3 unstable releases
0.3.0 | Dec 8, 2022 |
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0.2.1 | Nov 24, 2022 |
0.2.0 | Sep 29, 2022 |
#353 in Parser tooling
46 downloads per month
Used in alpine-core
79KB
2K
SLoC
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.
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_symmetric(1, 2), 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();
}
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 or Apache 2.0.
© Western Sydney Local Health District, NSW Health.
Dependencies
~0.5–1MB
~22K SLoC