========== apybiomart

.. image:: https://img.shields.io/pypi/v/apybiomart.svg :target: https://pypi.python.org/pypi/apybiomart

.. image:: https://www.repostatus.org/badges/latest/wip.svg :alt: Project Status: WIP – Initial development is in progress, but there has not yet been a stable, usable release suitable for the public. :target: https://www.repostatus.org/#wip

.. image:: https://travis-ci.com/robertopreste/apybiomart.svg?branch=master :target: https://travis-ci.com/robertopreste/apybiomart :alt: Travis CI build status

.. image:: https://circleci.com/gh/robertopreste/apybiomart.svg?style=svg :target: https://circleci.com/gh/robertopreste/apybiomart :alt: CircleCI build status

.. image:: https://codecov.io/gh/robertopreste/apybiomart/branch/master/graph/badge.svg :target: https://codecov.io/gh/robertopreste/apybiomart :alt: Codecov status

.. image:: https://readthedocs.org/projects/apybiomart/badge/?version=latest :target: https://apybiomart.readthedocs.io/en/latest/?badge=latest :alt: Documentation Status

.. image:: https://pyup.io/repos/github/robertopreste/apybiomart/shield.svg :target: https://pyup.io/repos/github/robertopreste/apybiomart/ :alt: Updates

.. image:: https://pyup.io/repos/github/robertopreste/apybiomart/python-3-shield.svg :target: https://pyup.io/repos/github/robertopreste/apybiomart/ :alt: Python 3

.. image:: https://pepy.tech/badge/apybiomart :target: https://pepy.tech/project/apybiomart :alt: Downloads

Async pythonic interface to BioMart.

• Free software: MIT license
• Documentation: https://apybiomart.readthedocs.io
• GitHub repo: https://github.com/robertopreste/apybiomart

Features

apybiomart is a Python module which provides a simple asynchronous interface to Ensembl BioMart_. Users can exploit the async interface to schedule multiple queries using all the commodities offered by Python's asyncio library.

Depending on specific needs, apybiomart offers different entry points:

• an asynchronous aquery() function, to schedule multiple queries in the same event loop;

• a synchronous query() function, which can be used for exploratory queries, executed in real time;

• a set of synchronous find_*() functions, which can be used to retrieve the list of available marts (find_marts()), datasets for a specific mart (find_datasets()), attributes (find_attributes()) and filters (find_filters()) for a specific dataset.

  • a set of related CLI commands also exists to allow exploration of these data from the command line; these are, respectively, apybiomart marts, apybiomart datasets, apybiomart attributes and apybiomart filters. Run apybiomart --help for further details.

Please refer to the Usage_ section of the documentation for further information.

Background

apybiomart was originally born as a fork of the great pybiomart_ package.

I was working on a project that employed a series of async calls to several online resources, but I couldn't manage to perform asynchronous calls to BioMart using that package, so I decided to modify it to better suit my needs. However, it gradually evolved into a very different thing: the original implementation was rewritten and the structure of the package changed a bit, in a way that I found most useful for my purpose.

This said, all the credits go to jrderuiter_, which created the original pybiomart_ package.

Installation

apybiomart only supports Python 3, and can be installed using pip::

pip install apybiomart

Please refer to the Installation_ section of the documentation for further information.

Credits

This package was created with Cookiecutter_ and the cc-pypackage_ project template.

.. _BioMart: https://www.ensembl.org/biomart/martview .. _Usage: https://apybiomart.readthedocs.io/en/latest/usage.html .. _pybiomart: https://github.com/jrderuiter/pybiomart .. _jrderuiter: https://github.com/jrderuiter .. _Installation: https://apybiomart.readthedocs.io/en/latest/installation.html .. _Cookiecutter: https://github.com/audreyr/cookiecutter .. _cc-pypackage: https://github.com/robertopreste/cc-pypackage