Metadata-Version: 2.1
Name: allfreqs
Version: 0.3.0
Summary: Calculate allele frequency from a sequence multialignment.
Home-page: https://github.com/robertopreste/allfreqs
Author: Roberto Preste
Author-email: robertopreste@gmail.com
License: MIT license
Description: ========
        allfreqs
        ========
        
        
        .. image:: https://img.shields.io/pypi/v/allfreqs.svg
                :target: https://pypi.python.org/pypi/allfreqs
        
        .. image:: https://www.repostatus.org/badges/latest/wip.svg
            :alt: Project Status: WIP – Initial development is in progress, but there has not yet been a stable, usable release suitable for the public.
            :target: https://www.repostatus.org/#wip
        
        .. image:: https://travis-ci.com/robertopreste/allfreqs.svg?branch=master
                :target: https://travis-ci.com/robertopreste/allfreqs
        
        .. image:: https://readthedocs.org/projects/allfreqs/badge/?version=latest
                :target: https://allfreqs.readthedocs.io/en/latest/?badge=latest
                :alt: Documentation Status
        
        
        Calculate allele frequencies from a sequence multialignment.
        
        
        * Free software: MIT license
        * Documentation: https://allfreqs.readthedocs.io
        * GitHub repo: https://github.com/robertopreste/allfreqs
        
        
        Features
        ========
        
        Calculate allele frequencies from a nucleotide multialignment in fasta or csv format.
        
        Allele frequencies will be returned as a table in which each row is a nucleotide position (based on
        the provided reference sequence) and columns are A, C, G, T frequencies as well as gaps and other
        non-canonical nucleotides.
        
        For example, given the following multialignment:
        
        +------+----------+
        | ID   | Sequence |
        +======+==========+
        | ref  | ACGTACGT |
        +------+----------+
        | seq1 | A-GTAGGN |
        +------+----------+
        | seq2 | ACCAGCGT |
        +------+----------+
        
        the resulting allele frequencies will be:
        
        +----------+-----+-----+-----+-----+-----+-----+
        | position | A   | C   | G   | T   | gap | oth |
        +==========+=====+=====+=====+=====+=====+=====+
        | 1.0_A    | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 |
        +----------+-----+-----+-----+-----+-----+-----+
        | 2.0_C    | 0.0 | 0.5 | 0.0 | 0.0 | 0.5 | 0.0 |
        +----------+-----+-----+-----+-----+-----+-----+
        | 3.0_G    | 0.0 | 0.5 | 0.5 | 0.0 | 0.0 | 0.0 |
        +----------+-----+-----+-----+-----+-----+-----+
        | 4.0_T    | 0.5 | 0.0 | 0.0 | 0.5 | 0.0 | 0.0 |
        +----------+-----+-----+-----+-----+-----+-----+
        | 5.0_A    | 0.5 | 0.0 | 0.5 | 0.0 | 0.0 | 0.0 |
        +----------+-----+-----+-----+-----+-----+-----+
        | 6.0_C    | 0.0 | 0.5 | 0.5 | 0.0 | 0.0 | 0.0 |
        +----------+-----+-----+-----+-----+-----+-----+
        | 7.0_G    | 0.0 | 0.0 | 1.0 | 0.0 | 0.0 | 0.0 |
        +----------+-----+-----+-----+-----+-----+-----+
        | 8.0_T    | 0.0 | 0.0 | 0.0 | 0.5 | 0.0 | 0.5 |
        +----------+-----+-----+-----+-----+-----+-----+
        
        Frequencies of non-canonical (ambiguous) nucleotides are by default squashed into the ``oth``
        column, but they can also be shown separately using a simple flag.
        
        allfreqs can be used either as a command line tool or through its Python API.
        
        For more information, please refer to the Usage_ section of the documentation.
        
        Installation
        ============
        
        **PLEASE NOTE: allfreqs only supports Python >= 3.6!**
        
        The preferred installation method for allfreqs is using ``pip``:
        
        .. code-block:: console
        
            $ pip install allfreqs
        
        For more information, please refer to the Installation_ section of the documentation.
        
        Credits
        =======
        
        This package was created with Cookiecutter_ and the `cc-pypackage`_ project template.
        
        .. _Usage: https://allfreqs.readthedocs.io/en/latest/usage.html
        .. _Installation: https://allfreqs.readthedocs.io/en/latest/installation.html
        .. _Cookiecutter: https://github.com/audreyr/cookiecutter
        .. _`cc-pypackage`: https://github.com/robertopreste/cc-pypackage
        
        
        =======
        History
        =======
        
        0.1.0 (2019-07-08)
        ==================
        
        * First release.
        
        0.1.1 (2019-08-08)
        ------------------
        
        * Read and process multialignments from fasta and csv files (Python module only).
        
        0.1.2 (2019-10-17)
        ------------------
        
        * Add tests with and without reference included in multialignments;
        * Add tests with real datasets (coming from haplogroup-specific multialignments).
        
        0.1.3 (2019-10-18)
        ------------------
        
        * Add more detailed tests for real datasets;
        * Implement more efficient frequency calculation;
        * Add dunder methods and sanity checks;
        * Fix requirements and testing framework;
        * Clean code.
        
        0.2.0 (2020-03-07)
        ==================
        
        * Remove `numpy` and `pandas` from requirements as they are installed by `scikit-bio`;
        * Move `tests` module inside `allfreqs`;
        * Add `ci` module for internal management;
        * Clean code.
        
        0.3.0 (2020-04-02)
        ==================
        
        * Add option to allow ambiguous nucleotides shown separately.
        
Keywords: allfreqs
Platform: UNKNOWN
Classifier: Development Status :: 2 - Pre-Alpha
Classifier: Intended Audience :: Developers
Classifier: License :: OSI Approved :: MIT License
Classifier: Natural Language :: English
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Description-Content-Type: text/x-rst
