Alphabeta (but it's fast)

This repostiory contains a fast implementation of the AlphaBeta algorithm first proposed by Yadollah Shahryary, Frank Johannes and Rashmi Hazarika. The original R implemtation is accessible on Github here. I matched the original parameters needed for the program, to the old documentation is still useful.

Additionally, this repository also contains a program for creating metaprofiles of (epi)genetic data. They are connected, so output from the metaprofile program can automcatically be fed into AlphaBeta.

In Action

How to use

You'll need to install Rust, the programming language used for this project. Then enter the following commands into your terminal:

cargo install alphabeta

This will install the programs on your system. You can then ensure everything works by running:

alphabeta --help
# and
metaprofile --help

Windows

Windows is currently not supported, but using WSL2 on Windows works.

Open powershell and run:

wsl --install -d ubuntu

Configure your user, open Ubuntu and then install the dependencies and the program:

sudo apt update
sudo apt install build-essential pkg-config libssl-dev
curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh
cargo install alphabeta

cargo run --release --bin alphabeta
# or
cargo run --release --bin metaprofile

Updating

If you want to use a new version of the program, just run the following command again:

cargo install alphabeta

Parameters

Alphabeta

I tried to make this as easy to use as possible, so every parameter as a (hopefully) sensible default. You can see all the options by running alphabeta --help:

When you are in a directory with a nodelist.txt and edgelist.txt file, you can just run alphabeta and it will use default values for everything. If you want to use a different directory, you can supply the --nodes and --edges as well as the --output parameters manually.

Metaprofile

When using the metaprofile, you will need to supply a methylome directory, a genome annotation file, all other parameters have defaults which you can of course overwrite. You can see all the options by running metaprofile --help:

If you want to run AlphaBeta on the metaprofile output, use the alphabeta subcommand, which takes the AlphaBeta parameters from above. Note that alphabeta must come after the metaprofile options. The full order is: metaprofile [metaprofile options] alphabeta [alphabeta options]. The minimum command is therefore:

metaprofile --methylome [methylome directory] --genome [genome annotation file] alphabeta

About window step and size:

Size determines the "length" of each window, for example for --window-size 5, each window will span 5% of the length of the gene it is in. If you supply --absolute, the size will be interpreted as the number of basepairs instead of a percentage, so 5 bp.

Step determines the distance between the start of each window. If you supply --window-step 1 and --window-size 5, the first window will go from 0% to 5% and the second from 1% to 6% and so on. If you supply --window-step 5 and --window-size 5, the first window will go from 0% to 5% and the second from 5% to 10% and so on. In the latter case, you can also omit the step paramter, as it will default to the same value as size.

Examples

Run alphabeta

alphabeta \
--edges ./data/edgelist.txt \
--nodes ./data/nodelist.txt \
--output ./data/output

Create a metaprofile and feed it into AlphaBeta

metaprofile \
--methylome ../methylome/within_gbM_genes/ \
--genome ../methylome/gbM_gene_anotation_extract_Arabidopsis.bed \
--output-dir /mnt/extStorage/workingDir/./windows/wt \
--name wildtype \
--window-step 1 --window-size 5 \
alphabeta
--edges ../methylome/edgelist.txt \
--nodes ../methylome/nodelist.txt