API reference¶
Find a class below. To find a query method by what it returns, use the method overview. For installation and runnable examples, start on the home page. The command-line interface has a separate reference.
| Interface | Purpose | Complete reference |
|---|---|---|
EnsemblRelease |
Select a species and numbered release | Select data |
EnsemblAnnotation |
Select an assembly and dated annotation | Select data |
Genome |
Shared annotation queries and custom data | Query a genome |
Gene, Transcript, Exon, Protein, Locus |
Annotated features and intervals | Features |
GeneNameAliases |
Explicit alias source | Aliases |
DownloadCache, Database, SequenceData |
Local data and indexing | Data and caches |
| Reference and species helpers | Assembly/species normalization and selection | Helpers |
Coordinates in the annotation API are one-based and inclusive. The optional
pyfaidx reader exposed by Genome.fasta
uses zero-based half-open slicing. Consult reference DNA
before mixing those interfaces. Installed annotation queries read local data;
setup methods explicitly download and index files.