MSAnalysis

msanalysis is a lightweight python package to read and process mass spectra, specifically those in the mzXML format.

• General
  • Build Info
  • Python Versions Tested
• Dependencies
• Installation
  • Fresh install
  • Patches
• Testing
• Copyright
• Acknowledgements

General

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Build Info

OS	Build Status
Linux
OSX

Python Versions Tested

OS	3.5	3.6	3.7	3.8
Linux	✔️	✔️	✔️	✔️
OSX	✔️	✔️	✔️	❌

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Dependencies

• pytest-cov
• matplotlib
• seaborn
• numpy
• scipy
• pandas
• pyopenms
• black (only required for contributors)

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Installation

Set up is meant to be easy! First we suggest installing all of prerequisites in a clean Conda env (run this inside the main directory of the package):

conda env create -f devtools/conda-envs/msanalysis_env.yaml

Then install using pip and we're done!

python -m pip install -e .

If you aren't doing this in a conda env and don't have root user privileges use:

python -m pip install -e . --user

Fresh install

git clone https://github.com/jamesETsmith/msanalysis.git
cd msanalysis
conda env create -f devtools/conda-envs/msanalysis_env.yaml
python -m pip install -e .
cd patches
python add_elements.py

Patches

Currently there is one patch while we wait to hear back on an issue from PyOpenMS. If you want to work with species like Indium, run the python script to patch up msanalysis.

cd patches
python add_elements.py

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Testing

To check that everything is working, run the following from the main project directory:

pytest -v msanalysis --cov=msanalysis

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Copyright

Copyright (c) 2019, James E. T. Smith/ CU Boulder

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Acknowledgements

Project based on the Computational Molecular Science Python Cookiecutter version 1.1.