Module to parse mzML data in Python based on cElementTree

Copyright 2010-2018 by:

M. Kösters,

J. Leufken,

T. Bald,

A. Niehues,

S. Schulze,

K. Sugimoto,

R.P. Zahedi,

M. Hippler,

S.A. Leidel,

C. Fufezan,

Please refer to:

Dr. Christian Fufezan

Group Leader Experimental Bioinformatics

Cellzome GmbH

R&D Platform Technology & Science

GSK

Germany

eMail: [email protected]

https:// <in transition >

pymzML is an extension to Python that offers

• 1. easy access to mass spectrometry (MS) data that allows the rapid development of tools
• 2. a very fast parser for mzML data, the standard mass spectrometry data format
• 3. a set of functions to compare and/or handle spectra
• 4. random access in compressed files
• 5. interactive data visualization

pymzML requires Python3.4+. The module is freely available on pymzml.github.com or pypi, published under GPL and requires no additional modules to be installed, but can optionally use numpy.

Get the latest version via github

https://github.com/pymzml/pymzML

The complete Documentation can be found as pdf

https://pymzml.github.com/dist/pymzml.pdf

M Kösters, J Leufken, S Schulze, K Sugimoto, J Klein, R P Zahedi, M Hippler, S A Leidel, C Fufezan; pymzML v2.0: introducing a highly compressed and seekable gzip format, Bioinformatics, doi: https://doi.org/10.1093/bioinformatics/bty046

pymzML requires Python 3.4 or higher.

Download pymzML using GitHub or the zip file:

• GitHub version: Start by cloning the GitHub repository:

  user@localhost:~$ git clone https://github.com/pymzML/pymzml.git
  user@localhost:~$ cd pymzml
  user@localhost:~$ pip install -r requirements.txt
  user@localhost:~$ python setup.py install
  

If you have troubles installing the dependencies, install numpy first separately, since pynumpress requires numpy to be installed.

If you use Windows 7 please use the 'SDK7.1 command prompt' for installation of pymzML to assure correct compiling of the C extensions.

To test the package and correct installation:

nosetests tests/*.py