Lun4m / PeptideBuilder

A simple Python library to generate model peptides

PeptideBuilder: A simple Python library to generate model peptides.

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

Installation

You can install PeptideBuilder with pip:

pip install PeptideBuilder

PeptideBuilder has one required dependency: 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
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.