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.