omicverse.utils.convert2gene_id¶

omicverse.utils.convert2gene_id(input_names, species=None, ensembl_release=None, force_rebuild=False, multi='first')[source]¶

Convert official gene symbols to Ensembl gene IDs using pyensembl.

Parameters:

input_names (List[str]) – List of official gene symbols (e.g. ['TP53', 'GAPDH', 'BRCA1']).
species (str or None, optional) – Target species. Supported values: 'human', 'mouse', 'rat', 'zebrafish', 'fly', 'chicken', 'dog', 'pig', 'cow', 'macaque'. Defaults to 'human' when None.
ensembl_release (int or None, optional) – Ensembl release number. Defaults to 77 when None.
force_rebuild (bool, optional) – Force re-download and re-index the local database. Default is False.
multi ({'first', 'all', 'join'}, optional) –
Strategy when a symbol maps to multiple Ensembl IDs (e.g. due to gene duplication):
- 'first' — return only the first ID (default).
- 'all' — return a Python list of all IDs.
- 'join' — return all IDs concatenated with '|'.

Returns:

DataFrame indexed by 'query' (original symbol) with column:

'gene_id' — Ensembl gene ID, or the original symbol when no match is found.

Return type:

pandas.DataFrame

Examples

>>> df = ov.utils.convert2gene_id(['TP53', 'GAPDH'])
>>> df = ov.utils.convert2gene_id(
...     ['Trp53', 'Gapdh'],
...     species='mouse',
...     ensembl_release=102,
... )
>>> df = ov.utils.convert2gene_id(['TP53'], multi='join')