This tool is inspired by the original implementation of the bali-score tool which accompanies the BAliBASE 3 database.
Currently this tool only works for BAliBASE 3 reference alignments in .xml format which have core blocks declared. It is not possible to declare a threshold instead of core blocks.
The tool can be used as a library for other projects or as a CLI tool. Installing it as a CLI tool depends on a stable Rust toolchain being available (recommended install via rustup) and can be done by executing
cargo install --path .
at the top level of the project.
Execute
bali-score -h
to see the available options. Scoring a test alignment in fasta format against a BAliBASE v3 reference alignment in xml format is as easy as running:
bali-score -t <test fasta file> -r <reference xml> [-o <output file>]
If no output file path is provided, the result is written to stdout, otherwise the scores are written as a json file at the provided path.
The tool has been reimplemented because I simply could not get the original one running and I had the necessary code mostly written already. I simply extracted it from my thesis to make it reusable.
Most importantly it is not dependant upon the Expat xml parser or any other dynamic dependency (except libc).
If you'd like a feature that is currently not available, e.g. using other file formats like msf as input, please open an issue describing the use case and if it sounds useful/interesting I might implement it :) No guarantees though.
- add license
- is it problematic that original bali-score contains no license? This tool shares no code with it, but currently has the same name...
- accept other file formats as input
- document library
- publish as binary and clearly documented lib on crates.io
- provide c compatible methods
- allow evaluation against reference alignments without core block information (see original tool)
- write some tests
- write some benchmarks
- set up CI
- are there other scores/databases that could be supported? Maybe this tool could become more general than just BAliBASE