acidgenomes.make_ensembl_genes

acidgenomes.make_ensembl_genes(df: DataFrame, organism: str | None = None, genome_build: str | None = None, release: int | None = None, ignore_version: bool = True) → EnsemblGenes

Create an EnsemblGenes object from a DataFrame.

Parameters:

  • df (pd.DataFrame) – Gene-level annotations, as returned by GFF parsing.

  • organism (str or None) – Latin organism name. Auto-detected from gene_id if None.

  • 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 df’s gene identifiers have version suffixes stripped.

Returns:

Validated Ensembl gene annotations, enriched with metadata from the Ensembl FTP server when available.

Return type:

EnsemblGenes