joyliu-q / rust-genomics

A library related to analyzing genomic data (reading files, parsing sequences, etc).

rust-genomics

About

A Rust library related to analyzing genomic data (reading files, parsing sequences, etc).

RustGenomics contains tools to help with some of the major analysis of genes and genomes, including:

• parsing fasta files
• reviewing sequence validity
• viewing sequences in various reading frames
• finding open reading frames and longest open reading frames in genes
• Genome Related Structs (e.g. Sequence) with methods and associated functions

Some of these functions, such as file parsing and sequence analysis have various versions (e.g. concurrent/normal) that you can use for different sizes. These functions are benchmarked and tested with the criterion crate.

For more information, see the documentation generated here or run cargo doc on your terminal.

Main Technologies Used

• rayon: for concurrency in reading files
• criterion: for benchmarking and testing

Usage Example

use rust_genomics::{Sequence, FASTA};

fn main() {
    let file_path = "data/haha-1.fasta";

    // Generate an instance of the FASTA struct by reading data from the given file
    let mut fasta = FASTA::rayon_read_fasta(file_path);

    // The FASTA instance has the Display trait, allowing it to be visualized in a clean fashion
    println!("{}", fasta);

    println!("Epic");

    // Find all longest open reading frame for fasta, with concurrency
    let lorfs = fasta.find_lorfs(true);

    println!("{}", lorfs.len());
}