acidgenomes.download_gencode_genome

acidgenomes.download_gencode_genome(organism: str, *, genome_build: str | None = None, release: str | None = None, output_dir: Path | None = None, cache: bool = False) → dict[str, Path]

Download GENCODE genome FASTA, transcriptome FASTA, GTF, and GFF3.

Parameters:

  • organism (str) – "Homo sapiens" or "Mus musculus".

  • genome_build (str or None) – Genome build (e.g. "GRCh38"). Auto-detected if None.

  • release (str or None) – GENCODE release (e.g. "44" for human, "M33" for mouse). Auto-detected if None.

  • output_dir (Path or None) – Parent directory for the download. Defaults to the current working directory at call time if None.

  • cache (bool) – If True, skip downloading files that already exist.

Returns:

Mapping of file type to local path.

Return type:

dict[str, Path]