pypath.inputs.oma.oma_orthologs§
- pypath.inputs.oma.oma_orthologs(organism_a: str | int = 'human', organism_b: str | int = 'mouse', id_type: str | None = None, rel_type: set[Literal['1:1', '1:n', 'm:1', 'm:n']] | None = None, score: float | None = None, return_df: bool = False) list[tuple] | DataFrame[source]§
Retrieves pairwise relations between two genomes from the OMA (Orthologous Matrix) database (https://omabrowser.org/oma/home/).
- Parameters:
organism_a – Name or NCBI Taxonomy ID of the first organism.
organism_b – Name or NCBI Taxonomy ID of the second organism.
id_type – OMA by default uses UniProt entry IDs and sometimes other identifiers for genes. Set this parameter to control which ID type all the identifiers are to be mapped to.
rel_type – Restrict relations to certain types.
score – Lower threshold for similarity metric.
return_df – If True, returns a data frame instead of a list of tuples.
- Returns:
A list with tuples of pairwise orthologous relationships or a data frame with the same records.