kozo2 / pywikipathways

Python Client Package for WikiPathways

pywikipathways

Python Client Package for the WikiPathways API

Use this package to interface with the WikiPathways API. It provides programmatic access to WikiPathways content.

This is a Python port of rWikiPathways R (Bioconductor) package. The names of functions and their arguments are unified between the two. (However, there is a difference between a camel case and a snake case.)

This project is inspired by py4cytoscape for RCy3. Just as py4cytoscape ports RCy3 and function specifications to Python, pywikipathways also ports rWikiPathways functions to Python.

Try pywikipathways with Google Colab

Installation

pip install pywikipathways

Instructions for installing the development version

1. Install Python and pip
2. Install Git
3. Install the development version of pywikipathways with the following command.

pip install git+https://github.com/kozo2/pywikipathways.git

Documentation

https://pywikipathways.readthedocs.io

pywikipathways's Issues

Update functions to work with new JSON API

See the corresponding rWikiPathways branch for examples of all the changes:
https://github.com/wikipathways/rwikipathways/tree/json_api