Metadata-Version: 2.1
Name: blosum
Version: 1.1.0
Summary: A simple BLOSUM toolbox without dependencies.
Home-page: https://github.com/not-a-feature/blosum
Author: Jules Kreuer / not_a_feature
License: gpl-3.0
Description: ![blosum](https://github.com/not-a-feature/blosum/raw/main/blosum.png)
        
        A small module for easy access to BLOSUM matrices without dependencies.
        
        ![Test Badge](https://github.com/not-a-feature/blosum/actions/workflows/tests.yml/badge.svg)
        ![Python Version Badge](https://img.shields.io/pypi/pyversions/blosum)
        ![Download Badge](https://img.shields.io/pypi/dm/blosum.svg)
        
        The BLOcks SUbstitution Matrices (BLOSUM) are used to score alignments between protein sequences and are therefore mainly used in bioinformatics.
        
        Reading such matrices is not particularly difficult, yet most off the shelf packages are overloaded with strange dependencies.
        And why do we need to implement the same reader again if there is a simple module for that.
        
        `blosum` offers a robust and easy-to-expand implementation without relying on third-party libraries. 
        
        
        ## Installation
        Using pip  / pip3:
        ```bash
        pip install blosum
        ```
        Or by source:
        ```bash
        git clone git@github.com:not-a-feature/blosum.git
        cd blosum
        pip install .
        ```
        
        ## How to use
        
        ### Default BLOSUM 
        This package comes with the most commonly used BLOSUM matrices built in.
        You can choose from BLOSUM 45, 50, 62, 80 and 90.
        
        To load a matrix:
        ```python
        import blosum as bl
        matrix = bl.BLOSUM(62)
        ``` 
        
        ### Custom Matrix
        In addition, own matrices can be loaded. For this, the path is given as an argument.
        
        ```python
        import blosum as bl
        matrix = bl.BLOSUM("path/to/blosum.file")
        ```
        
        The matrices are required to have following format:
        
        ```
        # One Header Line
           A  R  N  D
        A  5 -2 -1 -2
        R -2  7  0 -1
        N -1  0  6  2
        D -2 -1  2  7
        ```
        
        ### Getting Values.
        To get a value use:
        
        ```python
        val = matrix["AY"]
        ```
        
        Or get the dictionary representation of the BLOSUM matrix.
        
        ```python
        blosum_dict = dict(matrix)
        ```
        
        If the key cannot be found, the default value is returned. It is `float("-inf")`.
        It is possible to set a custom default score:
        ```python
        matrix = bl.BLOSUM(62, default=0)
        ```
        
        ## License
        ```
        Copyright (C) 2021 by Jules Kreuer - @not_a_feature
        This piece of software is published unter the GNU General Public License v3.0
        TLDR:
        
        | Permissions      | Conditions                   | Limitations |
        | ---------------- | ---------------------------- | ----------- |
        | ✓ Commercial use | Disclose source              | ✕ Liability |
        | ✓ Distribution   | License and copyright notice | ✕ Warranty  |
        | ✓ Modification   | Same license                 |             |
        | ✓ Patent use     | State changes                |             |
        | ✓ Private use    |                              |             |
        ```
        Go to [LICENSE.md](https://github.com/not-a-feature/blosum/blob/main/LICENSE) to see the full version.
        
        ## Dependencies
        In addition to packages included in Python 3, this piece of software uses 3rd-party software packages for development purposes that are not required in the published version.
        Go to [DEPENDENCIES.md](https://github.com/not-a-feature/blosum/blob/main/DEPENDENCIES.md) to see all dependencies and licenses.
Keywords: BLOSUM,reader,bio,bioinformatics
Platform: unix
Platform: linux
Platform: osx
Platform: cygwin
Platform: win32
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Requires-Python: >=3.8
Description-Content-Type: text/markdown
Provides-Extra: testing
