Struct bio::io::fasta::Reader

pub struct Reader<B> { /* private fields */ }

A FASTA reader.

Implementations

impl Reader<BufReader<File>>

pub fn from_file<P: AsRef<Path> + Debug>(path: P) -> Result<Self>

Read FASTA from given file path.

pub fn from_file_with_capacity<P: AsRef<Path> + Debug>(
    capacity: usize,
    path: P
) -> Result<Self>

Read FASTA from give file path and a capacity

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

pub fn new(reader: R) -> Self

Create a new Fasta reader given an instance of io::Read.

Example

let reader = Reader::new(fasta_file);

pub fn with_capacity(capacity: usize, reader: R) -> Self

Create a new Fasta reader given a capacity and an instance of io::Read.

Example

let reader = Reader::with_capacity(16384, fasta_file);

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

pub fn from_bufread(bufreader: B) -> Self

Create a new Fasta reader with an object that implements io::BufRead.

Example

let buffer = io::BufReader::with_capacity(16384, fasta_file);
let reader = Reader::from_bufread(buffer);

pub fn records(self) -> Records<B>

Return an iterator over the records of this Fasta file.

Example

for record in reader.records() {
    let record = record.unwrap();
    assert_eq!(record.id(), "id");
    assert_eq!(record.desc().unwrap(), "desc");
    assert_eq!(record.seq().to_vec(), b"AAAA");
}

Trait Implementations

impl<B: Debug> Debug for Reader<B>

fn fmt(&self, f: &mut Formatter<'_>) -> Result

Formats the value using the given formatter.

impl<B> FastaRead for Reader<B> where
    B: BufRead, 

fn read(&mut self, record: &mut Record) -> Result<()>

Read the next FASTA record into the given Record. An empty record indicates that no more records can be read.

Use this method when you want to read records as fast as possible because it allows the reuse of a Record allocation.

The records iterator provides a more ergonomic approach to accessing FASTA records.

Errors

This function will return an error if the record is incomplete, syntax is violated or any form of I/O error is encountered.

Example

use bio::io::fasta::Record;
use bio::io::fasta::{FastaRead, Reader};

const fasta_file: &'static [u8] = b">id desc
AAAA
";
let mut reader = Reader::new(fasta_file);
let mut record = Record::new();

// Check for errors parsing the record
reader
    .read(&mut record)
    .expect("fasta reader: got an io::Error or could not read_line()");

assert_eq!(record.id(), "id");
assert_eq!(record.desc().unwrap(), "desc");
assert_eq!(record.seq().to_vec(), b"AAAA");