Source code for PairTON.
Execute the repository's Snakemake workflows with the following command (example):
snakemake -s workflow/workflow_name.smk --workflow-profile workflow/profile/There are three separate workflows, one for running the main configuration and getting uncertainties, and then two workflows the architecture ablation and iteration ablation studies.
The root files containing the data published with HyPER (https://zenodo.org/records/10653837)
are processed with scripts/hyper_to_h5_cli.py.
Configuration files live under configs/ (for example configs/data/sequence_hyper.yaml).
Some configuration files contain absolute, hardcoded dataset paths that must be adapted to your system before running the workflows.
This repository currently contains absolute paths that start with /srv/. Before running anything, search the tree and update paths as needed. For a quick check run:
grep -R --line-number "/srv/" .Replace occurrences with paths valid on your system or use relative paths/configuration overrides.
This project is distributed under the MIT License. See LICENSE for details.