Cnv.get_gene_names

missionbio.mosaic.cnv.Cnv.get_gene_names

Cnv.get_gene_names(max_workers: int = 10, species: str = 'homo_sapiens') → None

Fetch gene names from Ensembl for all the amplicons.

The data is stored in the “gene_name” column attribute.

Note

A direct connection to https://grch37.rest.ensembl.org is needed to download gene names. While proxy support has been added to our wish list, the current version does not support it. Use a network that does not require a proxy. Alternatively, ask your network admin to add firewall rules that allow direct connections to https://grch37.rest.ensembl.org.

Parameters:

max_workersint

The maximum number of parallel process to run.

speciesstr, optional

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

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< Class Cnv