https://github.com/robertopreste/allfreqs

Calculate allele frequencies from a sequence multialignment.
https://github.com/robertopreste/allfreqs

allele-frequencies bioinformatics csv fasta python

Last synced: 2 months ago
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Calculate allele frequencies from a sequence multialignment.

• Host: GitHub
• URL: https://github.com/robertopreste/allfreqs
• Owner: robertopreste
• License: mit
• Created: 2019-07-08T09:34:42.000Z (over 6 years ago)
• Default Branch: master
• Last Pushed: 2024-11-23T10:29:54.000Z (over 1 year ago)
• Last Synced: 2025-10-30T14:38:16.513Z (5 months ago)
• Topics: allele-frequencies, bioinformatics, csv, fasta, python
• Language: Python
• Homepage: https://allfreqs.readthedocs.io
• Size: 360 KB
• Stars: 1
• Watchers: 0
• Forks: 0
• Open Issues: 59
• Metadata Files:
  • Readme: README.rst
  • Changelog: HISTORY.rst
  • Contributing: CONTRIBUTING.rst
  • License: LICENSE
  • Authors: AUTHORS.rst

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README

          
========

allfreqs

========

.. image:: https://img.shields.io/pypi/v/allfreqs.svg

        :target: https://pypi.python.org/pypi/allfreqs

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    :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