https://github.com/cidm-ph/distmat

Distance matrix data types and file formats for Rust
https://github.com/cidm-ph/distmat

bioinformatics data-structures distance-matrix

Last synced: 7 months ago
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Distance matrix data types and file formats for Rust

• Host: GitHub
• URL: https://github.com/cidm-ph/distmat
• Owner: cidm-ph
• License: apache-2.0
• Created: 2022-09-29T01:55:27.000Z (over 3 years ago)
• Default Branch: main
• Last Pushed: 2024-11-11T09:46:29.000Z (over 1 year ago)
• Last Synced: 2025-08-30T08:53:14.146Z (7 months ago)
• Topics: bioinformatics, data-structures, distance-matrix
• Language: Rust
• Homepage:
• Size: 118 KB
• Stars: 0
• Watchers: 2
• Forks: 0
• Open Issues: 1
• Metadata Files:
  • Readme: README.md
  • Changelog: CHANGELOG.md
  • License: LICENSE-APACHE

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README

          
# distmat

[![crates-io-v](https://img.shields.io/crates/v/distmat)](https://crates.io/crates/distmat)

![crates-io-l](https://img.shields.io/crates/l/distmat)

[![docs-rs](https://img.shields.io/docsrs/distmat)](https://docs.rs/distmat)

> **Distance matrix data types and file formats**

Matrix types specialised for storing pairwise distance data, and parsers for

some common file formats for storing such data.

```rust

use distmat::{DistMatrix, SquareMatrix};

use distmat::formats::{PhylipDialect, Separator, TabularShape};

fn main() {

    // A symmetric matrix stored as the lower triangle:

    //   _1__5__3

    // 1|

    // 5| 4

    // 3| 2  2

    let matrix1 = DistMatrix::from_pw_distances(&[1, 5, 3]);

    assert_eq!(matrix1.get(1, 2), Some(&2));

    assert_eq!(matrix1.get(2, 1), None);

        assert_eq!(

            matrix1.get_symmetric(2, 1).map(|x| x.get_or_default()),

            Some(2)

        );

    // A square matrix stored in row major order:

    //   _1___5___3

    // 1| 0  -4  -2

    // 5| 4   0   2

    // 3| 2  -2   0

    let matrix2 = SquareMatrix::from_pw_distances_with(&[1, 5, 3], |x, y| x - y);

    let mut total = 0;

    for row in matrix2.iter_rows() {

        total += row.sum::();

    }

    assert_eq!(total, 0);

    let _matrix =

        SquareMatrix::from_tabular_file("snp-dists.dat", Separator::Char('\t'), TabularShape::Wide).unwrap();

    let _matrix =

        SquareMatrix::from_phylip_file("phylip.dist", PhylipDialect::Strict).unwrap();

    let _matrix =

        DistMatrix::from_phylip_file("phylip_lt.dist", PhylipDialect::Relaxed).unwrap();

}

```

## Purpose

Goals:

  * Read and write pairwise distance data from any reasonable formats,

    especially those used in bioinformatics.

  * Provide a convenient API to interact with distance data.

Non-goals:

  * Linear algebra. There are many linear algebra libraries available with

    matrix data structures. At most distmat will help you export your data to

    these libraries.

  * Algorithms. You can provide a closure to distmat to construct a distance

    matrix, but any specialised algorithms or distance measures are best

    implemented elsewhere.

## License

Dual-licensed under [MIT](LICENSE-MIT) or [Apache 2.0](LICENSE-APACHE).

© Western Sydney Local Health District, NSW Health.