pyOpenMS are the Python bindings to the OpenMS library which are available for Windows, Linux and macOS. You can download them from PyPI or directly through pip or conda:

pip install pyopenms


conda install -c bioconda -c conda-forge pyopenms

Getting started

After installation, you should be able to import pyopenms as a package in your python script

import pyopenms

which should now give you access to all of pyopenms. You should now be able to interact with the OpenMS library and, for example, read and write mzML files:

import pyopenms
exp = pyopenms.MSExperiment()
pyopenms.MzMLFile().store("testfile.mzML", exp)

which will create an empty mzML file called testfile.mzML.

For further help, please also consult the extensive pyOpenMS Documentation.

Older versions

Download of older versions: Historic versions of pyOpenMS