Struct noodles_fasta::reader::Reader

pub struct Reader<R> { /* fields omitted */ }

A FASTA reader.

Implementations

impl<R> Reader<R> where
    R: BufRead, 

pub fn new(inner: R) -> Self

Creates a FASTA reader.

Examples

use noodles_fasta as fasta;
let data = b">sq0\nACGT\n>sq1\nNNNN\nNNNN\nNN\n";
let mut reader = fasta::Reader::new(&data[..]);

pub fn read_definition(&mut self, buf: &mut String) -> Result<usize>

Reads a raw definition line.

The given buffer will not include the trailing newline. It can subsequently be parsed as a crate::record::Definition.

The position of the stream is expected to be at the start or at the start of another definition.

If successful, this returns the number of bytes read from the stream. If the number of bytes read is 0, the stream reached EOF.

Examples

use noodles_fasta as fasta;

let data = b">sq0\nACGT\n>sq1\nNNNN\nNNNN\nNN\n";
let mut reader = fasta::Reader::new(&data[..]);

let mut buf = String::new();
reader.read_definition(&mut buf)?;

assert_eq!(buf, ">sq0");

pub fn read_sequence(&mut self, buf: &mut Vec<u8>) -> Result<usize>

Reads a sequence.

The given buffer consumes a sequence without newlines until another definition or EOF is reached.

The position of the stream is expected to be at the start of a sequence, which is directly after a definition.

If successful, this returns the number of bytes read from the stream. If the number of bytes read is 0, the stream reached EOF (though this case is likely an error).

Examples

use noodles_fasta as fasta;

let data = b">sq0\nACGT\n>sq1\nNNNN\nNNNN\nNN\n";
let mut reader = fasta::Reader::new(&data[..]);
reader.read_definition(&mut String::new())?;

let mut buf = Vec::new();
reader.read_sequence(&mut buf)?;

assert_eq!(buf, b"ACGT");

pub fn records(&mut self) -> Records<'_, R>

Returns an iterator over records starting from the current stream position.

The position of the stream is expected to be at the start or at the start of another definition.

use noodles_fasta::{self as fasta, record::{Definition, Sequence}};

let data = b">sq0\nACGT\n>sq1\nNNNN\nNNNN\nNN\n";
let mut reader = fasta::Reader::new(&data[..]);

let mut records = reader.records();

assert_eq!(records.next().transpose()?, Some(fasta::Record::new(
    Definition::new("sq0", None),
    Sequence::from(b"ACGT".to_vec()),
)));

assert_eq!(records.next().transpose()?, Some(fasta::Record::new(
    Definition::new("sq1", None),
    Sequence::from(b"NNNNNNNNNN".to_vec()),
)));

assert!(records.next().is_none());

impl<R> Reader<Reader<R>> where
    R: Read, 

pub fn virtual_position(&self) -> VirtualPosition

Returns the current virtual position of the underlying BGZF reader.

Examples

use noodles_bgzf as bgzf;
use noodles_fasta as fasta;

let data = Vec::new();
let reader = fasta::Reader::new(bgzf::Reader::new(&data[..]));
let virtual_position = reader.virtual_position();

assert_eq!(virtual_position.compressed(), 0);
assert_eq!(virtual_position.uncompressed(), 0);

impl<R> Reader<R> where
    R: BufRead + Seek, 

pub fn query(&mut self, index: &[Record], region: &Region) -> Result<Record>

Returns a record of the given region.

Examples

use noodles_core::Region;
use noodles_fasta::{self as fasta, fai, record::{Definition, Sequence}};

let data = b">sq0\nNNNN\n>sq1\nACGT\n>sq2\nNNNN\n";
let index = vec![
    fai::Record::new(String::from("sq0"), 4, 5, 4, 5),
    fai::Record::new(String::from("sq1"), 4, 15, 4, 5),
    fai::Record::new(String::from("sq2"), 4, 25, 4, 5),
];

let mut reader = fasta::Reader::new(Cursor::new(data));

let region = Region::mapped("sq1", ..);
let record = reader.query(&index, &region)?;
assert_eq!(record, fasta::Record::new(
    Definition::new("sq1", None),
    Sequence::from(b"ACGT".to_vec()),
));

let region = Region::mapped("sq1", 2..=3);
let record = reader.query(&index, &region)?;
assert_eq!(record, fasta::Record::new(
    Definition::new("sq1:2-3", None),
    Sequence::from(b"CG".to_vec()),
));

impl<R> Reader<Reader<R>> where
    R: Read + Seek, 

pub fn seek(&mut self, pos: VirtualPosition) -> Result<VirtualPosition>

Seeks the underlying BGZF stream to the given virtual position.

Virtual positions typically come from an associated index.

Examples

use noodles_bgzf as bgzf;
use noodles_fasta as fasta;

let mut reader = File::open("sample.fa.gz")
    .map(bgzf::Reader::new)
    .map(fasta::Reader::new)?;

let virtual_position = bgzf::VirtualPosition::from(102334155);
reader.seek(virtual_position)?;

Trait Implementations

impl<R> Seek for Reader<R> where
    R: Read + Seek, 

fn seek(&mut self, pos: SeekFrom) -> Result<u64>

Seeks the underlying stream to the given position.

These positions typically come from an associated index, which start at the sequence and not the definition.

Examples

use noodles_fasta as fasta;

let data = b">sq0\nACGT\n>sq1\nNNNN\nNNNN\nNN\n";
let cursor = Cursor::new(&data[..]);
let mut reader = fasta::Reader::new(cursor);
reader.seek(SeekFrom::Start(14));

let mut buf = Vec::new();
reader.read_sequence(&mut buf)?;

assert_eq!(buf, b"NNNNNNNNNN");

fn rewind(&mut self) -> Result<(), Error>

Rewind to the beginning of a stream.

fn stream_len(&mut self) -> Result<u64, Error>

🔬 This is a nightly-only experimental API. (seek_stream_len)

Returns the length of this stream (in bytes).

fn stream_position(&mut self) -> Result<u64, Error>

Returns the current seek position from the start of the stream.