Struct needletail::parser::FastaReader

pub struct FastaReader<R: Read> { /* private fields */ }

Parser for FASTA files. Only use this directly if you know your file is FASTA and that it is not compressed as it does not handle decompression. If you are unsure, it’s better to use parse_fastx_file.

Implementations

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

pub fn new(reader: R) -> Reader<R>

Creates a new reader with the default buffer size of 64 KiB

Example:

use needletail::parser::{FastaReader, FastxReader};
let fasta = b">id\nSEQUENCE";

let mut reader = FastaReader::new(&fasta[..]);
let record = reader.next().unwrap().unwrap();
assert_eq!(record.id(), b"id")

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

Creates a new reader with a given buffer capacity. The minimum allowed capacity is 3.

impl Reader<File>

pub fn from_path<P: AsRef<Path>>(path: P) -> Result<Reader<File>>

Creates a reader from a file path.

Example:

use needletail::parser::{FastaReader, FastxReader};

let mut reader = FastaReader::from_path("seqs.fasta").unwrap();

// (... do something with the reader)

Trait Implementations

impl<R: Read + Send> FastxReader for Reader<R>

fn next(&mut self) -> Option<Result<SequenceRecord<'_>, ParseError>>

Gets the next record in the stream. This imitates the Iterator API but does not support any iterator functions. This returns None once we reached the EOF.

fn position(&self) -> &Position

Returns the current line/byte in the stream we are reading from

fn line_ending(&self) -> Option<LineEnding>

Returns whether the current stream uses Windows or Unix style line endings It is None only before calling next, once next has been called it will always return a line ending.