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::io::Reader::new)?;

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

Re-exports

pub use self::io::indexed_reader;

pub use self::io::reader;

pub use self::io::writer;

pub use self::record::Record;

pub use self::repository::Repository;

pub use self::fs::index;

pub use self::io::IndexedReader;

pub use self::io::Reader;

pub use self::io::Writer;

pub use self::async::io::Reader as AsyncReader;

Modules

async

Async FASTA.

fai

FASTA index (FAI) and fields.

fs

FASTA filesystem operations.

io

FASTA I/O.

record

FASTA record and definition.

repository

Sequence repository and adapters.

sequence

Sequence format.