# 🎼🧬 `lightmotif-tfmpvalue` [![Star me](https://img.shields.io/github/stars/althonos/lightmotif.svg?style=social&label=Star&maxAge=3600)](https://github.com/althonos/lightmotif/stargazers) *A Rust port of the [TFMPvalue](https://bioinfo.lifl.fr/TFM/TFMpvalue/) algorithm for the [`lightmotif`](https://crates.io/crates/lightmotif) crate.*. [![Actions](https://img.shields.io/github/actions/workflow/status/althonos/lightmotif/rust.yml?branch=main&logo=github&style=flat-square&maxAge=300)](https://github.com/althonos/lightmotif/actions) [![Coverage](https://img.shields.io/codecov/c/gh/althonos/lightmotif?logo=codecov&style=flat-square&maxAge=3600)](https://codecov.io/gh/althonos/lightmotif/) [![License](https://img.shields.io/badge/license-MIT-blue.svg?style=flat-square&maxAge=2678400)](https://choosealicense.com/licenses/mit/) [![Crate](https://img.shields.io/crates/v/lightmotif-tfmpvalue.svg?maxAge=600&style=flat-square)](https://crates.io/crates/lightmotif-tfmpvalue) [![Docs](https://img.shields.io/docsrs/lightmotif-tfmpvalue?maxAge=600&style=flat-square)](https://docs.rs/lightmotif-tfmpvalue) [![Source](https://img.shields.io/badge/source-GitHub-303030.svg?maxAge=2678400&style=flat-square)](https://github.com/althonos/lightmotif/tree/main/lightmotif-tfmpvalue) [![Mirror](https://img.shields.io/badge/mirror-EMBL-009f4d?style=flat-square&maxAge=2678400)](https://git.embl.de/larralde/lightmotif/) [![GitHub issues](https://img.shields.io/github/issues/althonos/lightmotif.svg?style=flat-square&maxAge=600)](https://github.com/althonos/lightmotif/issues) [![Changelog](https://img.shields.io/badge/keep%20a-changelog-8A0707.svg?maxAge=2678400&style=flat-square)](https://github.com/althonos/lightmotif/blob/master/CHANGELOG.md) ## 🗺️ Overview **TFMPvalue** is an algorithm proposed by Touzet & Varré[\[1\]](#ref1) for computing a [*p-value*](https://en.wikipedia.org/wiki/P-value) from a score obtained with a position weight matrix. It uses discretization to compute an approximation of the score distribution for the position weight matrix, iterating with growing levels of accuracy until convergence is reached. This approach outperforms [dynamic-programming](https://en.wikipedia.org/wiki/Dynamic_programming) based methods such as **LazyDistrib** by Beckstette *et al.*[\[2\]](#ref2). `lightmotif-tfmpvalue` provides an implementation of the **TFMPvalue** algorithm to use with position weight matrices from the `lightmotif` crate. ## 💡 Example Use `lightmotif` to create a position specific scoring matrix, and then use the TFMPvalue algorithm to compute the exact P-value for a given score, or a score threshold for a given P-value: ```rust extern crate lightmotif; extern crate lightmotif_tfmpvalue; use lightmotif::pwm::CountMatrix; use lightmotif::abc::Dna; use lightmotif::seq::EncodedSequence; use lightmotif_tfmpvalue::TfmPvalue; // Use a ScoringMatrix from `lightmotif` let pssm = CountMatrix::::from_sequences(&[ EncodedSequence::encode("GTTGACCTTATCAAC").unwrap(), EncodedSequence::encode("GTTGATCCAGTCAAC").unwrap(), ]) .unwrap() .to_freq(0.25) .to_scoring(None); // Initialize the TFMPvalue algorithm for the given PSSM // (the `pssm` reference must outlive `tfmp`). let mut tfmp = TfmPvalue::new(&pssm); // Compute the exact p-value for a given score let pvalue = tfmp.pvalue(19.3); assert_eq!(pvalue, 1.4901161193847656e-08); // Compute the exact score for a given p-value let score = tfmp.score(pvalue); assert_eq!(score, 19.3); ``` *Note that in the example above, the computation is not bounded, so for certain particular matrices the algorithm may require a large amount of memory to converge. Use the `TfmPvalue::approximate_pvalue` and `TfmPvalue::approximate_score` methods to obtain an iterator over the algorithm iterations, allowing you to stop at any given time based on external criterion such as total memory usage.* ## 💭 Feedback ### ⚠️ Issue Tracker Found a bug ? Have an enhancement request ? Head over to the [GitHub issue tracker](https://github.com/althonos/lightmotif/issues) if you need to report or ask something. If you are filing in on a bug, please include as much information as you can about the issue, and try to recreate the same bug in a simple, easily reproducible situation. ## 📋 Changelog This project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html) and provides a [changelog](https://github.com/althonos/lightmotif/blob/master/CHANGELOG.md) in the [Keep a Changelog](http://keepachangelog.com/en/1.0.0/) format. ## ⚖️ License This library is provided under the open-source [GNU General Public License v3.0](https://choosealicense.com/licenses/gpl-3.0/). The original TFMPvalue implementation was written by the [BONSAI team](https://bioinfo.univ-lille.fr/) of [CRISTaL](https://www.cristal.univ-lille.fr/), [Université de Lille](http://www.univ-lille.fr/) and [is available](https://bioinfo.univ-lille.fr/tfm-pvalue/tfm-pvalue.php) under the terms of the [GNU General Public License v2.0](https://choosealicense.com/licenses/gpl-2.0/). *This project is in no way not affiliated, sponsored, or otherwise endorsed by the [original TFMPvalue authors](https://bioinfo.univ-lille.fr/). It was developed by [Martin Larralde](https://github.com/althonos/) during his PhD project at the [European Molecular Biology Laboratory](https://www.embl.de/) in the [Zeller team](https://github.com/zellerlab).* ## 📚 References - \[1\] Touzet, Hélène and Jean-Stéphane Varré. ‘Efficient and accurate P-value computation for Position Weight Matrices’. Algorithms for Molecular Biology 2, 1–12 (2007). [doi:10.1186/1748-7188-2-15](https://doi.org/10.1186/1748-7188-2-15). - \[2\] Beckstette, Michael, Robert Homann, and Robert Giegerich. ‘Fast index based algorithms and software for matching position specific scoring matrices’. BMC Bioinformatics 7, 389 (2006). [doi:10.1186/1471-2105-7-389](https://doi.org/10.1186/1471-2105-7-389).