1.1. General information¶
Module to parse mzML data in Python based on cElementTree
Copyright 2010-2021 by:
M. Kösters,J. Leufken,T. Bald,A. Niehues,S. Schulze,K. Sugimoto,R.P. Zahedi,M. Hippler,S.A. Leidel,C. Fufezan,
1.1.1. Contact information¶
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 Python3.7+. The module is freely available on pymzml.github.com or pypi, published under MIT license and only requires numpy and regex, however there are several optional dependencies for extended functionality like interactive plotting and deconvolution.
- 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 3.7 or higher.
Consider to use a Python virtual environment for easy installation and use. Further, usage of python3.7+ 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
user@localhost:~$ pip install pymzml # install standard version user@localhost:~$ pip install "pymzml[plot]" # with plotting support user@localhost:~$ pip install "pymzml[pynumpress]" # with pynumpress support user@localhost:~$ pip install "pymzml[deconvolution]" # with deconvolution support using ms_deisotope user@localhost:~$ pip install "pymzml[full]" # full featured
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:
Please read the contribution guidelines before contributing here
1.8. Code of Conduct¶
Since pymzML is an open source project maintained by the community, we established a code of conduct in order to facilitate an inclusive environment for all users, contributors and project memebers. Before contributing to pymzML, please read the code of conduct here
The latest Documentation was generated on: Sep 15, 2023