https://github.com/jamesetsmith/msanalysis
Python Tools for Mass Spec. Analysis
https://github.com/jamesetsmith/msanalysis
mass-spectrometry matplotlib mzxml python scipy
Last synced: 20 days ago
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Python Tools for Mass Spec. Analysis
- Host: GitHub
- URL: https://github.com/jamesetsmith/msanalysis
- Owner: jamesETsmith
- License: mit
- Created: 2019-10-21T16:30:56.000Z (over 5 years ago)
- Default Branch: master
- Last Pushed: 2021-09-23T13:58:57.000Z (over 3 years ago)
- Last Synced: 2025-04-13T06:08:37.743Z (20 days ago)
- Topics: mass-spectrometry, matplotlib, mzxml, python, scipy
- Language: Python
- Size: 5.29 MB
- Stars: 3
- Watchers: 2
- Forks: 2
- Open Issues: 1
-
Metadata Files:
- Readme: README.md
- Contributing: .github/CONTRIBUTING.md
- License: LICENSE
- Code of conduct: CODE_OF_CONDUCT.md
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README
# MSAnalysis
`msanalysis` is a lightweight python package to read and process mass spectra, specifically those in the mzXML format.
- [General](#general)
- [Build Info](#build-info)
- [Python Versions Tested](#python-versions-tested)
- [Dependencies](#dependencies)
- [Installation](#installation)
- [Fresh install](#fresh-install)
- [Patches](#patches)
- [Testing](#testing)
- [Copyright](#copyright)
- [Acknowledgements](#acknowledgements)
## General
---
### Build Info
| OS | Build Status |
| :---: | :-------------------------------------------------------------------------------------------------------------------------------: |
| Linux | [](https://travis-ci.com/jamesETsmith/MSAnalysis) |
| OSX | [](https://travis-ci.com/jamesETsmith/MSAnalysis) |
### Python Versions Tested
| OS | 3.5 | 3.6 | 3.7 | 3.8 |
| :---: | :----------------: | :----------------: | :----------------: | :----------------: |
| Linux | :heavy_check_mark: | :heavy_check_mark: | :heavy_check_mark: | :heavy_check_mark: |
| OSX | :heavy_check_mark: | :heavy_check_mark: | :heavy_check_mark: | :x: |
---
## Dependencies
- [pytest-cov](https://docs.pytest.org/en/latest/)
- [matplotlib](https://matplotlib.org/)
- [seaborn](https://seaborn.pydata.org/)
- [numpy](https://numpy.org/)
- [scipy](https://www.scipy.org/)
- [pandas](https://pandas.pydata.org/)
- [pyopenms](https://pyopenms.readthedocs.io/en/latest/)
- [black](https://black.readthedocs.io/en/stable/) (only required for contributors)
---
## Installation
Set up is meant to be easy! First we suggest installing all of prerequisites in a clean [Conda](https://docs.conda.io/projects/conda/en/latest/user-guide/install/) env (run this inside the main directory of the package):
```bash
conda env create -f devtools/conda-envs/msanalysis_env.yaml
```
Then install using pip and we're done!
```bash
python -m pip install -e .
```
If you aren't doing this in a conda env and don't have root user privileges use:
```bash
python -m pip install -e . --user
```
### Fresh install
```bash
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`.
```bash
cd patches
python add_elements.py
```
---
## Testing
To check that everything is working, run the following from the main project directory:
```bash
pytest -v msanalysis --cov=msanalysis
```
---
## Copyright
Copyright (c) 2019, James E. T. Smith/ CU Boulder
---
## Acknowledgements
Project based on the
[Computational Molecular Science Python Cookiecutter](https://github.com/molssi/cookiecutter-cms) version 1.1.