allfreqs 0.3.0

Calculate allele frequency from a sequence multialignment.

allfreqs

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:

$ 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.

0.3.0 (2020-04-02)

• Add option to allow ambiguous nucleotides shown separately.