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//! Efficient FASTA reading and writing
//!
//! # Example
//!
//! This example reads some content, writes it back and compares the output
//! (should be the same):
//!
//! ```
//! use seq_io::fasta::{Reader, Record};
//!
//! let input = b">id1
//! ACGT
//! ACGT
//! >id2
//! TGCA
//! TGCA
//! ";
//!
//! let mut reader = Reader::new(&input[..]);
//! let mut output = vec![];
//!
//! while let Some(record) = reader.next() {
//! let record = record.expect("Error reading record");
//! println!("id: {}", record.id().unwrap());
//! record.write_wrap(&mut output, 4);
//! }
//!
//! assert_eq!(input, output.as_slice());
//! ```
//!
//! # Details on parsing behaviour
//!
//! * The parser handles UNIX (LF) and Windows (CRLF) line endings, but not old
//! Mac-style (CR) endings. However, FASTA writing currently always uses UNIX
//! line endings.
//! * Empty lines are allowed anywhere in the file, they will just be ignored.
//! The first non-empty line must start with `>`, indicating the first header.
//! * Whitespace at the end of header and sequence lines is never removed.
//! * If two consecutive FASTA header lines (starting with `>`) are encountered
//! without intermediate sequence line, the first record will have an empty
//! sequence. The same is true if the input ends with a header line.
//! * Empty input will result in `None` being returned immediately by
//! `fasta::Reader::next()` and in empty iterators for `RecordsIter` /
//! `RecordsIntoIter`.
//! * Comment lines starting with `;` are not supported.
//! If at the start of a file, there will be an error, since `>` is expected.
//! Intermediate comments are appended to the sequence.
use std::borrow::Cow;
use std::fs::File;
use std::io::{self, BufRead, Seek};
use std::iter;
use std::path::Path;
use std::slice;
use std::str::{self, Utf8Error};
use buffer_redux;
use memchr::Memchr;
use super::policy::{BufPolicy, StdPolicy};
use super::*;
type DefaultPolicy = StdPolicy;
const BUFSIZE: usize = 64 * 1024;
/// Parser for FASTA files.
pub struct Reader<R: io::Read, P = DefaultPolicy> {
buf_reader: buffer_redux::BufReader<R>,
buf_pos: BufferPosition,
position: Position,
search_pos: usize,
finished: bool,
buf_policy: P,
}
impl<R> Reader<R, DefaultPolicy>
where
R: io::Read,
{
/// 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"))
/// ```
#[inline]
pub fn new(reader: R) -> Reader<R, StdPolicy> {
Reader::with_capacity(reader, BUFSIZE)
}
/// Creates a new reader with a given buffer capacity. The minimum allowed
/// capacity is 3.
#[inline]
pub fn with_capacity(reader: R, capacity: usize) -> Reader<R, DefaultPolicy> {
assert!(capacity >= 3);
Reader {
buf_reader: buffer_redux::BufReader::with_capacity(capacity, reader),
buf_pos: BufferPosition {
start: 0,
seq_pos: Vec::with_capacity(1),
},
position: Position::new(0, 0),
search_pos: 0,
finished: false,
buf_policy: StdPolicy,
}
}
}
impl Reader<File, DefaultPolicy> {
/// Creates a reader from a file path.
///
/// # Example:
///
/// ```no_run
/// use seq_io::fasta::Reader;
///
/// let mut reader = Reader::from_path("seqs.fasta").unwrap();
///
/// // (... do something with the reader)
/// ```
#[inline]
pub fn from_path<P: AsRef<Path>>(path: P) -> io::Result<Reader<File>> {
File::open(path).map(Reader::new)
}
}
impl<R, P> Reader<R, P>
where
R: io::Read,
P: BufPolicy,
{
/// Returns a reader with the given buffer policy applied
#[inline]
pub fn set_policy<T: BufPolicy>(self, policy: T) -> Reader<R, T> {
Reader {
buf_reader: self.buf_reader,
buf_pos: self.buf_pos,
position: self.position,
search_pos: self.search_pos,
finished: self.finished,
buf_policy: policy,
}
}
/// Returns the `BufPolicy` of the reader
#[inline]
pub fn policy(&self) -> &P {
&self.buf_policy
}
/// Searches the next FASTA record and returns a [RefRecord](struct.RefRecord.html) that
/// borrows its data from the underlying buffer of this reader.
///
/// # Example:
///
/// ```no_run
/// 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());
/// }
/// ```
#[allow(clippy::should_implement_trait)]
#[inline]
pub fn next(&mut self) -> Option<Result<RefRecord, Error>> {
if self.finished || !self.initialized() && !try_opt!(self.init()) {
return None;
}
if !self.buf_pos.is_new() {
self.next_pos();
}
if !try_opt!(self.search()) && !try_opt!(self.next_complete()) {
return None;
}
Some(Ok(RefRecord {
buffer: self.get_buf(),
buf_pos: &self.buf_pos,
}))
}
/// Updates a [RecordSet](struct.RecordSet.html) 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.
#[inline]
pub fn read_record_set(&mut self, rset: &mut RecordSet) -> Option<Result<(), Error>> {
if self.finished {
return None;
}
if !self.initialized() {
if !try_opt!(self.init()) {
return None;
}
if !try_opt!(self.search()) {
return Some(Ok(()));
}
} else if !try_opt!(self.next_complete()) {
return None;
};
// copy buffer AFTER call to next_complete (initialization of buffer is done there)
rset.buffer.clear();
rset.buffer.extend(self.get_buf());
// Update records that are already in the positions vector
let mut n = 0;
for pos in &mut rset.positions {
n += 1;
pos.update(&self.buf_pos);
self.next_pos();
if self.finished || !try_opt!(self.search()) {
rset.npos = n;
return Some(Ok(()));
}
}
// Add more positions if necessary
loop {
n += 1;
rset.positions.push(self.buf_pos.clone());
self.next_pos();
if self.finished || !try_opt!(self.search()) {
rset.npos = n;
return Some(Ok(()));
}
}
}
// Sets starting points for next position
fn next_pos(&mut self) {
self.position.line += self.buf_pos.seq_pos.len() as u64;
self.position.byte += (self.search_pos - self.buf_pos.start) as u64;
self.buf_pos.start = self.search_pos;
self.buf_pos.seq_pos.clear();
}
fn get_buf(&self) -> &[u8] {
self.buf_reader.buffer()
}
fn initialized(&self) -> bool {
self.position.line != 0
}
// moves to the first record positon, ignoring newline characters
#[inline(never)]
fn init(&mut self) -> Result<bool, Error> {
if let Some((line_num, pos, byte)) = self.first_byte()? {
if byte == b'>' {
self.buf_pos.start = pos;
self.position.byte = pos as u64;
self.position.line = line_num as u64;
self.search_pos = pos + 1;
return Ok(true);
} else {
self.finished = true;
return Err(Error::InvalidStart {
line: line_num,
found: byte,
});
}
}
self.finished = true;
Ok(false)
}
fn first_byte(&mut self) -> Result<Option<(usize, usize, u8)>, Error> {
let mut line_num = 0;
while fill_buf(&mut self.buf_reader)? > 0 {
let mut pos = 0;
let mut last_line_len = 0;
for line in self.get_buf().split(|b| *b == b'\n') {
line_num += 1;
if !line.is_empty() && line != b"\r" {
return Ok(Some((line_num, pos, line[0])));
}
pos += line.len() + 1;
last_line_len = line.len();
}
// If an orphan '\r' is found at the end of the buffer,
// we need to move it to the start and re-search the line
self.buf_reader.consume(pos - 1 - last_line_len);
self.buf_reader.make_room();
}
Ok(None)
}
/// Finds the position of the next record
/// and returns true if found; false if end of buffer reached.
fn search(&mut self) -> Result<bool, Error> {
if self._search() {
return Ok(true);
}
// nothing found
if self.get_buf().len() < self.buf_reader.capacity() {
// EOF reached, there will be no next record
self.finished = true;
self.buf_pos.seq_pos.push(self.search_pos);
return Ok(true);
}
Ok(false)
}
// returns true if complete position found, false if end of buffer reached.
fn _search(&mut self) -> bool {
let bufsize = self.get_buf().len();
for pos in Memchr::new(b'\n', &self.buf_reader.buffer()[self.search_pos..]) {
let pos = self.search_pos + pos;
let next_line_start = pos + 1;
if next_line_start == bufsize {
// cannot check next byte -> treat as incomplete
self.search_pos = pos; // make sure last byte is re-searched next time
return false;
}
self.buf_pos.seq_pos.push(pos);
if self.get_buf()[next_line_start] == b'>' {
// complete record was found
self.search_pos = next_line_start;
return true;
}
}
// record end not found
self.search_pos = bufsize;
false
}
/// To be called when the end of the buffer is reached and `next_pos` does not find
/// the next record. Incomplete bytes will be moved to the start of the buffer.
/// If the record still doesn't fit in, the buffer will be enlarged.
/// After calling this function, the position will therefore always be 'complete'.
/// this function assumes that the buffer was fully searched
fn next_complete(&mut self) -> Result<bool, Error> {
loop {
if self.buf_pos.start == 0 {
// first record -> buffer too small
self.grow()?;
} else {
// not the first record -> buffer may be big enough
self.make_room();
}
// fill up remaining buffer
fill_buf(&mut self.buf_reader)?;
if self.search()? {
return Ok(true);
}
}
}
// grow buffer
fn grow(&mut self) -> Result<(), Error> {
let cap = self.buf_reader.capacity();
let new_size = self.buf_policy.grow_to(cap).ok_or(Error::BufferLimit)?;
let additional = new_size - cap;
self.buf_reader.reserve(additional);
Ok(())
}
// move incomplete bytes to start of buffer
fn make_room(&mut self) {
let consumed = self.buf_pos.start;
self.buf_reader.consume(consumed);
self.buf_reader.make_room();
self.buf_pos.start = 0;
self.search_pos -= consumed;
for s in &mut self.buf_pos.seq_pos {
*s -= consumed;
}
}
/// Returns the current position (useful with `seek()`).
/// If `next()` has not yet been called, `None` will be returned.
///
/// # Example
///
/// ```
/// # fn main() {
/// 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)));
/// # }
/// ```
#[inline]
pub fn position(&self) -> Option<&Position> {
if self.buf_pos.is_new() {
return None;
}
Some(&self.position)
}
/// Returns a borrowed iterator over all FASTA records. The records
/// are owned (`OwnedRecord`), this is therefore slower than using
/// `Reader::next()`.
///
/// # Example
///
/// ```
/// # fn main() {
/// 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()}
/// ]
/// );
/// # }
/// ```
#[inline]
pub fn records(&mut self) -> RecordsIter<R, P> {
RecordsIter { rdr: self }
}
/// Returns an iterator over all FASTA records like `Reader::records()`,
/// but with the difference that it owns the underlying reader.
#[inline]
pub fn into_records(self) -> RecordsIntoIter<R, P> {
RecordsIntoIter { rdr: self }
}
}
impl<R, P> Reader<R, P>
where
R: io::Read + Seek,
P: BufPolicy,
{
/// 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
///
/// ```
/// # fn main() {
/// 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);
/// # }
/// ```
#[inline]
pub fn seek(&mut self, pos: &Position) -> Result<(), Error> {
self.finished = false;
let diff = pos.byte as i64 - self.position.byte as i64;
let rel_pos = self.buf_pos.start as i64 + diff;
if rel_pos >= 0 && rel_pos < (self.get_buf().len() as i64) {
// position reachable within buffer -> no actual seeking necessary
self.search_pos = rel_pos as usize;
self.buf_pos.reset(rel_pos as usize);
self.position = pos.clone();
return Ok(());
}
self.position = pos.clone();
self.search_pos = 0;
self.buf_reader.seek(io::SeekFrom::Start(pos.byte))?;
fill_buf(&mut self.buf_reader)?;
self.buf_pos.reset(0);
Ok(())
}
}
/// Borrowed iterator of `OwnedRecord`
pub struct RecordsIter<'a, R, P = DefaultPolicy>
where
P: 'a,
R: io::Read + 'a,
{
rdr: &'a mut Reader<R, P>,
}
impl<'a, R, P> Iterator for RecordsIter<'a, R, P>
where
P: BufPolicy + 'a,
R: io::Read + 'a,
{
type Item = Result<OwnedRecord, Error>;
#[inline]
fn next(&mut self) -> Option<Self::Item> {
self.rdr.next().map(|rec| rec.map(|r| r.to_owned_record()))
}
}
/// Iterator of `OwnedRecord` that owns the underlying reader
pub struct RecordsIntoIter<R: io::Read, P = DefaultPolicy> {
rdr: Reader<R, P>,
}
impl<R, P> Iterator for RecordsIntoIter<R, P>
where
P: BufPolicy,
R: io::Read,
{
type Item = Result<OwnedRecord, Error>;
#[inline]
fn next(&mut self) -> Option<Self::Item> {
self.rdr.next().map(|rec| rec.map(|r| r.to_owned_record()))
}
}
/// Holds line number and byte offset of a FASTA record
#[derive(Debug, Clone, PartialEq, Eq, PartialOrd, Ord)]
pub struct Position {
line: u64,
byte: u64,
}
impl Position {
#[inline]
pub fn new(line: u64, byte: u64) -> Position {
Position { line, byte }
}
/// Line number (starting with 1)
#[inline]
pub fn line(&self) -> u64 {
self.line
}
/// Byte offset within the file
#[inline]
pub fn byte(&self) -> u64 {
self.byte
}
}
/// FASTA parsing error
#[derive(Debug)]
pub enum Error {
/// io::Error
Io(io::Error),
/// First non-empty line does not start with `>`
InvalidStart {
/// line number (1-based)
line: usize,
/// byte that was found instead
found: u8,
},
/// Size limit of buffer was reached, which happens if `policy::BufPolicy::grow_to()` returned
/// `None`. This does not happen with the default `struct.DoubleUntil.html` policy.
BufferLimit,
}
impl fmt::Display for Error {
#[inline]
fn fmt(&self, f: &mut fmt::Formatter) -> fmt::Result {
match *self {
Error::Io(ref e) => e.fmt(f),
Error::InvalidStart { line, found } => write!(
f,
"FASTA parse error: expected '>' but found '{}' at file start, line {}.",
(found as char).escape_default(),
line
),
Error::BufferLimit => write!(f, "FASTA parse error: buffer limit reached."),
}
}
}
impl From<io::Error> for Error {
#[inline]
fn from(e: io::Error) -> Error {
Error::Io(e)
}
}
impl error::Error for Error {
#[inline]
fn source(&self) -> Option<&(dyn error::Error + 'static)> {
match *self {
Error::Io(ref err) => Some(err),
_ => None,
}
}
}
#[derive(Clone, Debug, Serialize, Deserialize)]
struct BufferPosition {
/// index of '>'
start: usize,
/// Indicate line start, but actually it is one byte before (start - 1), which is usually
/// the line terminator of the header (if there is one). The last index in the Vec is always
/// the last byte of the last sequence line (including line terminator if present).
/// Therefore, the length of this Vec should never be 0.
seq_pos: Vec<usize>,
}
impl BufferPosition {
#[inline]
fn is_new(&self) -> bool {
self.seq_pos.is_empty()
}
#[inline]
fn reset(&mut self, start: usize) {
self.seq_pos.clear();
self.start = start;
}
#[inline]
fn update(&mut self, other: &Self) {
self.start = other.start;
self.seq_pos.clear();
self.seq_pos.extend(&other.seq_pos);
}
}
/// FASTA record trait implemented by both `RefRecord` and `OwnedRecord`
pub trait Record {
/// Return the header line of the record as byte slice
fn head(&self) -> &[u8];
/// Return the FASTA sequence as byte slice
fn seq(&self) -> &[u8];
/// Write the record to the given `io::Write` instance. The sequence will occupy one line only.
fn write<W: io::Write>(&self, writer: W) -> io::Result<()>;
/// Write the record to the given `io::Write` instance. The sequence is wrapped to produce
/// multi-line FASTA with a maximum width specified by `wrap`.
fn write_wrap<W: io::Write>(&self, writer: W, wrap: usize) -> io::Result<()>;
#[inline]
fn id_bytes(&self) -> &[u8] {
self.head().split(|b| *b == b' ').next().unwrap()
}
/// Return the ID of the record (everything before an optional space) as string slice
#[inline]
fn id(&self) -> Result<&str, Utf8Error> {
str::from_utf8(self.id_bytes())
}
#[inline]
fn desc_bytes(&self) -> Option<&[u8]> {
self.head().splitn(2, |b| *b == b' ').nth(1)
}
/// Return the description of the record as string slice, if present. Otherwise, `None` is returned.
#[inline]
fn desc(&self) -> Option<Result<&str, Utf8Error>> {
self.desc_bytes().map(str::from_utf8)
}
/// Return both the ID and the description of the record (if present)
/// This should be faster than calling `id()` and `desc()` separately.
#[inline]
fn id_desc_bytes(&self) -> (&[u8], Option<&[u8]>) {
let mut h = self.head().splitn(2, |c| *c == b' ');
(h.next().unwrap(), h.next())
}
/// Return both the ID and the description of the record (if present)
/// This should be faster than calling `id()` and `desc()` separately.
#[inline]
fn id_desc(&self) -> Result<(&str, Option<&str>), Utf8Error> {
let mut h = str::from_utf8(self.head())?.splitn(2, ' ');
Ok((h.next().unwrap(), h.next()))
}
}
/// A FASTA record that borrows data from a buffer.
#[derive(Debug, Clone)]
pub struct RefRecord<'a> {
buffer: &'a [u8],
buf_pos: &'a BufferPosition,
}
impl<'a> Record for RefRecord<'a> {
#[inline]
fn head(&self) -> &[u8] {
trim_cr(&self.buffer[self.buf_pos.start + 1..*self.buf_pos.seq_pos.first().unwrap()])
}
/// Return the FASTA sequence as byte slice.
/// Note that this method of `RefRecord` returns
/// the **raw** sequence, which may contain line breaks.
/// Use `seq_lines()` to iterate over all lines without
/// breaks, or use [`full_seq()`](struct.RefRecord.html#method.full_seq)
/// to access the whole sequence at once.
#[inline]
fn seq(&self) -> &[u8] {
if self.buf_pos.seq_pos.len() > 1 {
let start = *self.buf_pos.seq_pos.first().unwrap() + 1;
let end = *self.buf_pos.seq_pos.last().unwrap();
trim_cr(&self.buffer[start..end])
} else {
b""
}
}
#[inline]
fn write<W: io::Write>(&self, mut writer: W) -> io::Result<()> {
write_head(&mut writer, self.head())?;
write_seq_iter(&mut writer, self.seq_lines())
}
#[inline]
fn write_wrap<W: io::Write>(&self, mut writer: W, wrap: usize) -> io::Result<()> {
write_head(&mut writer, self.head())?;
write_wrap_seq_iter(&mut writer, self.seq_lines(), wrap)
}
}
impl<'a> RefRecord<'a> {
/// Return an iterator over all sequence lines in the data
#[inline]
pub fn seq_lines(&self) -> SeqLines {
SeqLines {
data: self.buffer,
len: self.buf_pos.seq_pos.len() - 1,
pos_iter: self
.buf_pos
.seq_pos
.iter()
.zip(self.buf_pos.seq_pos.iter().skip(1)),
}
}
/// Returns the number of sequence lines.
/// Equivalent to `self.seq_lines().len()`
#[inline]
pub fn num_seq_lines(&self) -> usize {
self.seq_lines().len()
}
/// Returns the full sequence. If the sequence consists of a single line,
/// then the sequence will be borrowed from the underlying buffer
/// (equivalent to calling `RefRecord::seq()`). If there are multiple
/// lines, an owned copy will be created (equivalent to `RefRecord::owned_seq()`).
#[inline]
pub fn full_seq(&self) -> Cow<[u8]> {
if self.num_seq_lines() == 1 {
// only one line
self.seq().into()
} else {
self.owned_seq().into()
}
}
/// Returns the sequence as owned `Vec`. **Note**: This function
/// must be called in order to obtain a sequence that does not contain
/// line endings (as returned by `seq()`)
#[inline]
pub fn owned_seq(&self) -> Vec<u8> {
let mut seq = Vec::new();
for segment in self.seq_lines() {
seq.extend(segment);
}
seq
}
/// Creates an owned copy of the record.
#[inline]
pub fn to_owned_record(&self) -> OwnedRecord {
OwnedRecord {
head: self.head().to_vec(),
seq: self.owned_seq(),
}
}
/// Writes a record to the given `io::Write` instance
/// by just writing the unmodified input, which is faster than `RefRecord::write`
#[inline]
pub fn write_unchanged<W: io::Write>(&self, mut writer: W) -> io::Result<()> {
let data = &self.buffer[self.buf_pos.start..*self.buf_pos.seq_pos.last().unwrap()];
writer.write_all(data)?;
if *data.last().unwrap() != b'\n' {
writer.write_all(&[b'\n'])?;
}
Ok(())
}
}
/// Iterator over sequence the lines of a FASTA record.
pub struct SeqLines<'a> {
data: &'a [u8],
len: usize,
pos_iter: iter::Zip<slice::Iter<'a, usize>, iter::Skip<slice::Iter<'a, usize>>>,
}
impl<'a> Iterator for SeqLines<'a> {
type Item = &'a [u8];
#[inline]
fn next(&mut self) -> Option<&'a [u8]> {
self.pos_iter
.next()
.map(|(start, next_start)| trim_cr(&self.data[*start + 1..*next_start]))
}
#[inline]
fn size_hint(&self) -> (usize, Option<usize>) {
let l = self.len();
(l, Some(l))
}
}
impl<'a> DoubleEndedIterator for SeqLines<'a> {
#[inline]
fn next_back(&mut self) -> Option<&'a [u8]> {
self.pos_iter
.next_back()
.map(|(start, next_start)| trim_cr(&self.data[*start + 1..*next_start]))
}
}
impl<'a> ExactSizeIterator for SeqLines<'a> {
#[inline]
fn len(&self) -> usize {
self.len
}
}
/// A FASTA record that ownes its data (requiring two allocations)
#[derive(Debug, Clone, PartialEq, Eq, Serialize, Deserialize)]
pub struct OwnedRecord {
pub head: Vec<u8>,
pub seq: Vec<u8>,
}
impl Record for OwnedRecord {
#[inline]
fn head(&self) -> &[u8] {
&self.head
}
#[inline]
fn seq(&self) -> &[u8] {
&self.seq
}
#[inline]
fn write<W: io::Write>(&self, writer: W) -> io::Result<()> {
write_to(writer, &self.head, &self.seq)
}
#[inline]
fn write_wrap<W: io::Write>(&self, mut writer: W, wrap: usize) -> io::Result<()> {
write_head(&mut writer, &self.head)?;
write_wrap_seq(&mut writer, &self.seq, wrap)
}
}
/// Set of FASTA records that owns it'P buffer
/// and knows the positions of each record.
#[derive(Default, Clone, Debug, Serialize, Deserialize)]
pub struct RecordSet {
buffer: Vec<u8>,
positions: Vec<BufferPosition>,
npos: usize,
}
impl<'a> iter::IntoIterator for &'a RecordSet {
type Item = RefRecord<'a>;
type IntoIter = RecordSetIter<'a>;
#[inline]
fn into_iter(self) -> Self::IntoIter {
RecordSetIter {
buffer: &self.buffer,
pos: self.positions.iter().take(self.npos),
}
}
}
/// Iterator over record sets
pub struct RecordSetIter<'a> {
buffer: &'a [u8],
pos: iter::Take<slice::Iter<'a, BufferPosition>>,
}
impl<'a> Iterator for RecordSetIter<'a> {
type Item = RefRecord<'a>;
#[inline]
fn next(&mut self) -> Option<RefRecord<'a>> {
self.pos.next().map(|p| RefRecord {
buffer: self.buffer,
buf_pos: p,
})
}
}
/// Writes data (not necessarily stored in a `Record` instance) to the FASTA format.
#[inline]
pub fn write_to<W>(mut writer: W, head: &[u8], seq: &[u8]) -> io::Result<()>
where
W: io::Write,
{
write_head(&mut writer, head)?;
write_seq(&mut writer, seq)
}
/// Writes data to the FASTA format. ID and description parts of the header are supplied
/// separately instead of a whole header line.
#[inline]
pub fn write_parts<W>(mut writer: W, id: &[u8], desc: Option<&[u8]>, seq: &[u8]) -> io::Result<()>
where
W: io::Write,
{
write_id_desc(&mut writer, id, desc)?;
write_seq(&mut writer, seq)
}
/// Writes data to the FASTA format. Wraps the sequence to produce multi-line FASTA
/// with a maximum width specified by the `wrap` parameter.
#[inline]
pub fn write_wrap<W>(
mut writer: W,
id: &[u8],
desc: Option<&[u8]>,
seq: &[u8],
wrap: usize,
) -> io::Result<()>
where
W: io::Write,
{
write_id_desc(&mut writer, id, desc)?;
write_wrap_seq(&mut writer, seq, wrap)
}
/// Writes only the sequence header.
#[inline]
pub fn write_head<W>(mut writer: W, head: &[u8]) -> io::Result<()>
where
W: io::Write,
{
writer.write_all(b">")?;
writer.write_all(head)?;
writer.write_all(b"\n")
}
/// Writes only the sequence header given ID and description parts.
#[inline]
pub fn write_id_desc<W>(mut writer: W, id: &[u8], desc: Option<&[u8]>) -> io::Result<()>
where
W: io::Write,
{
writer.write_all(b">")?;
writer.write_all(id)?;
if let Some(d) = desc {
writer.write_all(b" ")?;
writer.write_all(d)?;
}
writer.write_all(b"\n")
}
/// Writes only the sequence line.
#[inline]
pub fn write_seq<W>(mut writer: W, seq: &[u8]) -> io::Result<()>
where
W: io::Write,
{
writer.write_all(seq)?;
writer.write_all(b"\n")
}
/// Writes the sequence line, and wraps the output to a maximum width specified by `wrap`.
#[inline]
pub fn write_wrap_seq<W>(mut writer: W, seq: &[u8], wrap: usize) -> io::Result<()>
where
W: io::Write,
{
assert!(wrap > 0);
for chunk in seq.chunks(wrap) {
writer.write_all(chunk)?;
writer.write_all(b"\n")?;
}
Ok(())
}
/// Writes the sequence line from an iterator (such as `SeqLines`)
#[inline]
pub fn write_seq_iter<'a, W, P>(mut writer: W, seq: P) -> io::Result<()>
where
W: io::Write,
P: Iterator<Item = &'a [u8]>,
{
for subseq in seq {
writer.write_all(subseq)?;
}
writer.write_all(b"\n")
}
/// Writes the sequence line from an iterator (such as `SeqLines`) and wraps the output
/// to a maximum width specified by `wrap`.
#[inline]
pub fn write_wrap_seq_iter<'a, W, P>(mut writer: W, seq: P, wrap: usize) -> io::Result<()>
where
W: io::Write,
P: IntoIterator<Item = &'a [u8]>,
{
assert!(wrap > 0);
let mut n_line = 0;
for subseq in seq {
let mut chunk = subseq;
loop {
let remaining = wrap - n_line;
if chunk.len() <= remaining {
writer.write_all(chunk)?;
n_line += chunk.len();
break;
}
// chunk longer than line -> break
let (line, rest) = chunk.split_at(remaining);
chunk = rest;
writer.write_all(line)?;
writer.write_all(b"\n")?;
n_line = 0;
}
}
writer.write_all(b"\n")?;
Ok(())
}