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A Python interface to the ProteomeXchange Repository

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ppx: A Python interface to the ProteomeXchange Repository

Overview

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

ppx is largely based on the rpx R package by Laurent Gatto (Bioconductor and GitHub).

For full documentation and examples, visit: https://ppx.readthedocs.io

Installation

ppx is pip installable. The ppx package is available for Python 3.5+ and only depends on packages in the Python Standard Library.

pip3 install ppx

Examples

First create a PXDataset object using a valid ProteomeXchange identifier:

dat = PXDataset("PXD000001")

We can then extract various data about the ProteomeXchange project from the PXDataset:

dat.pxref()
# ['Gatto L, Christoforou A. Using R and Bioconductor for proteomics data
# analysis. Biochim Biophys Acta. 2014 1844(1 pt a):42-51']

dat.pxurl()
# 'ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2012/03/PXD000001'

dat.pxtax()
# ['Erwinia carotovora']

dat.pxfiles()
# ['F063721.dat', 'F063721.dat-mztab.txt',
# 'PRIDE_Exp_Complete_Ac_22134.xml.gz', 'PRIDE_Exp_mzData_Ac_22134.xml.gz',
# 'PXD000001_mztab.txt', 'README.txt',
# 'TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01-20141210.mzML',
# 'TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01-20141210.mzXML',
# 'TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.mzXML',
# 'TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.raw',
# 'erwinia_carotovora.fasta', 'generated']

Lastly, we can download files that we're interested in:

# Download "README.txt" to the "test" directory
dat.pxget(files="README.txt", dest_dir="test")

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