Crate noodles_fasta

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 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()
    );
}

Re-exports

pub use self::reader::Reader;

pub use self::record::Record;

Modules

fai

FASTA index (FAI) and fields.

reader

FASTA reader and iterators.

record

FASTA record and definition.

Structs

Writer

A FASTA writer.

Functions

index

Indexes a FASTA file.