https://github.com/clauswilke/peptidebuilder

A simple Python library to generate model peptides
https://github.com/clauswilke/peptidebuilder

Last synced: 9 days ago
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A simple Python library to generate model peptides

• Host: GitHub
• URL: https://github.com/clauswilke/peptidebuilder
• Owner: clauswilke
• License: mit
• Created: 2013-04-21T03:59:06.000Z (over 11 years ago)
• Default Branch: master
• Last Pushed: 2020-11-29T05:58:09.000Z (about 4 years ago)
• Last Synced: 2024-12-21T02:52:04.683Z (15 days ago)
• Language: Python
• Homepage:
• Size: 1.18 MB
• Stars: 80
• Watchers: 8
• Forks: 30
• Open Issues: 7
• Metadata Files:
  • Readme: README.md
  • License: LICENSE.txt

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README

        
# PeptideBuilder: A simple Python library to generate model peptides.

*Matthew Z. Tien, Dariya K. Sydykova, Austin G. Meyer, and Claus O. Wilke*

[![PyPI version](https://badge.fury.io/py/PeptideBuilder.svg)](https://badge.fury.io/py/PeptideBuilder)

![PyPI - Downloads](https://img.shields.io/pypi/dm/PeptideBuilder)

![PyPI - License](https://img.shields.io/pypi/l/PeptideBuilder)

[![Build Status](https://travis-ci.org/clauswilke/PeptideBuilder.svg?branch=master)](https://travis-ci.org/clauswilke/PeptideBuilder)

[![Coverage Status](https://img.shields.io/codecov/c/github/clauswilke/PeptideBuilder/master.svg)](https://codecov.io/github/clauswilke/PeptideBuilder?branch=master)

## Installation

You can install PeptideBuilder with pip:

```

pip install PeptideBuilder

```

PeptideBuilder has one required dependency: [Biopython](https://pypi.org/project/biopython/)

## Examples

For example usage, we encourage you to checkout the scripts in the `examples` folder and in the `tests` folder. The `examples` folder contains two scripts showing typical usage. The script `simpleExample.py` is a brief example script demonstrating basic use of the PeptideBuilder library. The script `evaluation.py` reproduces the results presented in Table 1 of Tien et al. (2013).

The file `test_PeptideBuilder.py` in `tests` contains extensive tests for the various functions provided by this library and may also be useful if you're looking for example usage.

## Misc

The software is provided to you under the MIT license (see file `LICENSE.txt`).

The most up-to-date version of this software is available at

https://github.com/clauswilke/PeptideBuilder.

To test whether your installation works properly, run `pytest` in the top-level project folder.

## Contributing

Pull requests are welcome on GitHub. However, to be accepted, contributions must:

1. Be styled with [`black`](https://black.readthedocs.io/en/stable/)

2. Be linted with `pylint`

3. Be type-checked with `mypy`

4. Pass the `pytest` unit tests

Thus, before contributing code make sure the following commands exit without errors when run from the root directory of the Peptide Builder project:

- `pytest`

- `black .`

- `mypy PeptideBuilder/`

- `pylint --rcfile=setup.cfg PeptideBuilder/`

**Reference:**

M. Z. Tien, D. K. Sydykova, A. G. Meyer, C. O. Wilke (2013). PeptideBuilder:

A simple Python library to generate model peptides. PeerJ 1:e80.