Calculate allele frequency from a sequence multialignment.
Calculate allele frequencies from a sequence multialignment.
- Free software: MIT license
- Documentation: https://allfreqs.readthedocs.io
- GitHub repo: https://github.com/robertopreste/allfreqs
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:
the resulting allele frequencies will be:
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.
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.
- First release.
- Read and process multialignments from fasta and csv files (Python module only).
- Add tests with and without reference included in multialignments;
- Add tests with real datasets (coming from haplogroup-specific multialignments).
- 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.
- 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.
- Add option to allow ambiguous nucleotides shown separately.
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