genomepy.annotation.mygene.query_mygene

genomepy.annotation.mygene.query_mygene(query: Iterable[str], tax_id: Union[str, int], field: str = 'genomic_pos') → DataFrame

Use mygene.info to map gene identifiers to another type.

Parameters

• query (iterable) – a list or list-like of gene identifiers

• tax_id (str or int) – Target genome taxonomy id

• field (str, optional) – Target identifier to map the query genes to. Valid fields are: ensembl.gene, entrezgene, symbol, name, refseq, entrezgene. Note that refseq will return the protein refseq_id by default, use refseq.translation.rna to return the RNA refseq_id. Currently, mapping to Ensembl transcript ids is not supported.

Returns

mapped gene annotation.

Return type

pandas.DataFrame