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April 22, 2016 20:45
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benchmarksgame-rs regex-dna entry with byte matching
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// The Computer Language Benchmarks Game | |
// http://benchmarksgame.alioth.debian.org/ | |
// | |
// contributed by the Rust Project Developers | |
// contributed by TeXitoi | |
// contributed by BurntSushi | |
extern crate regex; | |
use regex::bytes::Regex; | |
use std::io::{self, Read}; | |
use std::sync::Arc; | |
use std::thread; | |
macro_rules! regex { ($re:expr) => { Regex::new($re).unwrap() } } | |
fn main() { | |
let mut seq = Vec::with_capacity(50 * (1 << 20)); | |
io::stdin().read_to_end(&mut seq).unwrap(); | |
let ilen = seq.len(); | |
seq = regex!(r">[^\n]*\n|\n").replace_all(&seq, &b""[..]); | |
let clen = seq.len(); | |
let seq_arc = Arc::new(seq.clone()); | |
let variants = vec![ | |
regex!(r"agggtaaa|tttaccct"), | |
regex!(r"[cgt]gggtaaa|tttaccc[acg]"), | |
regex!(r"a[act]ggtaaa|tttacc[agt]t"), | |
regex!(r"ag[act]gtaaa|tttac[agt]ct"), | |
regex!(r"agg[act]taaa|ttta[agt]cct"), | |
regex!(r"aggg[acg]aaa|ttt[cgt]ccct"), | |
regex!(r"agggt[cgt]aa|tt[acg]accct"), | |
regex!(r"agggta[cgt]a|t[acg]taccct"), | |
regex!(r"agggtaa[cgt]|[acg]ttaccct"), | |
]; | |
let mut counts = Vec::with_capacity(9); | |
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![ | |
(regex!(r"B"), &b"(c|g|t)"[..]), | |
(regex!(r"D"), &b"(a|g|t)"[..]), | |
(regex!(r"H"), &b"(a|c|t)"[..]), | |
(regex!(r"K"), &b"(g|t)"[..]), | |
(regex!(r"M"), &b"(a|c)"[..]), | |
(regex!(r"N"), &b"(a|c|g|t)"[..]), | |
(regex!(r"R"), &b"(a|g)"[..]), | |
(regex!(r"S"), &b"(c|g)"[..]), | |
(regex!(r"V"), &b"(a|c|g)"[..]), | |
(regex!(r"W"), &b"(a|t)"[..]), | |
(regex!(r"Y"), &b"(c|t)"[..]), | |
]; | |
let mut seq = seq; | |
for (re, replacement) in substs.into_iter() { | |
seq = re.replace_all(&seq, replacement); | |
} | |
let rlen = seq.len(); | |
for (variant, count) in counts { | |
println!("{} {}", variant, count.join().unwrap()); | |
} | |
println!("\n{}\n{}\n{}", ilen, clen, rlen); | |
} |
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