nom-fasta

FASTA parser implemented in Rust with nom.

nom is a performant yet easy-to-use parser combinators library written in Rust. nom can handle either text or binary data. Here, based on nom, I implemented a parser for the FASTA, a text file format containing one more more protein/DNA/RNA sequences.

Example

extern crate fasta;
use fasta::Records;
use std::fs::File;
use std::io::prelude::*;

fn main() {
    let mut f = File::open("e.fasta").unwrap();
    let mut data = String::with_capacity(512);
    f.read_to_string(&mut data).unwrap();
    let a: Vec<_> = Records(&data).into_iter().collect();
    println!("{:?}", a);
}

[Ok(Record { id: "gi|2765644|emb|Z78519.1|CPZ78519", desc: Some("C.pubescens 5.8S rRNA gene and ITS1 and ITS2 DNA"), seq: "ATATGATCGAGTGAATCTGGTGGACTTGTGGTTACTCAGCTCGCCATAGGCTTTGCTTTTGCGGTGACCCTAATTTGTCATTGGGCCTCCTCCCAAGCTTTCCTTGTGGGTTTGAACCTCTAGCACGGTGCAGTA" }), Ok(Record { id: "gi|2765643|emb|Z78518.1|CRZ78518", desc: Some("C.reginae 5.8S rRNA gene and ITS1 and ITS2 DNA"), seq: "CGTAACAAGGTTTCCGTAGGTGAACCTGCGGGAGGATCATTGTTGAGATAGTAGAATATTCGATCGAGTGAATCCGGAGGACTTGTGGTTACTCGGCTCGTCGAAGGCTTAACTTTTGTGGTGACCCTGATTTGT" }), Ok(Record { id: "gi|2765642|emb|Z78517.1|CFZ78517", desc: Some("C.flavum 5.8S rRNA gene and ITS1 and ITS2 DNA"), seq: "CGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTGTTGA...

// --snip-- //

...TTAGTTGGGCC" })]

Comparison With bio::io::fasta

As of 2020-08-24, bio::io::fasta is faster.

test tests::bench_read_bio_io_fasta ... bench:     157,047 ns/iter (+/- 19,803)
test tests::bench_read_my_fasta     ... bench:     467,353 ns/iter (+/- 53,507)