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https://github.com/openvax/pyensembl
Python interface to access reference genome features (such as genes, transcripts, and exons) from Ensembl
https://github.com/openvax/pyensembl
Last synced: 3 months ago
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Python interface to access reference genome features (such as genes, transcripts, and exons) from Ensembl
- Host: GitHub
- URL: https://github.com/openvax/pyensembl
- Owner: openvax
- License: apache-2.0
- Created: 2014-04-14T15:23:02.000Z (over 10 years ago)
- Default Branch: main
- Last Pushed: 2024-06-04T23:13:40.000Z (5 months ago)
- Last Synced: 2024-07-25T11:46:39.012Z (4 months ago)
- Language: Python
- Homepage:
- Size: 976 KB
- Stars: 365
- Watchers: 22
- Forks: 66
- Open Issues: 67
-
Metadata Files:
- Readme: README.md
- Contributing: CONTRIBUTING.md
- License: LICENSE
Awesome Lists containing this project
- Awesome-Bioinformatics - pyensembl - Pythonic Access to the Ensembl database. [ [web](https://pyensembl.readthedocs.io/en/latest/pyensembl.html) ] (Next Generation Sequencing / Python Modules)
README
[](https://github.com/openvax/pyensembl/actions/workflows/tests.yml)
[](https://coveralls.io/github/openvax/pyensembl?branch=main)
# PyEnsembl
PyEnsembl is a Python interface to [Ensembl](http://www.ensembl.org) reference genome metadata such as exons and transcripts. PyEnsembl downloads [GTF](https://en.wikipedia.org/wiki/Gene_transfer_format) and [FASTA](https://en.wikipedia.org/wiki/FASTA_format) files from the [Ensembl FTP server](ftp://ftp.ensembl.org) and loads them into a local database. PyEnsembl can also work with custom reference data specified using user-supplied GTF and FASTA files.
# Example Usage
```python
from pyensembl import EnsemblRelease
# release 77 uses human reference genome GRCh38
data = EnsemblRelease(77)
# will return ['HLA-A']
gene_names = data.gene_names_at_locus(contig=6, position=29945884)
# get all exons associated with HLA-A
exon_ids = data.exon_ids_of_gene_name('HLA-A')
```
# Installation
You can install PyEnsembl using [pip](https://pip.pypa.io/en/latest/quickstart.html):
```sh
pip install pyensembl
```
This should also install any required packages such as [datacache](https://github.com/openvax/datacache).
Before using PyEnsembl, run the following command to download and install
Ensembl data:
```
pyensembl install --release --species
```
For example, `pyensembl install --release 75 76 --species human` will download and install all
human reference data from Ensembl releases 75 and 76.
Alternatively, you can create the `EnsemblRelease` object from inside a Python
process and call `ensembl_object.download()` followed by `ensembl_object.index()`.
## Cache Location
By default, PyEnsembl uses the platform-specific `Cache` folder
and caches the files into the `pyensembl` sub-directory.
You can override this default by setting the environment key `PYENSEMBL_CACHE_DIR`
as your preferred location for caching:
```sh
export PYENSEMBL_CACHE_DIR=/custom/cache/dir
```
or
```python
import os
os.environ['PYENSEMBL_CACHE_DIR'] = '/custom/cache/dir'
# ... PyEnsembl API usage
```
# Usage tips
## List installed genomes
To see the genomes for which PyEnsembl has already downloaded and indexed metadata you can run:
```sh
pyensembl list
```
Or equivalently do this in Python:
```python
from pyensembl.shell import collect_all_installed_ensembl_releases
collect_all_installed_ensembl_releases()
```
## Load genome in Python
Here's an example Python snippet that loads fly genome data from Ensembl release v100:
```python
from pyensembl import EnsemblRelease
data = EnsemblRelease(release=100, species='drosophila_melanogaster')
```
## Data structures
### Gene
```python
gene = genome.gene_by_id(gene_id='FBgn0011747')
```
### Transcript
```python
transcript = gene.transcripts[0]
```
### Protein information
```python
transcript.protein_id
transcript.protein_sequence
```
# Non-Ensembl Data
PyEnsembl also allows arbitrary genomes via the specification
of local file paths or remote URLs to both Ensembl and non-Ensembl GTF
and FASTA files. (Warning: GTF formats can vary, and handling of
non-Ensembl data is still very much in development.)
For example:
```python
from pyensembl import Genome
data = Genome(
reference_name='GRCh38',
annotation_name='my_genome_features',
# annotation_version=None,
gtf_path_or_url='/My/local/gtf/path_to_my_genome_features.gtf', # Path or URL of GTF file
# transcript_fasta_paths_or_urls=None, # List of paths or URLs of FASTA files containing transcript sequences
# protein_fasta_paths_or_urls=None, # List of paths or URLs of FASTA files containing protein sequences
# cache_directory_path=None, # Where to place downloaded and cached files for this genome
)
# parse GTF and construct database of genomic features
data.index()
gene_names = data.gene_names_at_locus(contig=6, position=29945884)
```
# API
The `EnsemblRelease` object has methods to let you access all possible
combinations of the annotation features _gene_name_, _gene_id_,
_transcript_name_, _transcript_id_, _exon_id_ as well as the location of
these genomic elements (contig, start position, end position, strand).
## Genes
- genes(contig=None, strand=None)
- Returns a list of Gene objects, optionally restricted to a particular contig
or strand. - genes_at_locus(contig, position, end=None, strand=None)
- Returns a list of Gene objects overlapping a particular position on a contig,
optionally extend into a range with the end parameter and restrict to
forward or backward strand by passing strand='+' or strand='-'. - gene_by_id(gene_id)
- Return a Gene object for given Ensembl gene ID (e.g. "ENSG00000068793").
- gene_names(contig=None, strand=None)
- Returns all gene names in the annotation database, optionally restricted
to a particular contig or strand. - genes_by_name(gene_name)
- Get all the unqiue genes with the given name (there might be multiple
due to copies in the genome), return a list containing a Gene object for each
distinct ID. - gene_by_protein_id(protein_id)
- Find Gene associated with the given Ensembl protein ID (e.g. "ENSP00000350283")
- gene_names_at_locus(contig, position, end=None, strand=None)
- Names of genes overlapping with the given locus, optionally restricted by strand.
(returns a list to account for overlapping genes) - gene_name_of_gene_id(gene_id)
- Returns name of gene with given genen ID.
- gene_name_of_transcript_id(transcript_id)
- Returns name of gene associated with given transcript ID.
- gene_name_of_transcript_name(transcript_name)
- Returns name of gene associated with given transcript name.
- gene_name_of_exon_id(exon_id)
- Returns name of gene associated with given exon ID.
- gene_ids(contig=None, strand=None)
- Return all gene IDs in the annotation database, optionally restricted by
chromosome name or strand. - gene_ids_of_gene_name(gene_name)
- Returns all Ensembl gene IDs with the given name.
## Transcripts
- transcripts(contig=None, strand=None)
- Returns a list of Transcript objects for all transcript entries in the
Ensembl database, optionally restricted to a particular contig or strand. - transcript_by_id(transcript_id)
- Construct a Transcript object for given Ensembl transcript ID (e.g. "ENST00000369985")
- transcripts_by_name(transcript_name)
- Returns a list of Transcript objects for every transcript matching the given name.
- transcript_names(contig=None, strand=None)
- Returns all transcript names in the annotation database.
- transcript_ids(contig=None, strand=None)
- Returns all transcript IDs in the annotation database.
- transcript_ids_of_gene_id(gene_id)
- Return IDs of all transcripts associated with given gene ID.
- transcript_ids_of_gene_name(gene_name)
- Return IDs of all transcripts associated with given gene name.
- transcript_ids_of_transcript_name(transcript_name)
- Find all Ensembl transcript IDs with the given name.
- transcript_ids_of_exon_id(exon_id)
- Return IDs of all transcripts associatd with given exon ID.
## Exons
- exon_ids(contig=None, strand=None)
- Returns a list of exons IDs in the annotation database, optionally restricted
by the given chromosome and strand. - exon_by_id(exon_id)
- Construct an Exon object for given Ensembl exon ID (e.g. "ENSE00001209410")
- exon_ids_of_gene_id(gene_id)
- Returns a list of exon IDs associated with a given gene ID.
- exon_ids_of_gene_name(gene_name)
- Returns a list of exon IDs associated with a given gene name.
- exon_ids_of_transcript_id(transcript_id)
- Returns a list of exon IDs associated with a given transcript ID.
- exon_ids_of_transcript_name(transcript_name)
- Returns a list of exon IDs associated with a given transcript name.