Skip to main content

Calculate allele frequency from a sequence multialignment.

Project description

allfreqs

https://img.shields.io/pypi/v/allfreqs.svg Project Status: WIP – Initial development is in progress, but there has not yet been a stable, usable release suitable for the public. https://travis-ci.com/robertopreste/allfreqs.svg?branch=master Documentation Status

Calculate allele frequencies from a sequence multialignment.

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

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:

$ 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.

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.

Project details


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

allfreqs-0.2.0.tar.gz (12.5 kB view hashes)

Uploaded Source

Built Distribution

allfreqs-0.2.0-py2.py3-none-any.whl (7.9 kB view hashes)

Uploaded Python 2 Python 3

Supported by

AWS AWS Cloud computing and Security Sponsor Datadog Datadog Monitoring Fastly Fastly CDN Google Google Download Analytics Microsoft Microsoft PSF Sponsor Pingdom Pingdom Monitoring Sentry Sentry Error logging StatusPage StatusPage Status page