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 allfreqsFor 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.
1 maintainer
Metadata
1 maintainer
Release files for allfreqs 0.3.0
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