kseq

kseq is a simple fasta/fastq (fastx) format parser library for Rust, its main function is to iterate over the records from fastx files (similar to kseq in C). It uses shared buffer to read and store records, so the speed is very fast. It supports a plain or gz fastx file or io::stdin, as well as a fofn (file-of-file-names) file, which contains multiple plain or gz fastx files (one per line).

Using kseq is very simple. Users only need to call parse_path to parse the path, and then use iter_record method to get each record.

• parse_path This function takes a path (Option<String>) as input, a path can be a fastx file, None or - for io::stdin, or a fofn file. It returns a Result type:

  • Ok(T): A struct T with the iter_record method.
  • Err(E): An error E including can't open or read, wrong fastx format or invalid path or file errors.

• iter_record This function can be called in a loop, it returns a Result<Option<Record>> type:

  • Ok(Some(Record)): A struct Record with methods:

    • head -> &str: get sequence id/identifier
    • seq -> &str: get sequence
    • des -> &str: get sequence description/comment
    • sep -> &str: get separator
    • qual -> &str: get quality scores
    • len -> usize: get sequence length

    Note: call des, sep and qual will return "" if Record doesn't have these attributes.

  • Ok(None): Stream has reached EOF.

  • Err(ParseError): An error ParseError including IO, TruncateFile, InvalidFasta or InvalidFastq errors.

Example

use std::env::args;
use kseq::parse_path;

fn main(){
	let path: Option<String> = args().nth(1);
	let mut records = parse_path(path).unwrap();
	while let Some(record) = records.iter_record().unwrap() {
		println!("head:{} des:{} seq:{} qual:{} len:{}", 
			record.head(), record.des(), record.seq(), record.qual(), record.len());
	}
}

Benchmark

cargo bench

We benchmarked kseq against Needletail v0.4.1 to parse 500 megabases in multi-line fasta format and 4-line fastq format. The results are as follows:

FASTQ parsing/kseq      time:   [945.98 ms 974.99 ms 1.0052 s]                              
FASTQ parsing/needletail                                                                          
                        time:   [1.0133 s 1.0323 s 1.0527 s]

FASTA parsing/kseq      time:   [531.90 ms 544.50 ms 559.56 ms]                             
FASTA parsing/needletail                                                                          
                        time:   [620.42 ms 632.76 ms 649.72 ms]
Found 2 outliers among 10 measurements (20.00%)
  2 (20.00%) high severe

Installation

[dependencies]
kseq = "0.2"