Metadata-Version: 2.1
Name: ppx
Version: 0.4.1
Summary: A Python interface to the ProteomeXchange Repository
Home-page: https://github.com/wfondrie/ppx
Author: William E Fondrie
Author-email: fondriew@gmail.com
License: MIT
Description: [![tests](https://github.com/wfondrie/ppx/workflows/tests/badge.svg?branch=master)](https://github.com/wfondrie/ppx/actions?query=workflow%3Atests)[![Documentation Status](https://readthedocs.org/projects/ppx/badge/?version=latest)](https://ppx.readthedocs.io/en/latest/?badge=latest)  
        
        
        # ppx: A Python interface to ProteomeXchange  
        
        ## Overview  
        ppx provides a simple means to access the
        [ProteomeXchange](http://www.proteomexchange.org/) repository from Python. Using
        ProteomeXchange identifiers, you can retrieve the metadata associated with a
        project and download project files from
        [PRIDE](https://www.ebi.ac.uk/pride/archive/),
        [MassIVE](https://massive.ucsd.edu/ProteoSAFe/static/massive.jsp), 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:
        ```Python
        >>> dat = PXDataset("PXD000001")
        ```
        
        We can then extract various data about the ProteomeXchange project from the PXDataset:
        ```Python
        >>> 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:
        ```Python
        # 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](http://bioconductor.org/packages/release/bioc/html/rpx.html) and
        [GitHub](https://github.com/lgatto/rpx).
        
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Description-Content-Type: text/markdown
