pub struct Reader<R: Read, P = StdPolicy> { /* private fields */ }
Expand description
Parser for FASTA files.
Implementations§
source§impl<R> Reader<R, StdPolicy>where
R: Read,
impl<R> Reader<R, StdPolicy>where R: Read,
sourcepub fn new(reader: R) -> Reader<R, StdPolicy>
pub fn new(reader: R) -> Reader<R, StdPolicy>
Creates a new reader with the default buffer size of 64 KiB
Example:
use seq_io::fasta::{Reader,Record};
let fasta = b">id\nSEQUENCE";
let mut reader = Reader::new(&fasta[..]);
let record = reader.next().unwrap().unwrap();
assert_eq!(record.id(), Ok("id"))
sourcepub fn with_capacity(reader: R, capacity: usize) -> Reader<R, StdPolicy>
pub fn with_capacity(reader: R, capacity: usize) -> Reader<R, StdPolicy>
Creates a new reader with a given buffer capacity. The minimum allowed capacity is 3.
source§impl<R, P> Reader<R, P>where
R: Read,
P: BufPolicy,
impl<R, P> Reader<R, P>where R: Read, P: BufPolicy,
sourcepub fn set_policy<T: BufPolicy>(self, policy: T) -> Reader<R, T>
pub fn set_policy<T: BufPolicy>(self, policy: T) -> Reader<R, T>
Returns a reader with the given buffer policy applied
sourcepub fn next(&mut self) -> Option<Result<RefRecord<'_>, Error>>
pub fn next(&mut self) -> Option<Result<RefRecord<'_>, Error>>
Searches the next FASTA record and returns a RefRecord that borrows its data from the underlying buffer of this reader.
Example:
use seq_io::fasta::{Reader,Record};
let mut reader = Reader::from_path("seqs.fasta").unwrap();
while let Some(record) = reader.next() {
let record = record.unwrap();
println!("{}", record.id().unwrap());
}
sourcepub fn read_record_set(
&mut self,
rset: &mut RecordSet
) -> Option<Result<(), Error>>
pub fn read_record_set( &mut self, rset: &mut RecordSet ) -> Option<Result<(), Error>>
Updates a RecordSet with new data. The contents of the internal
buffer are just copied over to the record set and the positions of all records are found.
Old data will be erased. Returns None
if the input reached its end.
sourcepub fn position(&self) -> Option<&Position>
pub fn position(&self) -> Option<&Position>
Returns the current position (useful with seek()
).
If next()
has not yet been called, None
will be returned.
Example
use seq_io::fasta::{Reader,Position};
let fasta = b">id1
ACGT
>id2
TGCA";
let mut reader = Reader::new(&fasta[..]);
// skip one record
reader.next().unwrap();
// second position
reader.next().unwrap();
assert_eq!(reader.position(), Some(&Position::new(3, 10)));
sourcepub fn records(&mut self) -> RecordsIter<'_, R, P> ⓘ
pub fn records(&mut self) -> RecordsIter<'_, R, P> ⓘ
Returns a borrowed iterator over all FASTA records. The records
are owned (OwnedRecord
), this is therefore slower than using
Reader::next()
.
Example
use seq_io::fasta::{Reader,OwnedRecord};
let fasta = b">id1
ACGT
>id2
TGCA";
let mut reader = Reader::new(&fasta[..]);
let records: Result<Vec<_>, _> = reader
.records()
.collect();
assert_eq!(records.unwrap(),
vec![
OwnedRecord {head: b"id1".to_vec(), seq: b"ACGT".to_vec()},
OwnedRecord {head: b"id2".to_vec(), seq: b"TGCA".to_vec()}
]
);
sourcepub fn into_records(self) -> RecordsIntoIter<R, P> ⓘ
pub fn into_records(self) -> RecordsIntoIter<R, P> ⓘ
Returns an iterator over all FASTA records like Reader::records()
,
but with the difference that it owns the underlying reader.
source§impl<R, P> Reader<R, P>where
R: Read + Seek,
P: BufPolicy,
impl<R, P> Reader<R, P>where R: Read + Seek, P: BufPolicy,
sourcepub fn seek(&mut self, pos: &Position) -> Result<(), Error>
pub fn seek(&mut self, pos: &Position) -> Result<(), Error>
Seeks to a specified position. Keeps the underyling buffer if the seek position is
found within it, otherwise it has to be discarded.
If an error was returned before, seeking to that position will return the same error.
The same is not always true with None
. If there is no newline character at the end of the
file, the last record will be returned instead of None
.
Example
use seq_io::fasta::{Reader,Position,OwnedRecord};
use std::io::Cursor;
let fasta = b">id1
ACGT
>id2
TGCA";
let mut cursor = Cursor::new(&fasta[..]);
let mut reader = Reader::new(cursor);
// read the first record and get its position
let record1 = reader.next().unwrap().unwrap().to_owned_record();
let pos1 = reader.position().unwrap().to_owned();
// read the second record
reader.next().unwrap().unwrap();
// now seek to position of first record
reader.seek(&pos1);
assert_eq!(reader.next().unwrap().unwrap().to_owned_record(), record1);