Package: apybiomart
apybiomartAsync pythonic interface to BioMart.Free software: MIT licenseDocumentation:https://apybiomart.readthedocs.ioGitHub repo:https://github.com/robertopreste/apybiomartFeaturesapybiomart is a Python module which provides a simple asynchronous interface to EnsemblBioMart. 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 asynchronousaquery()function, to schedule multiple queries in the same event loop;a synchronousquery()function, which can be used for exploratory queries, executed in real time;a set of synchronousfind_*()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 attributesandapybiomart filters. Runapybiomart--helpfor further
details.Please refer to theUsagesection of the documentation for further information.Backgroundapybiomart was originally born as a fork of the greatpybiomartpackage.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 tojrderuiter, which created the originalpybiomartpackage.Installationapybiomart only supports Python 3, and can be installed using pip:pip install apybiomartPlease refer to theInstallationsection of the documentation for further information.CreditsThis package was created withCookiecutterand thecc-pypackageproject template.History0.1.0 (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;Syncqueryand asyncaqueryfunctions to query Biomart;Synclist_*functions to retrieve availablemarts,datasets,filtersandattributes.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)Changelist_*functions names tofind_*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 forquery()andaquery()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 deprecatedpd.npoccurrencies;Update test files.