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//! This library provides an(other) attempt at high performance FASTA and FASTQ parsing and writing. //! The FASTA parser can read and write multi-line files. The FASTQ parser supports only single //! lines. The sequence length of records in the FASTA/FASTQ files //! is not limited by the size of the buffer. Instead, the buffer will grow until //! the record fits, allowing parsers with a minimum amount of copying required. //! How it grows can be configured (see [`BufStrategy`](trait.BufStrategy.html)). //! //! See also the documentation for the [FASTA Reader](fasta/struct.Reader.html) and the //! [FASTQ Reader](fastq/struct.Reader.html). The methods for writing are documented //! [here](fasta/index.html#functions) for FASTA and [here](fastq/index.html#functions) //! for FASTQ. //! //! # Example FASTQ parser: //! This code prints the ID string from each FASTQ record. //! //! ```no_run //! use seq_io::fastq::{Reader,Record}; //! //! let mut reader = Reader::from_path("seqs.fasta").unwrap(); //! //! while let Some(record) = reader.next() { //! let record = record.expect("Error reading record"); //! println!("{}", record.id().unwrap()); //! } //! ``` //! //! # Example FASTA parser calculating mean sequence length: //! The FASTA reader works just the same. One challenge with the FASTA //! format is that the sequence can be broken into multiple lines. //! Therefore, it is not always possible to get a slice to the whole sequence //! without copying the data. But it is possible to use `seq_lines()` //! for efficiently iterating over each sequence line: //! //! ```no_run //! use seq_io::fasta::{Reader,Record}; //! //! let mut reader = Reader::from_path("seqs.fasta").unwrap(); //! //! let mut n = 0; //! let mut sum = 0; //! while let Some(record) = reader.next() { //! let record = record.expect("Error reading record"); //! for s in record.seq_lines() { //! sum += s.len(); //! } //! n += 1; //! } //! println!("mean sequence length of {} records: {:.1} bp", n, sum as f32 / n as f32); //! ``` //! If the whole sequence is required at once, there is the //! [`full_seq`](fasta/struct.RefRecord.html#method.full_seq), //! which will only allocate the sequence if there are multiple lines. //! use seq_io::fasta::{Reader,OwnedRecord}; //! //! # Owned records //! Both readers also provide iterators similar to *Rust-Bio*, which return owned data. This //! is slower, but make sense, e.g. if the records are collected in to a vector: //! //! ```no_run //! use seq_io::fasta::Reader; //! //! let mut reader = Reader::from_path("input.fasta").unwrap(); //! //! let records: Result<Vec<_>, _> = reader.records().collect(); //! ``` //! //! # Parallel processing //! Functions for parallel processing can be found in the [`parallel`](parallel/index.html) module extern crate buf_redux; extern crate memchr; #[macro_use] extern crate serde_derive; extern crate serde; use std::error; use std::fmt; use std::io; pub use strategy::*; mod strategy; macro_rules! try_opt { ($expr: expr) => { match $expr { Ok(item) => item, Err(e) => return Some(Err(::std::convert::From::from(e))) } }; } macro_rules! unwrap_or { ($expr:expr, $or:block) => { match $expr { Some(item) => item, None => $or } }; } pub mod parallel; pub mod fasta; pub mod fastq; /// used by more than one module #[derive(Default, Debug)] struct ReadAlways; impl buf_redux::strategy::ReadStrategy for ReadAlways { fn should_read(&self, _: &buf_redux::Buffer) -> bool { true } } /// Remove a final '\r' from a byte slice #[inline] fn trim_cr(line: &[u8]) -> &[u8] { if let Some((&b'\r', remaining)) = line.split_last() { remaining } else { line } } /// Makes sure the buffer is full after this call (unless EOF reached) /// code adapted from `io::Read::read_exact` fn fill_buf<R, Rs, Ms>(reader: &mut buf_redux::BufReader<R, Rs, Ms>) -> io::Result<usize> where R: io::Read, Rs: buf_redux::strategy::ReadStrategy, Ms: buf_redux::strategy::MoveStrategy { let mut num_read = reader.get_buf().len(); while num_read < reader.capacity() { match reader.read_into_buf() { Ok(0) => break, Ok(n) => num_read += n, Err(ref e) if e.kind() == io::ErrorKind::Interrupted => {} Err(e) => return Err(e), } } Ok(num_read) }