Cnv.get_gene_names#
missionbio.mosaic.cnv.Cnv.get_gene_names
- Cnv.get_gene_names(max_workers: int = 10, species: str = 'homo_sapiens') ndarray #
Fetch gene names from Ensembl for all the amplicons.
The data is stored in the “gene_name” column attribute.
Note
max_workers and species are no longer used. The annotations are stored locally and not pulled using the ensembl API. They are only available for hg19 and hg38. All other genomes will mark the gene names as “Unknown” The relevant genome version is pulled from the “genome_version” metadata of the assay.
- Parameters:
- max_workersint (No longer used)
The maximum number of parallel process to run.
- speciesstr, optional (No longer used)
The species such as homo_sapiens, mus_musculus_129s1svimj. When the value is homo_sapiens, the assembly version is estimated from the genome_version metadata. ‘hg19’ and ‘hg38’ can also be passed to force a specific genome assembly. A list of all the species supported by Ensembl can be found at https://rest.ensembl.org/info/species - use the
name
value of the species of interest
- Returns:
- np.ndarray: The gene_name column attribute values
< Class Cnv