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 2.28.3
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-2.28.3.tar.gz | 215.3 kB | Without provenance | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| pyensembl-2.28.3-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 326.0 kB
Release files / pyensembl-2.28.3.tar.gz
| Download URL | pyensembl-2.28.3.tar.gz |
|---|---|
| Size | 215.3 kB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
0e72549a0bb82518024571e1473a8b0bb53df0489fae46d6e1031c8b8de1b1fe
|
|
BLAKE2b-256 checksum How to use checksums |
b2bc6e576c82e13d24148c4468f7a14ed464ef048fc3d38a4b14252fa79c6d8f
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/7.0.0 CPython/3.12.6
|
Release files / pyensembl-2.28.3-py3-none-any.whl
| Download URL | pyensembl-2.28.3-py3-none-any.whl |
|---|---|
| Size | 110.6 kB |
| Tags | Python 3 |
|
SHA-256 checksum How to use checksums |
1d0dbc4837e4334fc74fd2977eef1ff3b45a1202ca02dde9b2a3929ee7d06cb0
|
|
BLAKE2b-256 checksum How to use checksums |
961ee7439276a53493ce983bd2e12945cbc486f44a076d69f1e05829fc20d7d1
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/7.0.0 CPython/3.12.6
|
Security for pyensembl 2.28.3
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.
