Python interface to ensembl reference genome metadata
Project description
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 BioPython.
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().
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:
data = Genome reference_name='GRCh38', annotation_name='my_genome_features', gtf_path_or_url='/My/local/gtf/path_to_my_genome_features.gtf')) # 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 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 list of exons IDs in the annotation database, optionally restricted by the given chromosome and strand
- exon_ids_of_gene_id(gene_id)
returns list of exon IDs associated with a given gene ID
- exon_ids_of_gene_name(gene_name)
returns list of exon IDs associated with a given gene name
- exon_ids_of_transcript_id(transcript_id)
returns list of exon IDs associated with a given transcript ID
- exon_ids_of_transcript_name(transcript_name)
returns list of exon IDs associated with a given transcript name
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