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 3.9 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 2.27.1
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| pyensembl-2.27.1.tar.gz | 194.5 kB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| pyensembl-2.27.1-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 299.9 kB
Release files / pyensembl-2.27.1.tar.gz
| Download URL | pyensembl-2.27.1.tar.gz |
|---|---|
| Size | 194.5 kB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
80b03097b8163f4f26a0ca7d581984858a2b1dd14babe88a9d6c6291c810623e
|
|
BLAKE2b-256 checksum How to use checksums |
58a73e575633779200c936cbb777e89d94ae34ad1af4c0a16b614192ca41a617
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/7.0.0 CPython/3.12.6
|
Release files / pyensembl-2.27.1-py3-none-any.whl
| Download URL | pyensembl-2.27.1-py3-none-any.whl |
|---|---|
| Size | 105.4 kB |
| Tags | Python 3 |
|
SHA-256 checksum How to use checksums |
fe6da2516bc13274f3f2efe2af46fbd739a4b65cc17efa7674ed355a5d47ee59
|
|
BLAKE2b-256 checksum How to use checksums |
5f5adad14ccdd8baca79ade31199872e4fb7d640913e139dfff18bcd08f109db
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/7.0.0 CPython/3.12.6
|
