// The Computer Language Benchmarks Game // https://benchmarksgame-team.pages.debian.net/benchmarksgame/ // // contributed by the Rust Project Developers // contributed by TeXitoi // contributed by BurntSushi extern crate regex; use std::io::{self, Read}; 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 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"), ]; for re in variants { println!("{} {}", re.to_string(), re.find_iter(&seq).count()); } 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); 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 }