kseq 0.1.1

a simple fasta/fastq format parser library
Documentation 
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35

# kseq
`kseq` is a simple fasta/fastq (fastx) format parser library for [Rust](https://www.rust-lang.org/), its main function is to iterate over the records from fastx files (similar to [kseq](https://attractivechaos.github.io/klib/#Kseq%3A%20stream%20buffer%20and%20FASTA%2FQ%20parser) 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`](https://doc.rust-lang.org/std/io/fn.stdin.html), 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`](https://doc.rust-lang.org/std/io/fn.stdin.html), or a fofn file. It return a [`Result`](https://doc.rust-lang.org/std/result/) type:
	- `Ok(T)`: An 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 cyclically, it return an [`Option`](https://doc.rust-lang.org/std/option/index.html) type:
	- `Some(Record)`: An struct `Record` with methods:
		- `head`: get sequence id/identifier (`&str`)
		- `seq`:  get sequence  (`&str`)
		- `des`:  get sequence description/comment (`&str`)
		- `sep`:  get separator (`&str`)
		- `qual`: get quality scores (`&str`)
		- `len`:  get sequence length (`usize`)

		***Note:*** call `des`, `sep` and `qual` will return `""` if `Record` does have these attributes. `head`, `seq`, `des`, `sep` and `qual` use unsafe code [`str::from_utf8_unchecked`](https://doc.rust-lang.org/std/str/fn.from_utf8_unchecked.html).
	- `None`: Stream has reached `EOF`.

# Examples
```
use std::env::args;
use kseq::path::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() {
		println!("head:{} des:{} seq:{} qual:{} len:{}", 
			record.head(), record.des(), record.seq(), record.qual(), record.len());
	}
}
```