apybiomart

========== apybiomart

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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

======= History

0.1.0 (2019-03-26)

• First development release.

0.1.1 (2019-03-27)

• Requests are converted to async calls;
• Code style is clean and Python 3 compatible.

0.1.2 (2019-03-27)

• Add basic tests.

0.2.0 (2019-03-31)

• New version with different organisation of classes and functions;
• Sync query and async aquery functions to query Biomart;
• Sync list_* functions to retrieve available marts, datasets, filters and attributes.

0.2.1 (2019-04-01)

• Add tests.

0.2.2 (2019-04-01)

• Basic functions working and tested;
• Fix documentation;
• Update requirements.

0.2.3 (2019-04-02)

• Update requirements;
• Fix type hints for query functions;
• Reorganise query classes into a single class;
• Update documentation.

0.2.4 (2019-04-04)

• Fix type hints;
• Fix docstrings in classes;
• Add docstrings to main entry points.

0.2.5 (2019-04-09)

• Fix test files with new BioMart versions;
• Add script to create test files automatically.

0.2.6 (2019-04-29)

• Update test files;
• Fix and update documentation.

0.3.0 (2019-05-05)

• Change list_* functions names to find_* for better compliance;
• Update documentation.

0.3.1 (2019-05-11)

• Fix requirements handling;
• Add function to check internet connection.

0.3.2 (2019-05-29)

• Correct minor typos;
• Update documentation and testfiles.

0.3.3 (2019-07-29)

• Fix #37 - issue with the requests module not installed.

0.3.4 (2019-08-23)

• Better handling of filters arguments for query() and aquery() functions;
• Convert docstrings to Google style;
• Fix documentation.

0.3.5 (2019-08-25)

• Relax requirement versions.

0.4.0 (2020-01-26)

• Add CLI commands for finding marts, datasets, attributes and filters;
• Change output dataframe column names.

0.5.0 (2020-03-22)

• Add CLI and Python module options to save outputs to CSV file.

0.5.1 (2020-04-04)

• Add option to specify the output CSV filename.

0.5.2 (2020-06-06)

• Update tests and test files;
• Clean code;
• Add CI module.

0.5.3 (2020-11-30)

• Remove deprecated pd.np occurrencies;
• Update test files.