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
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
|
// The Computer Language Benchmarks Game
// https://benchmarksgame-team.pages.debian.net/benchmarksgame/
//
// contributed by the Rust Project Developers
// contributed by TeXitoi
// contributed by BurntSushi
// This technically solves the problem posed in the `regex-dna` benchmark, but
// it cheats by combining all of the replacements into a single regex and
// replacing them with a single linear scan. i.e., it re-implements
// `replace_all`. As a result, this is around 25% faster. ---AG
use std::io::{self, Read};
use std::sync::Arc;
use std::thread;
macro_rules! regex {
($re:expr) => {
::regex::Regex::new($re).unwrap()
};
}
fn main() {
let mut seq = String::with_capacity(50 * (1 << 20));
io::stdin().read_to_string(&mut seq).unwrap();
let ilen = seq.len();
seq = regex!(">[^\n]*\n|\n").replace_all(&seq, "").into_owned();
let clen = seq.len();
let seq_arc = Arc::new(seq.clone());
let variants = vec![
regex!("agggtaaa|tttaccct"),
regex!("[cgt]gggtaaa|tttaccc[acg]"),
regex!("a[act]ggtaaa|tttacc[agt]t"),
regex!("ag[act]gtaaa|tttac[agt]ct"),
regex!("agg[act]taaa|ttta[agt]cct"),
regex!("aggg[acg]aaa|ttt[cgt]ccct"),
regex!("agggt[cgt]aa|tt[acg]accct"),
regex!("agggta[cgt]a|t[acg]taccct"),
regex!("agggtaa[cgt]|[acg]ttaccct"),
];
let mut counts = vec![];
for variant in variants {
let seq = seq_arc.clone();
let restr = variant.to_string();
let future = thread::spawn(move || variant.find_iter(&seq).count());
counts.push((restr, future));
}
let substs = vec![
(b'B', "(c|g|t)"),
(b'D', "(a|g|t)"),
(b'H', "(a|c|t)"),
(b'K', "(g|t)"),
(b'M', "(a|c)"),
(b'N', "(a|c|g|t)"),
(b'R', "(a|g)"),
(b'S', "(c|g)"),
(b'V', "(a|c|g)"),
(b'W', "(a|t)"),
(b'Y', "(c|t)"),
]; // combined into one regex in `replace_all`
let seq = replace_all(&seq, substs);
for (variant, count) in counts {
println!("{} {}", variant, count.join().unwrap());
}
println!("\n{}\n{}\n{}", ilen, clen, seq.len());
}
fn replace_all(text: &str, substs: Vec<(u8, &str)>) -> String {
let mut replacements = vec![""; 256];
let mut alternates = vec![];
for (re, replacement) in substs {
replacements[re as usize] = replacement;
alternates.push((re as char).to_string());
}
let re = regex!(&alternates.join("|"));
let mut new = String::with_capacity(text.len());
let mut last_match = 0;
for m in re.find_iter(text) {
new.push_str(&text[last_match..m.start()]);
new.push_str(replacements[text.as_bytes()[m.start()] as usize]);
last_match = m.end();
}
new.push_str(&text[last_match..]);
new
}
|
