The ppx Package

A Python interface to the ProteomeXchange Repository

https://travis-ci.org/wfondrie/ppx.svg?branch=master Documentation Status

The ppx package provides a simple means to access the ProteomeXchange [1] repository from Python. Using ProteomeXchange identifiers, the user can retrieve metadata associated with a project and download project files from the PRIDE Archive [2] .

ppx is based on the rpx R package by Laurent Gatto [3]. Our intent is that ppx would provide an efficient method to reuse proteomics data from ProteomeXchange, allowing easier access for those developing proteomics tools and analyses in Python.

Installation

ppx was developed and tested for Python 3.5+, and only requires packages that are distributed as part of the Python Standard Library. The release version of ppx can be installed with pip (or pip3):

pip install ppx

License

ppx is distributed under the MIT license.

API Reference

[1]Vizcaino J.A. et al. ProteomeXchange: globally co-ordinated proteomics data submission and dissemination, Nature Biotechnology 2014, 32, 223 – 226, doi:10.1038/nbt.2839.
[2]Vizcaíno JA, et al. 2016 update of the PRIDE database and related tools. Nucleic Acids Res. 2016, 44(D1): D447-D456. doi:10.1093/nar/gkv1145.
[3]Gatto L. rpx: R Interface to the ProteomeXchange Repository. 2018, R package version 1.16.0, https://github.com/lgatto/rpx.