Name | scoring-matrices JSON |
Version |
0.3.0
JSON |
| download |
home_page | None |
Summary | Dependency free, Cython-compatible scoring matrices to use with biological sequences. |
upload_time | 2024-10-20 15:11:58 |
maintainer | None |
docs_url | None |
author | None |
requires_python | >=3.7 |
license | MIT License Copyright (c) 2024 Martin Larralde <martin.larralde@embl.de> Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. |
keywords |
bioinformatics
sequence
substitution
matrix
score
|
VCS |
|
bugtrack_url |
|
requirements |
No requirements were recorded.
|
Travis-CI |
No Travis.
|
coveralls test coverage |
No coveralls.
|
# π§¬π `scoring-matrices` [![Stars](https://img.shields.io/github/stars/althonos/scoring-matrices.svg?style=social&maxAge=3600&label=Star)](https://github.com/althonos/scoring-matrices/stargazers)
*Dependency free, [Cython](https://cython.org/)-compatible scoring matrices to use with biological sequences.*
[![Actions](https://img.shields.io/github/actions/workflow/status/althonos/scoring-matrices/test.yml?branch=main&logo=github&style=flat-square&maxAge=300)](https://github.com/althonos/scoring-matrices/actions)
[![Coverage](https://img.shields.io/codecov/c/gh/althonos/scoring-matrices?style=flat-square&maxAge=3600&logo=codecov)](https://codecov.io/gh/althonos/scoring-matrices/)
[![License](https://img.shields.io/badge/license-MIT-blue.svg?style=flat-square&maxAge=2678400)](https://choosealicense.com/licenses/mit/)
[![PyPI](https://img.shields.io/pypi/v/scoring-matrices.svg?style=flat-square&maxAge=3600&logo=PyPI)](https://pypi.org/project/scoring-matrices)
[![Bioconda](https://img.shields.io/conda/vn/bioconda/scoring-matrices?style=flat-square&maxAge=3600&logo=anaconda)](https://anaconda.org/bioconda/scoring-matrices)
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[![Docs](https://img.shields.io/readthedocs/scoring-matrices/latest?style=flat-square&maxAge=600)](https://scoring-matrices.readthedocs.io)
[![Changelog](https://img.shields.io/badge/keep%20a-changelog-8A0707.svg?maxAge=2678400&style=flat-square)](https://github.com/althonos/scoring-matrices/blob/main/CHANGELOG.md)
[![Downloads](https://img.shields.io/pypi/dm/scoring-matrices?style=flat-square&color=303f9f&maxAge=86400&label=downloads)](https://pepy.tech/project/scoring-matrices)
## πΊοΈ 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 library
to handle and distribute common substitution matrices:
- **no external dependencies**: The matrices are distributed as-is: you don't
need the whole [Biopython](https://biopython.org) ecosystem, or even
[NumPy](https://numpy.org/).
- **Cython compatibility**: The `ScoringMatrix` is a Cython class that can be
inherited, and the matrix data can be accessed as either a raw pointer, or
a [typed memoryview](https://cython.readthedocs.io/en/latest/src/userguide/memoryviews.html).
- **most common matrices**: The package distributes most common matrices, such as
those used by the NCBI BLAST+ suite, including:
- [*PAM*](https://en.wikipedia.org/wiki/Point_accepted_mutation#) matrices by Dayhoff *et al.* (1978).
- [*BLOSUM*](https://en.wikipedia.org/wiki/BLOSUM) matrices by Henikoff & Henikoff (1992).
- *VTML* matrices by Muller *et al.* (2002).
- *BENNER* matrices by Benner *et al.* (1994).
## π§ Installing
`scoring-matrices` can be installed directly from [PyPI](https://pypi.org/project/scoring-matrices/),
which hosts some pre-built wheels for the x86-64 architecture (Linux/OSX/Windows)
and the Aarch64 architecture (Linux/OSX), as well as the code required to
compile from source with Cython:
```console
$ pip install scoring-matrices
```
Otherwise, `scoring-matrices` is also available as a [Bioconda](https://bioconda.github.io/)
package:
```console
$ conda install bioconda::scoring-matrices
```
## π‘ Usage
### Python
- Import the `ScoringMatrix` class from the installed module:
```python
from scoring_matrices import ScoringMatrix
```
- Load one of the built-in matrices:
```python
blosum62 = ScoringMatrix.from_name("BLOSUM62")
```
- Get individual matrix weights either by index or by alphabet letter:
```python
x = blosum62[0, 0]
y = blosum62['A', 'A']
```
- Get a row of the matrix either by index or by alphabet letter:
```python
row_x = blosum62[0]
row_y = blosum62['A']
```
### Cython
- Access the matrix weights as raw pointers to constant data:
```cython
from scoring_matrices cimport ScoringMatrix
cdef ScoringMatrix blosum = ScoringMatrix.from_name("BLOSUM62")
cdef const float* data = blosum.data_ptr() # dense array
cdef const float** matrix = blosum.matrix_ptr() # array of pointers
```
- Access the `ScoringMatrix` weights as a [typed memoryview](https://cython.readthedocs.io/en/latest/src/userguide/memoryviews.html)
using the *buffer protocol* in more recents versions of Python:
```cython
from scoring_matrices cimport ScoringMatrix
cdef ScoringMatrix blosum = ScoringMatrix.from_name("BLOSUM62")
cdef const float[:, :] weights = blosum
```
## π Feedback
### β οΈ Issue Tracker
Found a bug ? Have an enhancement request ? Head over to the [GitHub issue tracker](https://github.com/althonos/scoring-matrices/issues)
if you need to report or ask something. If you are filing in on a bug,
please include as much information as you can about the issue, and try to
recreate the same bug in a simple, easily reproducible situation.
### ποΈ Contributing
Contributions are more than welcome! See
[`CONTRIBUTING.md`](https://github.com/althonos/scoring-matrices/blob/main/CONTRIBUTING.md)
for more details.
## π Changelog
This project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html)
and provides a [changelog](https://github.com/althonos/scoring-matrices/blob/main/CHANGELOG.md)
in the [Keep a Changelog](http://keepachangelog.com/en/1.0.0/) format.
## βοΈ License
This library is provided under the [MIT License](https://choosealicense.com/licenses/mit/).
Matrices were collected from the [MMseqs2](https://github.com/soedinglab/MMseqs2),
[Biopython](https://github.com/biopython/biopython/tree/master/Bio/Align/substitution_matrices/data)
and [NCBI BLAST+](https://ftp.ncbi.nih.gov/blast/matrices/) sources and are believed to
be in the public domain.
*This project was developed by [Martin Larralde](https://github.com/althonos/)
during his PhD project at the [Leiden University Medical Center](https://www.lumc.nl/en/) in the [Zeller team](https://github.com/zellerlab).*
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"description": "# \ud83e\uddec\ud83d\udd20 `scoring-matrices` [![Stars](https://img.shields.io/github/stars/althonos/scoring-matrices.svg?style=social&maxAge=3600&label=Star)](https://github.com/althonos/scoring-matrices/stargazers)\n\n*Dependency free, [Cython](https://cython.org/)-compatible scoring matrices to use with biological sequences.*\n\n[![Actions](https://img.shields.io/github/actions/workflow/status/althonos/scoring-matrices/test.yml?branch=main&logo=github&style=flat-square&maxAge=300)](https://github.com/althonos/scoring-matrices/actions)\n[![Coverage](https://img.shields.io/codecov/c/gh/althonos/scoring-matrices?style=flat-square&maxAge=3600&logo=codecov)](https://codecov.io/gh/althonos/scoring-matrices/)\n[![License](https://img.shields.io/badge/license-MIT-blue.svg?style=flat-square&maxAge=2678400)](https://choosealicense.com/licenses/mit/)\n[![PyPI](https://img.shields.io/pypi/v/scoring-matrices.svg?style=flat-square&maxAge=3600&logo=PyPI)](https://pypi.org/project/scoring-matrices)\n[![Bioconda](https://img.shields.io/conda/vn/bioconda/scoring-matrices?style=flat-square&maxAge=3600&logo=anaconda)](https://anaconda.org/bioconda/scoring-matrices)\n[![AUR](https://img.shields.io/aur/version/python-scoring-matrices?logo=archlinux&style=flat-square&maxAge=3600)](https://aur.archlinux.org/packages/python-scoring-matrices)\n[![Wheel](https://img.shields.io/pypi/wheel/scoring-matrices.svg?style=flat-square&maxAge=3600)](https://pypi.org/project/scoring-matrices/#files)\n[![Python Versions](https://img.shields.io/pypi/pyversions/scoring-matrices.svg?style=flat-square&maxAge=600&logo=python)](https://pypi.org/project/scoring-matrices/#files)\n[![Python Implementations](https://img.shields.io/pypi/implementation/scoring-matrices.svg?style=flat-square&maxAge=600&label=impl)](https://pypi.org/project/scoring-matrices/#files)\n[![Source](https://img.shields.io/badge/source-GitHub-303030.svg?maxAge=2678400&style=flat-square)](https://github.com/althonos/scoring-matrices/)\n[![Issues](https://img.shields.io/github/issues/althonos/scoring-matrices.svg?style=flat-square&maxAge=600)](https://github.com/althonos/scoring-matrices/issues)\n[![Docs](https://img.shields.io/readthedocs/scoring-matrices/latest?style=flat-square&maxAge=600)](https://scoring-matrices.readthedocs.io)\n[![Changelog](https://img.shields.io/badge/keep%20a-changelog-8A0707.svg?maxAge=2678400&style=flat-square)](https://github.com/althonos/scoring-matrices/blob/main/CHANGELOG.md)\n[![Downloads](https://img.shields.io/pypi/dm/scoring-matrices?style=flat-square&color=303f9f&maxAge=86400&label=downloads)](https://pepy.tech/project/scoring-matrices)\n\n## \ud83d\uddfa\ufe0f Overview\n\n*Scoring Matrices* are matrices used to score the matches and mismatches between\ntwo characters are the same position in a sequence alignment. Some of these\nmatrices are derived from *substitution matrices*, which uses evolutionary \nmodeling.\n\nThe `scoring-matrices` package is a dependency-free, batteries included library\nto handle and distribute common substitution matrices:\n\n- **no external dependencies**: The matrices are distributed as-is: you don't \n need the whole [Biopython](https://biopython.org) ecosystem, or even \n [NumPy](https://numpy.org/).\n- **Cython compatibility**: The `ScoringMatrix` is a Cython class that can be\n inherited, and the matrix data can be accessed as either a raw pointer, or\n a [typed memoryview](https://cython.readthedocs.io/en/latest/src/userguide/memoryviews.html).\n- **most common matrices**: The package distributes most common matrices, such as \n those used by the NCBI BLAST+ suite, including:\n - [*PAM*](https://en.wikipedia.org/wiki/Point_accepted_mutation#) matrices by Dayhoff *et al.* (1978).\n - [*BLOSUM*](https://en.wikipedia.org/wiki/BLOSUM) matrices by Henikoff & Henikoff (1992).\n - *VTML* matrices by Muller *et al.* (2002).\n - *BENNER* matrices by Benner *et al.* (1994).\n\n## \ud83d\udd27 Installing\n\n`scoring-matrices` can be installed directly from [PyPI](https://pypi.org/project/scoring-matrices/),\nwhich hosts some pre-built wheels for the x86-64 architecture (Linux/OSX/Windows)\nand the Aarch64 architecture (Linux/OSX), as well as the code required to\ncompile from source with Cython:\n```console\n$ pip install scoring-matrices\n```\n\nOtherwise, `scoring-matrices` is also available as a [Bioconda](https://bioconda.github.io/)\npackage:\n```console\n$ conda install bioconda::scoring-matrices\n```\n\n## \ud83d\udca1 Usage\n\n### Python\n\n- Import the `ScoringMatrix` class from the installed module:\n ```python\n from scoring_matrices import ScoringMatrix\n ```\n- Load one of the built-in matrices:\n ```python\n blosum62 = ScoringMatrix.from_name(\"BLOSUM62\")\n ```\n- Get individual matrix weights either by index or by alphabet letter:\n ```python\n x = blosum62[0, 0]\n y = blosum62['A', 'A']\n ```\n- Get a row of the matrix either by index or by alphabet letter:\n ```python\n row_x = blosum62[0]\n row_y = blosum62['A']\n ```\n\n### Cython\n\n- Access the matrix weights as raw pointers to constant data:\n ```cython\n from scoring_matrices cimport ScoringMatrix\n\n cdef ScoringMatrix blosum = ScoringMatrix.from_name(\"BLOSUM62\")\n cdef const float* data = blosum.data_ptr() # dense array\n cdef const float** matrix = blosum.matrix_ptr() # array of pointers\n ```\n- Access the `ScoringMatrix` weights as a [typed memoryview](https://cython.readthedocs.io/en/latest/src/userguide/memoryviews.html) \n using the *buffer protocol* in more recents versions of Python:\n ```cython\n from scoring_matrices cimport ScoringMatrix\n\n cdef ScoringMatrix blosum = ScoringMatrix.from_name(\"BLOSUM62\")\n cdef const float[:, :] weights = blosum\n ```\n\n## \ud83d\udcad Feedback\n\n### \u26a0\ufe0f Issue Tracker\n\nFound a bug ? Have an enhancement request ? Head over to the [GitHub issue tracker](https://github.com/althonos/scoring-matrices/issues)\nif you need to report or ask something. If you are filing in on a bug,\nplease include as much information as you can about the issue, and try to\nrecreate the same bug in a simple, easily reproducible situation.\n\n### \ud83c\udfd7\ufe0f Contributing\n\nContributions are more than welcome! See\n[`CONTRIBUTING.md`](https://github.com/althonos/scoring-matrices/blob/main/CONTRIBUTING.md)\nfor more details.\n\n\n## \ud83d\udccb Changelog\n\nThis project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html)\nand provides a [changelog](https://github.com/althonos/scoring-matrices/blob/main/CHANGELOG.md)\nin the [Keep a Changelog](http://keepachangelog.com/en/1.0.0/) format.\n\n\n## \u2696\ufe0f License\n\nThis library is provided under the [MIT License](https://choosealicense.com/licenses/mit/). \nMatrices were collected from the [MMseqs2](https://github.com/soedinglab/MMseqs2), \n[Biopython](https://github.com/biopython/biopython/tree/master/Bio/Align/substitution_matrices/data)\nand [NCBI BLAST+](https://ftp.ncbi.nih.gov/blast/matrices/) sources and are believed to \nbe in the public domain.\n\n*This project was developed by [Martin Larralde](https://github.com/althonos/) \nduring his PhD project at the [Leiden University Medical Center](https://www.lumc.nl/en/) in the [Zeller team](https://github.com/zellerlab).*\n",
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