PyEnsembl
PyEnsembl queries Ensembl genes, transcripts, exons and sequences from local indexes. It supports numbered releases, dated new-platform annotations and custom matched GTF/FASTA files.
Installation
Use Python 3.11 or later. Install the package and one explicit annotation:
python -m pip install pyensembl
pyensembl install --release 93 --species human
This selects human GRCh38 and downloads and indexes its annotation, transcript and peptide files. Setup takes several minutes and disk space; whole-genome DNA is optional. See installation and first lookup.
Example Usage
After installing the data above:
from pyensembl import EnsemblRelease
with EnsemblRelease(93, species="human") as data:
gene = data.gene_by_id("ENSG00000141510")
print(gene.name, gene.contig, gene.start, gene.end, gene.strand)
TP53 17 7661779 7687550 -
Coordinates are one-based and inclusive; TP53 is on the minus strand. Pin the release you analyze: coordinates, IDs and sequences can change between releases, and a gene name can match several loci. The documentation continues with protein and transcript sequences.
Documentation
The documentation home page includes installation and getting-started examples. Use these guides for other tasks:
| Task | Guide |
|---|---|
| Find genes by name, position or biotype | Genes and transcripts |
| Protein, coding and transcript sequences; exons | Get protein and transcript sequences |
| Search additional gene names | Alias lookup |
| Read genomic DNA | Reference DNA |
| Choose an assembly, species and coverage | Assembly selection |
| Install from Python, check or delete data | Install and manage data |
| Use your own annotations | Custom genomes |
| Use dated Ensembl downloads | Dated annotations |
| Find a class or query method | API reference |
For contributions, see development setup,
documentation style and
releasing. Every PR includes a version bump, lint and
tests; maintainers merge through a PR and publish with ./deploy.sh from clean main.
5 maintainers
Metadata
5 maintainers
Release files for pyensembl 2.31.2
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | Provenance | |
|---|---|---|---|---|
| pyensembl-2.31.2.tar.gz | 479.9 kB | Without provenance | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| pyensembl-2.31.2-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 631.9 kB
Release files / pyensembl-2.31.2.tar.gz
| Download URL | pyensembl-2.31.2.tar.gz |
|---|---|
| Size | 479.9 kB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
734929c68a6ba4b26f73c0a6a4b9dfb1db1a544184fa6d7204338e125eb776c5
|
|
BLAKE2b-256 checksum How to use checksums |
8ecefe47d6ca32e491c57886e8f82d03a5448e29c7308d51dcbbc45e7cc77f3e
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/7.0.0 CPython/3.12.6
|
Release files / pyensembl-2.31.2-py3-none-any.whl
| Download URL | pyensembl-2.31.2-py3-none-any.whl |
|---|---|
| Size | 151.9 kB |
| Tags | Python 3 |
|
SHA-256 checksum How to use checksums |
b78e2be73b9b6349f58361a6b61693a839059a86721d3a674828f70df1ad5462
|
|
BLAKE2b-256 checksum How to use checksums |
05c2b56f66a8f503441e4c3169bc3baa7ce33e91bcd952ec54cc001073791b62
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/7.0.0 CPython/3.12.6
|
Security for pyensembl 2.31.2
Provenance
Provenance describes where a file came from. On PyPI, provenance is shared via attestations, which provide a verifiable record of the build or publishing details. View details, limitations and caveats.
No provenance found
None of the files in this release were uploaded with provenance metadata.
A note on package security
PyPI is a repository for distributing packages, not a service for auditing them. While third-party security researchers and our staff do their best to detect and remove malicious packages, PyPI cannot guarantee the quality, security or suitability of any given package.
To learn more about protecting yourself from malicious actors, visit our package security documentation.
