Metadata-Version: 2.0
Name: ensembl-rest
Version: 0.1.2
Summary: An interface to the Ensembl REST APIs, biological data at your fingertips.
Home-page: https://github.com/Ad115/EnsemblRest
Author: Ad115
Author-email: a.garcia230395@gmail.com
License: UNKNOWN
Project-URL: Say Thanks!, https://saythanks.io/to/Ad115
Project-URL: Documentation, https://ad115.github.io/EnsemblRest/
Project-URL: Author, https://agargar.wordpress.com/
Keywords: ensembl rest api client genomes
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Information Technology
Classifier: Intended Audience :: Science/Research
Classifier: Intended Audience :: Education
Classifier: Intended Audience :: Science/Research
Classifier: Intended Audience :: Developers
Classifier: Topic :: Scientific/Engineering :: Artificial Life
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3 :: Only
Provides-Extra: dev
Requires-Dist: importlib-resources
Requires-Dist: requests
Provides-Extra: dev
Requires-Dist: jupyter; extra == 'dev'
Requires-Dist: scrapy; extra == 'dev'

EnsemblRest
===========

.. image:: https://img.shields.io/badge/Say%20Thanks-!-1EAEDB.svg
    :target: https://saythanks.io/to/Ad115

A Python interface to the Ensembl REST APIs. A whole world of biological data 
at your fingertips.

The `Ensembl database <https://www.ensembl.org/index.html>`__ contains
reference biological data on almost any organism. Now it is easy to
access this data programatically through their REST API.

The specific documentation on the Ensembl REST API endpoints is on `their
website <https://rest.ensembl.org/>`__.

This library also includes some utilities built on top of the APIs designed to
ease working with them, including an 
`AssemblyMapper <https://ad115.github.io/EnsemblRest/#ensembl_rest.AssemblyMapper>`__
class that helps in the conversion between different genome assemblies.


This project uses code from `RESTEasy <https://github.com/rapidstack/RESTEasy>`__,
which made my life much easier. Thanks!



Installation
------------

You can install from `PyPI <https://pypi.org/project/ensembl-rest/>`_::

    $ pip install ensembl_rest


Examples
--------

The library exports two main classes: ``ensembl_rest.EnsemblClient`` and
``ensembl_rest.EnsemblGenomesClient`` that point respectively to the `main
REST API <http://rest.ensembl.org/>`__ and to the `Ensembl Genomes REST
API <http://rest.ensemblgenomes.org/>`__.

.. code-block:: python

    >>> import ensembl_rest

    >>> client = ensembl_rest.EnsemblClient()

If you want to use a method from the REST API, say:
``GET lookup/symbol/:species/:symbol`` 
(http://rest.ensembl.org/documentation/info/symbol\_lookup)
then the corresponding method on the class is called after the last
string in the link to the documentation page, in this case, ``symbol_lookup``.

.. code-block:: python

    >>> help(client.symbol_lookup)


::

    Help on method symbol_lookup in module ensembl_rest.core.baseclient:

    symbol_lookup(*args, **kwargs) method of ensembl_rest.core.baseclient.EnsemblClient instance
        ``GET lookup/symbol/:species/:symbol``

        Find the species and database for a symbol in a linked external database
        - More info: https://rest.ensembl.org/documentation/info/symbol_lookup



We can see from the resource string
``GET lookup/symbol/:species/:symbol`` that this method contains 2
parameters called species and symbol, so we can call the method in the
following way:

.. code-block:: python

    >>> client.symbol_lookup(species='homo sapiens',
                             symbol='TP53')

    # Or like this...
    >>> client.symbol_lookup('homo sapiens', 'TP53')


::

    {'source': 'ensembl_havana',
     'object_type': 'Gene',
     'logic_name': 'ensembl_havana_gene',
     'version': 16,
     'species': 'homo sapiens',
     'description': 'tumor protein p53 [Source:HGNC Symbol;Acc:HGNC:11998]',
     'display_name': 'TP53',
     'assembly_name': 'GRCh38',
     'biotype': 'protein_coding',
     'end': 7687550,
     'seq_region_name': '17',
     'db_type': 'core',
     'strand': -1,
     'id': 'ENSG00000141510',
     'start': 7661779}



Another common usage is to fetch sequences of known genes:

.. code-block:: python

    >>> client.sequence_id('ENSG00000157764')


::

    {'desc': 'chromosome:GRCh38:7:140719327:140924928:-1',
     'query': 'ENSG00000157764',
     'version': 13,
     'id': 'ENSG00000157764',
     'seq': 'TTCCCCCAATCCCCTCAGGCTCGGCTGCGCCCGGGGC...ACTGCTATAATAAAGATTGACTGCATGGAGAAGTCTTCA',
     'molecule': 'dna'}



Or to map betweeen assemblies...

.. code-block:: python

    >>> client.assembly_map(species='human',
                            asm_one='GRCh37',
                            region='X:1000000..1000100:1',
                            asm_two='GRCh38')


    # Or...
    >>> region_str = ensembl_rest.region_str(chom='X',
                                             start=1000000,
                                             end=1000100)

    >>> client.assembly_map(species='human',
                            asm_one='GRCh37',
                            region=region_str,
                            asm_two='GRCh38')

::

    {'mappings': [{'original': {'seq_region_name': 'X',
        'strand': 1,
        'coord_system': 'chromosome',
        'end': 1000100,
        'start': 1000000,
        'assembly': 'GRCh37'},
       'mapped': {'seq_region_name': 'X',
        'strand': 1,
        'coord_system': 'chromosome',
        'end': 1039365,
        'start': 1039265,
        'assembly': 'GRCh38'}}]}


The above problem (mapping from one assembly to another) is so frequent that 
the library provides a specialized class ``AssemblyMapper`` to efficiently
mapping large amounts of regions between assemblies. This class avoids the 
time-consuming task of making a web request every time a mapping is needed by 
fetching the mapping of the whole assembly right from the instantiation. This 
is a time-consuming operation by itself, but it pays off when one has to 
transform repeatedly betweeen assemblies.::


        >>> mapper = ensembl_rest.AssemblyMapper(from_assembly='GRCh37'
        ...                                      to_assembly='GRCh38')

        >>> mapper.map(chrom='1', pos=1000000)
        1064620



Meta
----

**Author**: `Ad115 <https://agargar.wordpress.com/>`_ -
`Github <https://github.com/Ad115/>`_ – a.garcia230395@gmail.com

Distributed under the MIT license. See
`LICENSE <https://github.com/Ad115/PyEnsembl/blob/master/LICENSE>`_
for more information.

Contributing
------------

1. Check for open issues or open a fresh issue to start a discussion
   around a feature idea or a bug.
2. Fork `the repository <https://github.com/Ad115/EnsemblRest/>`_
   on GitHub to start making your changes to a feature branch, derived
   from the **master** branch.
3. Write a test which shows that the bug was fixed or that the feature
   works as expected.
4. Send a pull request and bug the maintainer until it gets merged and
   published.


