pyensembl 0.5.4

Python interface to ensembl reference genome metadata

PyEnsembl

Python interface to Ensembl reference genome metadata (exons, transcripts, &c)

Example Usage

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:

pip install pyensembl

This should also install any required packages, such as datacache and pyfaidx.

The first time you use PyEnsembl, there will be a delay of several minutes while the library downloads and parses Ensembl data files.

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 list of Gene objects, optionally restricted to a particular contig or strand.

genes_at_locus(contig, position, end=None, strand=None) : returns 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 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 (returns a list to account for overlapping genes)

gene_name_of_gene_id(gene_id) : name of gene with given ID

gene_name_of_transcript_id(transcript_id) : name of gene associated with given transcript ID

gene_name_of_transcript_name(transcript_name) : name of gene associated with given transcript name

gene_name_of_exon_id(exon_id) : name of gene associated with given exon ID

gene_ids(contig=None, strand=None) : all gene IDs in the annotation database

gene_ids_of_gene_name(gene_name) : all Ensembl gene IDs with the given name

Transcripts

transcripts(contig=None, strand=None) : returns 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 Transcript object for given Ensembl transcript ID (e.g. “ENST00000369985”)

transcripts_by_name(transcript_name) : returns list of Transcript objects for every transcript matching the given name.

transcript_names(contig=None, strand=None) : 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 all transcript IDs in the annotation database

exon_ids_of_gene_id(gene_id)

exon_ids_of_gene_name(gene_name)

exon_ids_of_transcript_name(transcript_name)

exon_ids_of_transcript_id(transcript_id)