cellink.tl.external.generate_gene_coord_file

cellink.tl.external.generate_gene_coord_file(out_path, *, genome_build='GRCh37', gene_identifier_mode='ensembl', remove_version_suffix=True, add_chr_prefix=True, overwrite=False)

Generate a gene coordinate file for S-LDSC analysis from Ensembl BioMart.

Fetches all genes from Ensembl and creates a tab-delimited file with columns: GENE, CHR, START, END

Parameters:

• out_path (str | Path) – Output file path (e.g., “gene_coords.txt”).

• genome_build (Literal['GRCh37', 'GRCh38'] (default: 'GRCh37')) – Genome build version: “GRCh37” or “GRCh38”.

• gene_identifier_mode (str (default: 'ensembl')) – Gene identifier: “name” (gene symbols) or “ensembl” (Ensembl IDs).

• remove_version_suffix (bool (default: True)) – Whether to remove version suffixes from gene IDs (e.g., ENSG00000123456.7 → ENSG00000123456).

• add_chr_prefix (bool (default: True)) – Whether to add “chr” prefix to chromosome names (e.g., “1” → “chr1”).

• overwrite (bool (default: False)) – Whether to overwrite existing output file.

Raises:

• FileExistsError – If out_path exists and overwrite=False.

• ImportError – If pybiomart is not installed.

Return type:

DataFrame

Examples

>>> # Fetch all genes with Ensembl IDs from GRCh37
>>> coord_df = generate_gene_coord_file("gene_coords.txt", gene_identifier_mode="ensembl", genome_build="GRCh37")
>>> # Fetch with gene symbols from GRCh38
>>> coord_df = generate_gene_coord_file(
...     "gene_coords_grch38.txt", gene_identifier_mode="name", genome_build="GRCh38"
... )