Alias sources¶
See alias lookup for snapshot selection, ambiguity,
case sensitivity and species restrictions. The optional aliases= argument
is documented with Genome queries.
GeneNameAliases ¶
GeneNameAliases(aliases, *, species=None, source=None)
Read-only name-to-ID mapping with optional species/source metadata.
Ordinary mappings also work with Genome.genes_by_name(aliases=...).
Values may name several genes: aliases are not necessarily unique.
download_hgnc
classmethod
¶
download_hgnc(*, cache_directory_path=None, source_url=HGNC_COMPLETE_SET_URL, overwrite=False)
Download and load human HGNC aliases, reusing a cached snapshot.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
cache_directory_path
|
str or Path
|
Storage base directory. Defaults to aliases/homo_sapiens/hgnc under PyEnsembl's configured cache root. Each source URL has a separate subdirectory. |
None
|
source_url
|
str
|
Complete-set TSV or gzip TSV URL. Defaults to HGNC's current complete set; an archived snapshot or mirror can be selected. |
HGNC_COMPLETE_SET_URL
|
overwrite
|
bool
|
Download again even when this source is already cached. |
False
|
Returns:
| Type | Description |
|---|---|
GeneNameAliases
|
Human alias mapping whose source is the cached file path. |
Notes
Existing cached files are read without network access. Refresh is explicit; HGNC nomenclature is independent of the Ensembl release. Use from_hgnc(path) to load an already selected local snapshot.
from_hgnc
classmethod
¶
from_hgnc(path)
Load an HGNC complete-set TSV snapshot (plain or gzip).
Include symbols, aliases and previous symbols of approved human records with an Ensembl gene ID. Do not download or modify the file. HGNC nomenclature may be newer than the selected Ensembl annotation.