s --gene-loc argument: ENSG_ID  CHR  START  END (tab-separated, no header, numeric chromosome names). It is cached to <data_home>/magma/gene_loc_<genome_build>.txt and only re-fetched when overwrite=True.

Parameters:

• genome_build ({"GRCh38", "GRCh37"}, default "GRCh38") – Genome assembly to query from Ensembl BioMart.

• data_home (str or Path, optional) – Directory for caching. Defaults to ~/cellink_data (or the CELLINK_DATA environment variable).

• overwrite (bool, default False) – Re-fetch from BioMart even if the cached file already exists.

Return type:

str

Returns:

str Absolute path to the cached gene location file.

Examples

>>> from cellink.tl.external import get_magma_gene_loc
>>> gene_loc = get_magma_gene_loc()  # GRCh38, cached
>>> run_magma_annotate(snp_loc=..., gene_loc=gene_loc, out_prefix=...)

See also

generate_gene_coord_file

Headed GENE/CHR/START/END format for S-LDSC.

run_magma_annotate

MAGMA Step I — uses the gene location file.