Crates.io | kseq |
lib.rs | kseq |
version | 0.5.3 |
source | src |
created_at | 2021-08-02 06:27:14.451445 |
updated_at | 2024-03-01 01:34:28.451814 |
description | a simple fasta/fastq format parser library |
homepage | https://github.com/moold/kseq |
repository | https://github.com/moold/kseq |
max_upload_size | |
id | 430296 |
size | 33,132 |
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 a path or parse_reader
to parse a reader, and then use iter_record
method to get each record.
parse_path
This function takes a path that implements AsRef<std::path::Path>
as input, a path can be a fastx
file, -
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 missing input, can't open or read, wrong fastx format or invalid path or file errors.parse_reader
This function takes a reader that implements std::io::Read
as input. It returns a Result
type:
Ok(T)
: A struct T
with the iter_record
method.Err(E)
: An error E
including missing input, 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/identifierseq -> &str
: get sequencedes -> &str
: get sequence description/commentsep -> &str
: get separatorqual -> &str
: get quality scoreslen -> usize
: get sequence lengthNote: 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.
use std::env::args;
use std::fs::File;
use kseq::parse_path;
fn main(){
let path: String = args().nth(1).unwrap();
let mut records = parse_path(path).unwrap();
// let mut records = parse_reader(File::open(path).unwrap()).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());
}
}
cargo add kseq
cargo bench