The spectra-cluster-py project is a collection of tools and APIs that help analysing and working with MS/MS spectrum clustering results in the .clustering format.

For more information have a look at our documentation

• Python >= 3.4

The spectra-cluster-py package uses several external libraries. If you follow the installation instructions below, the will be installed but be build from source. This can take quite a while. Therefore, it is often better to install the binary versions of these libraries beforehand if available for your operating system:

• docopt
• pyinstaller
• pyteomics
• numpy
• lxml
• pandas
• maspy

The easiest way to install the spectra-cluster-py package is to use pip. pip is already installed if you downloaded python from python.org. In case it is not, follow these instructions to install it: https://pip.pypa.io/en/stable/installing/

Note: On some unix systems the pip command for python3 may be called pip3. In this case you need to use pip3 to install the spectra-cluster-py package.

pip install https://github.com/spectra-cluster/spectra-cluster-py/zipball/master

Download the .zip file using the button above or through this link. Extract the zip file and enter the directory. There, simply launch python3 ./setup.py install.

# Example for linux based systems with python3 installed
wget -O spectra_cluster_py.zip https://github.com/spectra-cluster/spectra-cluster-py/zipball/master
unzip spectra_cluster_py.zip
# enter the directory, the name will change based on the latest commit
cd spectra-cluster-spectra-cluster-py-ae3
python3 ./setup.py install

The .clustering format is currently used by the spectra-cluster algorithm (and API) and the output format of the derived tools:

• spectra-cluster-cli: Command line version of the spectra-cluster algorithm.
• spectra-cluster-gui: Graphical user interface for running the spectra-cluster-cli tool.
• spectra-cluster-hadoop: A Hadoop implementation of the spectra-cluster algorithm.

An up-to-date documentation of the .clustering format can be found at the Java API clustering-file-reader project page.

You can find the spectra-cluster-py's documentation at Read the Docs.

If you find a bug or encounter any problem with one of the tools or the API please send us your problem using the issue tracker.

If you have any other questions that doesn't fit the issue tracker don't hesitate to post a question at http://qa.proteomics-academy.org.