acidgenomes.make_granges_from_ensembl

acidgenomes.make_granges_from_ensembl(organism: str, *, level: Literal['genes', 'transcripts', 'exons'] = 'genes', genome_build: str | None = None, release: int | None = None, ignore_version: bool = False, extra_mcols: bool = False) → Any

Parse the Ensembl GTF into a BiocPy GenomicRanges object.

This is the Python equivalent of R’s makeGRangesFromEnsembl(). Downloads the Ensembl GTF for the organism and parses it using the full GFF parsing engine.

Parameters:

  • organism (str) – Latin organism name (e.g. 'Homo sapiens', 'Mus musculus').

  • level (str) – Feature level: "genes", "transcripts", or "exons".

  • genome_build (str or None) – Ensembl genome build. Auto-detected if None.

  • release (int or None) – Ensembl release version. Auto-detected if None.

  • ignore_version (bool) – Whether to strip version suffixes from identifiers.

  • extra_mcols (bool) – If True, add broad_class annotations.

Returns:

BiocPy GenomicRanges object.

Return type:

GenomicRanges