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Python interface to ensembl reference genome metadata

Project description

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
=============

.. code:: 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>`__:

.. code:: sh

pip install pyensembl

This should also install any required packages, such as
`datacache <https://github.com/openvax/datacache>`__ and
`BioPython <http://biopython.org/>`__.

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:

.. code:: sh

export PYENSEMBL_CACHE_DIR=/custom/cache/dir

or

.. code:: python

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:

.. code:: python

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
-----

.. raw:: html

<dl>

.. raw:: html

<dt>

genes(contig=None, strand=None)

.. raw:: html

</dt>

.. raw:: html

<dd>

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

.. raw:: html

</dd>

.. raw:: html

<dt>

genes_at_locus(contig, position, end=None, strand=None)

.. raw:: html

</dt>

.. raw:: html

<dd>

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=‘-’.

.. raw:: html

</dd>

.. raw:: html

<dt>

gene_by_id(gene_id)

.. raw:: html

</dt>

.. raw:: html

<dd>

Return a Gene object for given Ensembl gene ID (e.g. “ENSG00000068793”).

.. raw:: html

</dd>

.. raw:: html

<dt>

gene_names(contig=None, strand=None)

.. raw:: html

</dt>

.. raw:: html

<dd>

Returns all gene names in the annotation database, optionally restricted
to a particular contig or strand.

.. raw:: html

</dd>

.. raw:: html

<dt>

genes_by_name(gene_name)

.. raw:: html

</dt>

.. raw:: html

<dd>

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.

.. raw:: html

</dd>

.. raw:: html

<dt>

gene_by_protein_id(protein_id)

.. raw:: html

</dt>

.. raw:: html

<dd>

Find Gene associated with the given Ensembl protein ID (e.g.
“ENSP00000350283”)

.. raw:: html

</dd>

.. raw:: html

<dt>

gene_names_at_locus(contig, position, end=None, strand=None)

.. raw:: html

</dt>

.. raw:: html

<dd>

Names of genes overlapping with the given locus, optionally restricted
by strand. (returns a list to account for overlapping genes)

.. raw:: html

</dd>

.. raw:: html

<dt>

gene_name_of_gene_id(gene_id)

.. raw:: html

</dt>

.. raw:: html

<dd>

Returns name of gene with given genen ID.

.. raw:: html

</dd>

.. raw:: html

<dt>

gene_name_of_transcript_id(transcript_id)

.. raw:: html

</dt>

.. raw:: html

<dd>

Returns name of gene associated with given transcript ID.

.. raw:: html

</dd>

.. raw:: html

<dt>

gene_name_of_transcript_name(transcript_name)

.. raw:: html

</dt>

.. raw:: html

<dd>

Returns name of gene associated with given transcript name.

.. raw:: html

</dd>

.. raw:: html

<dt>

gene_name_of_exon_id(exon_id)

.. raw:: html

</dt>

.. raw:: html

<dd>

Returns name of gene associated with given exon ID.

.. raw:: html

</dd>

.. raw:: html

<dt>

gene_ids(contig=None, strand=None)

.. raw:: html

</dt>

.. raw:: html

<dd>

Return all gene IDs in the annotation database, optionally restricted by
chromosome name or strand.

.. raw:: html

</dd>

.. raw:: html

<dt>

gene_ids_of_gene_name(gene_name)

.. raw:: html

</dt>

.. raw:: html

<dd>

Returns all Ensembl gene IDs with the given name.

.. raw:: html

</dd>

.. raw:: html

</dl>

Transcripts
-----------

.. raw:: html

<dl>

.. raw:: html

<dt>

transcripts(contig=None, strand=None)

.. raw:: html

</dt>

.. raw:: html

<dd>

Returns a list of Transcript objects for all transcript entries in the
Ensembl database, optionally restricted to a particular contig or
strand.

.. raw:: html

</dd>

.. raw:: html

<dt>

transcript_by_id(transcript_id)

.. raw:: html

</dt>

.. raw:: html

<dd>

Construct a Transcript object for given Ensembl transcript ID (e.g.
“ENST00000369985”)

.. raw:: html

</dd>

.. raw:: html

<dt>

transcripts_by_name(transcript_name)

.. raw:: html

</dt>

.. raw:: html

<dd>

Returns a list of Transcript objects for every transcript matching the
given name.

.. raw:: html

</dd>

.. raw:: html

<dt>

transcript_names(contig=None, strand=None)

.. raw:: html

</dt>

.. raw:: html

<dd>

Returns all transcript names in the annotation database.

.. raw:: html

</dd>

.. raw:: html

<dt>

transcript_ids(contig=None, strand=None)

.. raw:: html

</dt>

.. raw:: html

<dd>

Returns all transcript IDs in the annotation database.

.. raw:: html

</dd>

.. raw:: html

<dt>

transcript_ids_of_gene_id(gene_id)

.. raw:: html

</dt>

.. raw:: html

<dd>

Return IDs of all transcripts associated with given gene ID.

.. raw:: html

</dd>

.. raw:: html

<dt>

transcript_ids_of_gene_name(gene_name)

.. raw:: html

</dt>

.. raw:: html

<dd>

Return IDs of all transcripts associated with given gene name.

.. raw:: html

</dd>

.. raw:: html

<dt>

transcript_ids_of_transcript_name(transcript_name)

.. raw:: html

</dt>

.. raw:: html

<dd>

Find all Ensembl transcript IDs with the given name.

.. raw:: html

</dd>

.. raw:: html

<dt>

transcript_ids_of_exon_id(exon_id)

.. raw:: html

</dt>

.. raw:: html

<dd>

Return IDs of all transcripts associatd with given exon ID.

.. raw:: html

</dd>

.. raw:: html

</dl>

Exons
-----

.. raw:: html

<dl>

.. raw:: html

<dt>

exon_ids(contig=None, strand=None)

.. raw:: html

</dt>

.. raw:: html

<dd>

Returns a list of exons IDs in the annotation database, optionally
restricted by the given chromosome and strand.

.. raw:: html

</dd>

.. raw:: html

<dt>

exon_ids_of_gene_id(gene_id)

.. raw:: html

</dt>

.. raw:: html

<dd>

Returns a list of exon IDs associated with a given gene ID.

.. raw:: html

</dd>

.. raw:: html

<dt>

exon_ids_of_gene_name(gene_name)

.. raw:: html

</dt>

.. raw:: html

<dd>

Returns a list of exon IDs associated with a given gene name.

.. raw:: html

</dd>

.. raw:: html

<dt>

exon_ids_of_transcript_id(transcript_id)

.. raw:: html

</dt>

.. raw:: html

<dd>

Returns a list of exon IDs associated with a given transcript ID.

.. raw:: html

</dd>

.. raw:: html

<dt>

exon_ids_of_transcript_name(transcript_name)

.. raw:: html

</dt>

.. raw:: html

<dd>

Returns a list of exon IDs associated with a given transcript name.

.. raw:: html

</dd>

.. raw:: html

</dl>

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