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//! This module provides types and functions for FASTX reading via dynamic //! dispatch. //! //! In contrast to [`fastx::Reader`](crate::fastx::Reader), which has an API //! equivalent to [`fasta::Reader`](crate::fasta::Reader) and //! [`fastq::Reader`](crate::fastq::Reader), this module provides the traits //! [`FastxReader`](FastxReader) and [`FastxSeekReader`](FastxSeekReader). //! These are implemented for all readers in the `fasta` and `fastq` modules. //! //! # Example //! //! This example uses the [`reader`](reader) function to obtain a //! [`Box<dyn FastxReader<...>`](FastxReader). The format is recognized based //! on the first byte of the first non-empty line, and an appropriate reader //! for the format is chosen and returned: //! //! ```rust //! use seq_io::prelude::*; //! use seq_io::fastx::dynamic::reader; //! use seq_io::fastx::SeqFormat; //! //! # fn main() { //! let fasta = b">id //! SEQUENCE //! "; //! //! let mut fasta_rdr = reader(&fasta[..], false).unwrap().expect("input empty"); //! // The format should be correctly recognized //! assert_eq!(fasta_rdr.format(), Some(SeqFormat::FASTA)); //! //! // The 'next' method is called 'next_fastx' here to prevent name clashes: //! let record = fasta_rdr.next_fastx().unwrap().unwrap(); //! assert_eq!(record.id(), Ok("id")); //! # } //! ``` //! //! An example with FASTQ: //! //! ```rust //! # use seq_io::prelude::*; //! # use seq_io::fastx::dynamic::reader; //! # use seq_io::fastx::SeqFormat; //! # fn main() { //! let fastq = b" //! @id //! SEQUENCE //! + //! QUALITYY //! "; //! //! let mut fastq_rdr = reader(&fastq[..], false).unwrap().expect("input empty"); //! // The format should be correctly recognized //! assert_eq!(fastq_rdr.format(), Some(SeqFormat::FASTQ)); //! //! // The 'next' method is called 'next_fastx' here to prevent name clashes: //! let record = fastq_rdr.next_fastx().unwrap().unwrap(); //! assert_eq!(record.id(), Ok("id")); //! # } //! ``` //! //! Empty input will lead to `None`: //! //! ```rust //! # use seq_io::prelude::*; //! # use seq_io::fastx::dynamic::reader; //! # use seq_io::fastx::SeqFormat; //! # fn main() { //! let empty_lines = b" //! //! //! "; //! //! assert!(reader(&empty_lines[..], false).unwrap().is_none()); //! # } //! ``` //! //! # Using ReaderBuilder //! //! [`ReaderBuilder`](ReaderBuilder) allows for applying different configuration //! options before the actual reader is created. This is different from the //! usual API in this crate, where reader options can be changed after creation. //! //! This example applies several non-default settings at once: //! //! ```rust //! use seq_io::fastx::dynamic::ReaderBuilder; //! use seq_io::fastx::SeqFormat; //! use seq_io::policy::DoubleUntil; //! //! # fn main() { //! let fastq = b" //! @id //! SEQUENCE //! + //! QUALITYY //! "; //! //! let policy = DoubleUntil(16 * 1024 * 1024); //! let capacity = 32 * 1024 * 1024; //! //! let mut reader = ReaderBuilder::new() //! .set_policy(policy) //! .set_capacity(capacity) //! .set_multiline_fastq(true) //! .from_reader(&fastq[..]) //! .unwrap() //! .expect("empty input"); //! //! assert_eq!(reader.format(), Some(SeqFormat::FASTQ)); //! # } //! ``` //! //! Another use of `ReaderBuilder` is to construct a //! [`FastxSeekReader`](FastxSeekReader) from a source other than [`File`](std::fs::File) //! (in which case you could use [`from_path`](from_path)): //! //! ```rust //! use seq_io::prelude::*; //! use seq_io::fastx::dynamic::ReaderBuilder; //! use std::io::Cursor; //! //! # fn main() { //! let fastq = b" //! >id1 //! SEQUENCE1 //! >id2 //! SEQUENCE2 //! "; //! let input = Cursor::new(&fastq[..]); //! //! let mut reader = ReaderBuilder::new() //! .from_seekable(input) //! .unwrap() //! .expect("empty input"); //! //! // first record //! let rec1 = reader.next_fastx().unwrap().expect("no record"); //! let id1 = rec1.id().unwrap().to_owned(); //! let pos1 = reader.position_fastx(); //! //! // proceed to second record //! let _ = reader.next_fastx().unwrap().expect("no record"); //! assert!(reader.next_fastx().is_none()); //! //! // now seek back //! reader.seek_fastx(&pos1); //! let rec1_again = reader.next_fastx().unwrap().expect("no record"); //! assert_eq!(rec1_again.id().unwrap(), &id1); //! # } //! ``` use std::convert::AsRef; use std::fs::File; use std::io; use std::marker::PhantomData; use std::path::Path; use crate::core::{BufReader, PositionStore, BUFSIZE}; use crate::fastx::{recognize_format, LineStore, SeqFormat}; use crate::policy::{BufPolicy, StdPolicy}; use crate::{fasta, fastq}; pub use super::error::{Error, Result}; pub use super::record::{OwnedRecord, Record, RecordSet, RefRecord}; /// Recognizes the sequence format of the input and returns an appropriate FASTA /// or FASTQ reader as [`Box<dyn FastxReader<...>`](FastxReader) or `None` if /// the input has only empty lines. /// /// `reader` is a convenience function for the most frequent case. If options /// need to be changed, use [`ReaderBuilder`](ReaderBuilder). The following two /// calls are equivalent: /// /// ```rust ignore /// // using the reader() function: /// let reader = seq_io::fastx::dynamic::reader(rdr, multiline_fastq).unwrap(); /// /// // using the builder API: /// let reader = ReaderBuilder::new() /// .set_multiline_fastq(multiline_fastq) /// .from_reader(rdr) /// .unwrap(); /// ``` /// /// If the first non-empty line starts with `>`, a /// [`fasta::Reader`](crate::fasta::Reader) is returned. If it starts with /// `@`, [`fastq::Reader`](crate::fastq::Reader) is returned if /// `multiline_fastq` is `false`, otherwise /// [`fastq::multiline::Reader`](crate::fastq::multiline::Reader) is returned, /// If the first non-empty line contains an invalid start byte, an error with /// `ErrorKind::InvalidStart` will be returned. pub fn reader<'s, R>( reader: R, multiline_fastq: bool, ) -> Result<Option<Box<dyn FastxReader<R, StdPolicy, LineStore> + 's>>> where R: io::Read + 's, { ReaderBuilder::new() .set_multiline_fastq(multiline_fastq) .from_reader(reader) } /// Recognizes the sequence format of the file and returns an appropriate FASTA /// or FASTQ reader as [`Box<dyn FastxSeekReader<...>`](FastxSeekReader) or `None` if /// the input has only empty lines. See [`reader`](reader) for more information /// about the behaviour. pub fn from_path<'s, P>( path: P, multiline_fastq: bool, ) -> Result<Option<Box<dyn FastxSeekReader<File, StdPolicy, LineStore> + 's>>> where P: AsRef<Path> + 's, { ReaderBuilder::new() .set_multiline_fastq(multiline_fastq) .from_path(path) } macro_rules! get_reader { ($builder:ident, $reader:expr, $ReaderType:ident) => {{ let mut buf_reader = BufReader::with_capacity($reader, $builder.capacity); recognize_format(&mut buf_reader)? .map(|(fmt, (byte, line))| { let out: Box<dyn $ReaderType<_, _, _>> = match fmt { SeqFormat::FASTA => Box::new( fasta::Reader::from_buf_reader(buf_reader, byte, line) .set_policy($builder.buf_policy) .set_store(), ), SeqFormat::FASTQ => { if $builder.multiline_fastq { Box::new( fastq::multiline::Reader::from_buf_reader(buf_reader, byte, line) .set_policy($builder.buf_policy) .set_store(), ) } else { // println!("new fastq {} {}", byte, line); Box::new( fastq::Reader::from_buf_reader(buf_reader, byte, line) .set_policy($builder.buf_policy) .set_store(), ) } } }; Ok(out) }) .transpose() }}; } /// Allows building a [`FastxReader`](FastxReader) /// or [`FastxSeekReader`](FastxReader) /// with various configuration options. #[derive(Debug)] pub struct ReaderBuilder<P: BufPolicy = StdPolicy, S: PositionStore = LineStore> { buf_policy: P, _store: PhantomData<S>, capacity: usize, multiline_fastq: bool, } impl ReaderBuilder { /// Creates a new `ReaderBuilder` #[inline] pub fn new() -> Self { ReaderBuilder { buf_policy: StdPolicy, _store: PhantomData, capacity: BUFSIZE, multiline_fastq: false, } } } impl<P, S> ReaderBuilder<P, S> where P: BufPolicy, S: PositionStore, { /// Creates a new [`FastxReader`](FastxReader) /// with the current configuration of the builder. /// See [`reader`](reader) for more information about the behaviour. #[inline] pub fn from_reader<'s, R>(self, reader: R) -> Result<Option<Box<dyn FastxReader<R, P, S> + 's>>> where R: io::Read + 's, P: 's, S: 's, { get_reader!(self, reader, FastxReader) } /// Creates a new [`FastxSeekReader`](FastxSeekReader) from the given path /// with the current configuration of the builder. #[inline] pub fn from_path<'s, Q>( self, path: Q, ) -> Result<Option<Box<dyn FastxSeekReader<File, P, S> + 's>>> where Q: AsRef<Path> + 's, P: 's, S: 's, { let f = File::open(path)?; self.from_seekable(f) } /// Creates a new [`FastxSeekReader`](FastxSeekReader) /// with the current configuration of the builder. #[inline] pub fn from_seekable<'s, R>( self, reader: R, ) -> Result<Option<Box<dyn FastxSeekReader<R, P, S> + 's>>> where R: io::Read + io::Seek + 's, P: 's, S: 's, { get_reader!(self, reader, FastxSeekReader) } /// Creates a new reader with a given /// [`core::PositionStore`](crate::core::PositionStore) /// as defined in the type argument of the method. The method consumes /// the reader and returns a new `Reader` instance. #[inline] pub fn set_store<T: crate::core::PositionStore>(self) -> ReaderBuilder<P, T> { ReaderBuilder { buf_policy: self.buf_policy, _store: PhantomData, capacity: self.capacity, multiline_fastq: self.multiline_fastq, } } /// Applies a [`BufPolicy`](crate::policy::BufPolicy) to the /// current reader. The method consumes the reader and returns a new /// `Reader` instance. #[inline] pub fn set_policy<T: crate::policy::BufPolicy>(self, buf_policy: T) -> ReaderBuilder<T, S> { ReaderBuilder { buf_policy, _store: self._store, capacity: self.capacity, multiline_fastq: self.multiline_fastq, } } /// Sets a reader capacity. #[inline] pub fn set_capacity(mut self, cap: usize) -> Self { self.capacity = cap; self } /// Sets whether multi-line FASTQ should be recognized by the reader. /// If `true`, the final reader will be /// [`fastq::multiline::Reader`](crate::fastq::multiline::Reader) /// in the case of FASTQ input. #[inline] pub fn set_multiline_fastq(mut self, multiline: bool) -> Self { self.multiline_fastq = multiline; self } } /// Trait for FASTX reading. /// /// Provides the same methods as individual `Reader` types, but in contrast of /// returning / operating on different `RefRecord` / `RecordSet` / /// `RecordsIter` ... types, types from the `fastx` module are used, allowing /// for FASTX functionality with dynamic dispatch. pub trait FastxReader<R, P, S> where R: io::Read, P: BufPolicy, S: PositionStore, { /// Returns the next [`fastx::RefRecord`](crate::fastx::RefRecord), if any. fn next_fastx(&mut self) -> Option<Result<RefRecord<S>>>; /// Updates a [`fastx::RecordSet`](crate::fastx::RecordSet) with new data. fn read_record_set_fastx(&mut self, record_set: &mut RecordSet<S>) -> Result<bool>; /// Returns the sequence format (`SeqFormat::FASTA` or `SeqFormat::FASTQ`) /// if known. For FASTA / FASTQ readers, the format is known in the /// beginning already, for FASTX readers, a first record has to be returned /// successfully (without error) before the format can be known. /// If not able to call this method in the middle of a parsing process /// because of borrowing issues, there is also /// [`has_quality()`](crate::BaseRecord::has_quality) /// method, which can be called on individual sequence records and /// essentially gives the same information. fn format(&self) -> Option<SeqFormat>; /// Returns a borrowed iterator over all records. fn fastx_records(&mut self) -> RecordsIter<R, P, S>; /// Returns an iterator over all records like `FastxReader::records()`, /// but with the difference that it owns the underlying reader. fn into_fastx_records<'a>(self) -> RecordsIntoIter<'a, R, P, S> where R: 'a, P: 'a, S: 'a; /// Returns the position of the current record (found by the previous call /// to [`next_fastx()`](#next_fastx)). Equivalent to the `position()` method /// of individual readers. Useful with [`seek_fastx()`](FastxSeekReader). fn position_fastx(&self) -> crate::Position; } // TODO: implementation for box not needed? // impl<'a, R, P, S> FastxReader<R, P, S> for Box<dyn FastxReader<R, P, S> + 'a> // where // R: io::Read, // P: BufPolicy, // S: PositionStore, // { // fn next_fastx(&mut self) -> Option<Result<RefRecord<S>>> { // (**self).next_fastx() // } // fn read_record_set_fastx(&mut self, record_set: &mut RecordSet<S>) -> Result<bool> { // (**self).read_record_set_fastx(record_set) // } // fn format(&self) -> Option<SeqFormat> { // (**self).format() // } // fn fastx_records(&mut self) -> RecordsIter<R, P, S> { // (**self).fastx_records() // } // fn into_fastx_records<'s>(self) -> RecordsIntoIter<'s, R, P, S> // where // R: 's, // P: 's, // S: 's // { // <Self as FastxReader<R, P, S>>::into_fastx_records(self) // } // fn position_fastx(&self) -> crate::Position { // (**self).position_fastx() // } // } pub trait FastxSeekReader<R, P, S>: FastxReader<R, P, S> where R: io::Read + io::Seek, P: BufPolicy, S: PositionStore, { /// Seeks to a specified position. Equivalent to the `seek()` method of the /// individual readers. fn seek_fastx(&mut self, pos: &crate::Position) -> io::Result<()>; } /// Borrowed iterator of `OwnedRecord` pub struct RecordsIter<'a, R, P, S> where P: crate::policy::BufPolicy + 'a, R: std::io::Read + 'a, S: crate::core::PositionStore + 'a, { rdr: &'a mut dyn FastxReader<R, P, S>, } impl<'a, R, P, S> RecordsIter<'a, R, P, S> where R: std::io::Read, P: crate::policy::BufPolicy, S: crate::core::PositionStore, { #[inline] pub(crate) fn new(rdr: &'a mut dyn FastxReader<R, P, S>) -> Self { RecordsIter { rdr } } } impl<'a, R, P, S> Iterator for RecordsIter<'a, R, P, S> where P: crate::policy::BufPolicy + 'a, R: std::io::Read + 'a, S: crate::core::PositionStore, { type Item = Result<OwnedRecord>; #[inline] fn next(&mut self) -> Option<Self::Item> { self.rdr .next_fastx() .map(|rec| rec.map(|r| r.to_owned_record())) } } /// Iterator of `OwnedRecord` that owns the underlying reader pub struct RecordsIntoIter<'a, R, P, S> where R: std::io::Read, P: crate::policy::BufPolicy, S: crate::core::PositionStore, { rdr: Box<dyn FastxReader<R, P, S> + 'a>, _s: std::marker::PhantomData<S>, } impl<'a, R, P, S> RecordsIntoIter<'a, R, P, S> where R: std::io::Read, P: crate::policy::BufPolicy, S: crate::core::PositionStore, { #[inline] pub(crate) fn new(rdr: Box<dyn FastxReader<R, P, S> + 'a>) -> Self { RecordsIntoIter { rdr, _s: std::marker::PhantomData, } } } impl<'a, R, P, S> Iterator for RecordsIntoIter<'a, R, P, S> where P: crate::policy::BufPolicy, R: std::io::Read, S: crate::core::PositionStore, { type Item = Result<OwnedRecord>; #[inline] fn next(&mut self) -> Option<Self::Item> { self.rdr .next_fastx() .map(|rec| rec.map(|r| r.to_owned_record())) } }