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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().

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:

export PYENSEMBL_CACHE_DIR=/custom/cache/dir

or

import os

os.environ['PYENSEMBL_CACHE_DIR'] = '/custom/cache/dir'
# ... PyEnsembl API usage

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
Release History

Release History

1.0.3

This version

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1.0.2

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1.0.1

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1.0.0

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0.9.7

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0.9.6

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0.9.5

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0.9.4

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0.9.3

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0.9.1

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0.9.0

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0.8.14

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0.8.13

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0.8.12

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0.8.11

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0.8.10

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0.8.9

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0.8.8

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0.8.7

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0.8.5

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0.8.4

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0.8.3

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0.8.2

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0.8.1

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0.7.0

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0.6.11

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0.6.10

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0.6.9

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0.6.8

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0.6.7

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0.6.5

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0.6.4

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0.6.3

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0.6.2

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0.6.1

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0.6.0

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0.5.13

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0.5.12

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0.5.11

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0.5.10

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0.5.9

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0.5.8

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0.5.7

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0.5.4

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0.5.3

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0.5.2

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0.5.1

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0.5.0

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0.4.0

History Node

TODO: Figure out how to actually get changelog content.

Changelog content for this version goes here.

Donec et mollis dolor. Praesent et diam eget libero egestas mattis sit amet vitae augue. Nam tincidunt congue enim, ut porta lorem lacinia consectetur. Donec ut libero sed arcu vehicula ultricies a non tortor. Lorem ipsum dolor sit amet, consectetur adipiscing elit.

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0.3.3

History Node

TODO: Figure out how to actually get changelog content.

Changelog content for this version goes here.

Donec et mollis dolor. Praesent et diam eget libero egestas mattis sit amet vitae augue. Nam tincidunt congue enim, ut porta lorem lacinia consectetur. Donec ut libero sed arcu vehicula ultricies a non tortor. Lorem ipsum dolor sit amet, consectetur adipiscing elit.

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0.3

History Node

TODO: Figure out how to actually get changelog content.

Changelog content for this version goes here.

Donec et mollis dolor. Praesent et diam eget libero egestas mattis sit amet vitae augue. Nam tincidunt congue enim, ut porta lorem lacinia consectetur. Donec ut libero sed arcu vehicula ultricies a non tortor. Lorem ipsum dolor sit amet, consectetur adipiscing elit.

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Download Files

Download Files

TODO: Brief introduction on what you do with files - including link to relevant help section.

File Name & Checksum SHA256 Checksum Help Version File Type Upload Date
pyensembl-1.0.3.tar.gz (58.6 kB) Copy SHA256 Checksum SHA256 Source Oct 11, 2016

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