ppx 0.5.0

A Python interface to the ProteomeXchange Repository

ppx: A Python interface to ProteomeXchange

Overview

ppx provides a simple means to access the ProteomeXchange repository from Python. Using ProteomeXchange identifiers, you can retrieve the metadata associated with a project and download project files from PRIDE, MassIVE, or other partner repositories.

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

Installation

ppx is pip installable. ppx requires Python 3.6+ 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.references
# ['Gatto L, Christoforou A. Using R and Bioconductor for proteomics data
# analysis. Biochim Biophys Acta. 2014 1844(1 pt a):42-51']

>>> dat.url
# 'ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2012/03/PXD000001'

>>> dat.taxonomies
# ['Erwinia carotovora']

>>> dat.list_files()
# ['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']

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

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

If you are an R user...

ppx was inpsired the rpx R package by Laurent Gatto. Check it out on Bioconductor and GitHub.