``scoring-matrices`` |Stars| ============================ .. |Stars| image:: https://img.shields.io/github/stars/althonos/scoring-matrices.svg?style=social&maxAge=3600&label=Star :target: https://github.com/althonos/scoring-matrices/stargazers *Dependency free, Cython-compatible scoring matrices to use with biological sequences.* |Actions| |Coverage| |PyPI| |Bioconda| |AUR| |Wheel| |Versions| |Implementations| |License| |Source| |Issues| |Docs| |Changelog| |Downloads| .. |Actions| image:: https://img.shields.io/github/actions/workflow/status/althonos/scoring-matrices/test.yml?branch=main&logo=github&style=flat-square&maxAge=300 :target: https://github.com/althonos/scoring-matrices/actions .. |Coverage| image:: https://img.shields.io/codecov/c/gh/althonos/scoring-matrices?style=flat-square&maxAge=600 :target: https://codecov.io/gh/althonos/scoring-matrices/ .. |PyPI| image:: https://img.shields.io/pypi/v/scoring-matrices.svg?style=flat-square&maxAge=3600 :target: https://pypi.python.org/pypi/scoring-matrices .. |Bioconda| image:: https://img.shields.io/conda/vn/bioconda/scoring-matrices?style=flat-square&maxAge=3600 :target: https://anaconda.org/bioconda/scoring-matrices .. |AUR| image:: https://img.shields.io/aur/version/python-scoring-matrices?logo=archlinux&style=flat-square&maxAge=3600 :target: https://aur.archlinux.org/packages/python-scoring-matrices .. |Wheel| image:: https://img.shields.io/pypi/wheel/scoring-matrices?style=flat-square&maxAge=3600 :target: https://pypi.org/project/scoring-matrices/#files .. |Versions| image:: https://img.shields.io/pypi/pyversions/scoring-matrices.svg?style=flat-square&maxAge=3600 :target: https://pypi.org/project/scoring-matrices/#files .. |Implementations| image:: https://img.shields.io/pypi/implementation/scoring-matrices.svg?style=flat-square&maxAge=3600&label=impl :target: https://pypi.org/project/scoring-matrices/#files .. |License| image:: https://img.shields.io/badge/license-MIT-blue.svg?style=flat-square&maxAge=3600 :target: https://choosealicense.com/licenses/mit/ .. |Source| image:: https://img.shields.io/badge/source-GitHub-303030.svg?maxAge=2678400&style=flat-square :target: https://github.com/althonos/scoring-matrices/ .. |Issues| image:: https://img.shields.io/github/issues/althonos/scoring-matrices.svg?style=flat-square&maxAge=600 :target: https://github.com/althonos/scoring-matrices/issues .. |Docs| image:: https://img.shields.io/readthedocs/scoring-matrices?style=flat-square&maxAge=3600 :target: http://scoring-matrices.readthedocs.io/en/stable/?badge=stable .. |Changelog| image:: https://img.shields.io/badge/keep%20a-changelog-8A0707.svg?maxAge=2678400&style=flat-square :target: https://github.com/althonos/scoring-matrices/blob/main/CHANGELOG.md .. |Downloads| image:: https://img.shields.io/pypi/dm/scoring-matrices?style=flat-square&color=303f9f&maxAge=86400&label=downloads :target: https://pepy.tech/project/scoring-matrices .. currentmodule:: scoring_matrices Overview -------- *Scoring Matrices* are matrices used to score the matches and mismatches between two characters are the same position in a sequence alignment. Some of these matrices are derived from *substitution matrices*, which uses evolutionary modeling. The ``scoring-matrices`` package is a dependency-free, batteries included Cython library to handle and distribute common substitution matrices: .. grid:: 1 2 3 3 :gutter: 1 .. grid-item-card:: :fas:`box` Self-contained The matrices are distributed as-is: you don't need the whole `Biopython `_ ecosystem, or even `NumPy `_. .. grid-item-card:: :fas:`gears` Cython Support The `ScoringMatrix` class is a Cython class that can be inherited, and the matrix data can be accessed as either a raw pointer, or a `typed memoryview `_. .. grid-item-card:: :fas:`battery-full` Batteries-included The package distributes most common matrices, such as those used by the NCBI BLAST+ suite, including: *PAM*, *BLOSUM*, *VTML*, *BENNER*, etc. .. grid-item-card:: :fas:`file-import` I/O Support Easily load a `ScoringMatrix` from a file, a file-like object, or by name for common matrices. .. grid-item-card:: :fas:`screwdriver-wrench` Configurable Easily build your own scoring matrices using the Python interface, including various shortcut constructors to create a `ScoringMatrix` from a diagonal or a pair of match/mismatch scores. .. grid-item-card:: :fas:`stamp` Versioned This library follows semantic versioning to guarantee compatibility between patch versions, allowing for a safe API and ABI that can be reused without recompiling on each install. Setup ----- ``scoring-matrices`` is available for all modern Python versions (3.7+). Run ``pip install scoring-matrices`` in a shell to download the latest release from PyPi, or have a look at the :doc:`Installation page ` to find other ways to install the package. Library ------- .. toctree:: :maxdepth: 2 User Guide API Reference Related Projects ---------------- The following Python libraries may be of interest for bioinformaticians. .. include:: related.rst License ------- This library is provided under the `MIT License `_. Matrices were collected from the `MMseqs2 `_, `Biopython `_ and `NCBI BLAST+ `_ sources and are believed to be in the public domain. *This project was developed by* `Martin Larralde `_ *during his PhD project at the* `Leiden University Medical Center `_ *in the* `Zeller team `_.