noodles-fasta handles and reading and writing of the FASTA format.

FASTA is a text format with no formal specification and only has de facto rules. It typically consists of a list of records, each with a definition on the first line and a sequence in the following lines.

The definition starts with a > (greater than) character, and directly after it is the reference sequence name. Optionally, whitespace may be used a delimiter for an extra description or metadata of the sequence. For example,

reference sequence name
| |
>sq0 LN:13
|   |
description

The sequence is effectively a byte array of characters representing a base. It is typically hard wrapped at an arbitrary width. For example, the following makes up the sequence ACGTNACTGG.

ACGT
NACT
GG

Examples

Read all records in a FASTA file

# use std::{fs::File, io::{self, BufReader}};
use noodles_fasta as fasta;

let mut reader = File::open("reference.fa")
.map(BufReader::new)
.map(fasta::Reader::new)?;

for result in reader.records() {
let record = result?;

println!(
"{}\t{}",
record.reference_sequence_name(),
record.sequence().len()
);
}
# Ok::<(), io::Error>(())