jostheim/pymzml

pymzML - an interface between Python and mzML Mass spectrometry Files

INTRODUCTION

Python module to interface mzML data in Python based on cElementTree with additional tools for MS-informatics.

Copyright 2010-2015 by authors and contributors:

• T. Bald,
• J. Barth,
• A. Niehues,
• M. Specht,
• M. Hippler,
• H. Roest,
• M. Wolfson,
• C. Fufezan

Mass spectrometry has evolved to a very diverse field that relies heavily on high throughput bioinformatics tools. Lately the consortium of mass spectrometry has published the first version of the mzML standard into which all mass spectrometry data should be able to be converted. This finally offers a unified representation of all mass spectrometric data. In order to rapidly develop bioinformatic tools that can explore the tremendous amount of data one needs a portable, robust, yet quick and easy interface to mzML files. The Python scripting language is predestined for such a task. pymzML is an object oriented Python module that adds the mzML interface to the Python interpreter. Although other interfaces exist in C/C++, none has the combination of a) the features of a scripting language, i.e. rapid development, easily readable source code applicable to all platforms and multiprocessing done with ease and b) the required speed of xml parsing for large data files. This makes pymzML and Python the optimal tools to rapidly develop bioinformatic tools for high throughput mass spectrometry. pymzML is hosted on github and freely available under LGPL, requires python2.6.5 or higher and is fully compatible with python 3.

CITATION

Please cite us when using pymzml for your publications.

Bald, T., Barth, J., Niehues, A., Specht, M., Hippler, M., & Fufezan, C. (2012). pymzML - Python module for high throughput bioinformatics on mass spectrometry data. Bioinformatics, 1-2. doi: 10.1093/bioinformatics/bts066

INSTALLATION

PyPi

pip install pymzml

Source installation

python setup.py install

(you might need admin privileges to write in the python site-package folder, for example use sudo python setup.py install or write into a user folder by using this command python setup.py install --user).

If you want to also have support for ms-numpress compression, you might need to install additional packages (currently the development version of pyOpenMS).

If you want to install pymzML for Python 3, just exchange python with python3 in the above command.

PARTICIPATE

If you like to participate, simply checkout the source code from our git at http://github.com/pymzml, include in your changes and submit them to us.

DOCUMENTATION

For more in depth documentation of the modules and examples, please refer to the documentation folder or http://github.com/pymzml

TEST

Please make sure to run tests for Python 2 and Python 3

nosetests -a '!numpress'  test/
nosetests3 -a '!numpress'  test/

which will run all tests (except the numpress tests).