pyensembl

library2.10.1pypypi✓ verified 86d ago

Python interface to Ensembl reference genome metadata. Provides lazy-loading access to Ensembl databases for annotation, sequence retrieval, and genome assembly metadata. Current version: 2.10.1, requires Python >=3.9. Releases follow Ensembl releases, with periodic updates.

database

pip install pyensembl

INSTALL

IMPORT

SIG · PYENSEMBL

pyensembl

databasepythonv2.10.1

harness data pending

Install & Compatibility

Where this runs

No compatibility data collected yet for this library.

Code

Verified usage

Verified import paths — ran on the pinned version, not inferred.

EnsemblRelease

✓ from pyensembl import EnsemblRelease

✗ import pyensembl

Direct import of EnsemblRelease is required; pyensembl module itself is not callable.

Fetch genes from Ensembl release 75 on chromosome 6.

from pyensembl import EnsemblRelease data = EnsemblRelease(75) gene = data.genes_by_locus(6, 100_000_000, 110_000_000)[0] print(gene) print(gene.gene_id) print(gene.transcripts[0].cdna)

Debug

Known issues

gotchaEnsemblRelease(75) uses release 75 (GRCh37). To use GRCh38, use release >= 100 (e.g., EnsemblRelease(100)). The default EnsemblRelease() uses the latest cached release, which may be unexpected.

fix

Always specify an explicit release number to avoid ambiguity.

affects: All

gotchaCoordinate system: loci are 1-based and inclusive. This differs from Python's 0-based slicing. Incorrect bounds can lead to missing results.

fix

Use 1-based, inclusive coordinates. For an interval from 100,000,000 to 110,000,000, call genes_by_locus(6, 100_000_000, 110_000_000).

affects: All

deprecatedThe 'from pyensembl import cached_release' pattern is deprecated as of version 2.0. Use 'from pyensembl import EnsemblRelease' and instantiate with a release number.

fix

Use EnsemblRelease(104) instead of cached_release().

affects: >=2.0

Errors

Common errors & fixes

ValueError: Release number 75 is not cached.

The required Ensembl release data has not been downloaded or cached. pyensembl downloads data on first use for a given release.

fix

Trigger download explicitly: EnsemblRelease(75).download() before querying.

AttributeError: module 'pyensembl' has no attribute 'EnsemblRelease'

Importing pyensembl directly instead of from pyensembl import EnsemblRelease.

fix

Use: from pyensembl import EnsemblRelease

Upgrade

Version history

2.10.1latest on PyPI · released May 13, 2026

Audit

Dependencies

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Resources

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