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:
- pymzML is an extension to Python that offers
- easy access to mass spectrometry (MS) data that allows the rapid development of tools
- a very fast parser for mzML data, the standard mass spectrometry data format
- a set of functions to compare and/or handle spectra
- random access in compressed files
- 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
- The complete Documentation can be found as 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.
Consider to use a Python virtual environment for easy installation and use. Further, usage of python3.4+ is recommended.
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: