PyEnsembl is a Python interface to Ensembl reference genome metadata such as exons and transcripts. PyEnsembl downloads GTF and FASTA files from the Ensembl FTP server and loads them into a local database. PyEnsembl can also work with custom reference data specified using user-supplied GTF and FASTA files.
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')PyEnsembl requires Python 3.9 or later. You can install PyEnsembl using pip:
pip install pyensemblThis should also install any required packages such as datacache.
Before using PyEnsembl, run the following command to download and install Ensembl data:
pyensembl install --release <list of Ensembl release numbers> --species <species-name>
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().
For development, install PyEnsembl in editable mode with development dependencies:
git clone https://github.com/openvax/pyensembl.git
cd pyensembl
pip install -e .[dev]This installs the package in development mode along with tools for testing, linting, and building:
pytestfor running testsruffandflake8for code lintingpytest-covfor coverage reportingbuildfor package building
Run tests with:
pytestBy 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:
export PYENSEMBL_CACHE_DIR=/custom/cache/diror
import os
os.environ['PYENSEMBL_CACHE_DIR'] = '/custom/cache/dir'
# ... PyEnsembl API usageTo see the genomes for which PyEnsembl has already downloaded and indexed metadata you can run:
pyensembl listOr equivalently do this in Python:
from pyensembl.shell import collect_all_installed_ensembl_releases
collect_all_installed_ensembl_releases()Here's an example Python snippet that loads fly genome data from Ensembl release v100:
from pyensembl import EnsemblRelease
data = EnsemblRelease(release=100, species='drosophila_melanogaster')gene = genome.gene_by_id(gene_id='FBgn0011747')transcript = gene.transcripts[0]transcript.protein_id
transcript.protein_sequencePyEnsembl 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:
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)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(contig=None, strand=None, biotype=None)
- Returns a list of Gene objects, optionally restricted to a particular contig,
strand, or
gene_biotype. - 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 unique 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 gene 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, biotype=None)
- Return all gene IDs in the annotation database, optionally restricted by
chromosome name, strand, or
gene_biotype. - gene_ids_of_gene_name(gene_name)
- Returns all Ensembl gene IDs with the given name.
- nearest_gene(contig, position, end=None, strand=None)
- Returns
(distance, Gene)for the gene whose locus is nearest to the position (or position..end interval) on the given contig — even when no gene overlaps. Returns(inf, None)when no candidates exist. - merged_gene_intervals(contig, strand=None)
- Returns the union of all gene loci on the contig as a sorted list of
non-overlapping
(start, end)tuples. Adjacent intervals (end+1 == next start) are merged into one.
- transcripts(contig=None, strand=None, biotype=None)
- Returns a list of Transcript objects for all transcript entries in the
Ensembl database, optionally restricted to a particular contig, strand, or
transcript_biotype. - 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, biotype=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 associated with given exon ID.
- nearest_transcript(contig, position, end=None, strand=None)
- Returns
(distance, Transcript)to the closest transcript on the contig. Returns(inf, None)when no candidates exist.
- exon_ids(contig=None, strand=None)
- Returns a list of exon 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.