https://github.com/robaina/brendapyrser

A Python parser for the BRENDA database
https://github.com/robaina/brendapyrser

biochemistry bioinformatics brenda computational-biology enzyme enzyme-kinetics metabolism python

Last synced: about 2 months ago
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A Python parser for the BRENDA database

• Host: GitHub
• URL: https://github.com/robaina/brendapyrser
• Owner: Robaina
• License: apache-2.0
• Created: 2020-09-28T19:51:59.000Z (about 4 years ago)
• Default Branch: master
• Last Pushed: 2023-09-15T17:50:18.000Z (over 1 year ago)
• Last Synced: 2024-10-23T00:28:57.481Z (2 months ago)
• Topics: biochemistry, bioinformatics, brenda, computational-biology, enzyme, enzyme-kinetics, metabolism, python
• Language: Python
• Homepage:
• Size: 702 KB
• Stars: 24
• Watchers: 2
• Forks: 5
• Open Issues: 2
• Metadata Files:
  • Readme: README.md
  • Contributing: CONTRIBUTING.md
  • License: LICENSE
  • Code of conduct: .github/CODE_OF_CONDUCT.md
  • Citation: CITATION.cff

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README

        
![logo](assets/logo.png)

## a Python package to parse and manipulate the BRENDA database

[![tests](https://github.com/Robaina/BRENDApyrser/actions/workflows/tests.yml/badge.svg)](https://github.com/Robaina/BRENDApyrser/actions/workflows/tests.yml)

[![codecov](https://codecov.io/gh/Robaina/BRENDApyrser/graph/badge.svg?token=214SPFXRTG)](https://codecov.io/gh/Robaina/BRENDApyrser)

![PyPI](https://img.shields.io/pypi/v/brendapyrser)

![GitHub release (latest by date)](https://img.shields.io/github/v/release/Robaina/Brendapyrser)

[![GitHub license](https://img.shields.io/github/license/Robaina/BRENDApyrser)](https://github.com/Robaina/BRENDApyrser/blob/master/LICENSE)

![Contributor Covenant](https://img.shields.io/badge/Contributor%20Covenant-v2.0%20adopted-ff69b4)

[![DOI](https://zenodo.org/badge/299416438.svg)](https://zenodo.org/badge/latestdoi/299416438)

## What is Brendapyrser?

This project provides python classes and functions to parse the text file containing the entire BRENDA enzyme database (https://www.brenda-enzymes.org)

This is an ongoing project!

## Installation

1. ```pip install brendapyrser```

or

2. Git clone project to local directory.

   In terminal navigate to directory and enter: ```python setup.py install```

## Usage

Due to BRENDA's license, BRENDA's database cannot be downloaded directly by the parser, instead, the user is asked to download the database as a text file after accepting usage conditions [here](https://www.brenda-enzymes.org/download.php).

You can find a jupyter notebook with usage examples [here](docs/examples.ipynb).

## Contribute

Contributions are always more than welcome! Feel free to fork, make changes and pull requests. If you don't know where to start, you can always browse open issues. Thanks!

## Citation

If you use this software, please cite it as below:

Robaina-Estévez, S. (2022). BRENDApyrser: a Python package to parse and manipulate the BRENDA database (Version 0.0.3)[Computer software]. https://doi.org/10.5281/zenodo.7026555