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// Copyright 2014 The Rust Project Developers. See the COPYRIGHT
// file at the top-level directory of this distribution and at
// http://rust-lang.org/COPYRIGHT.
//
// Licensed under the Apache License, Version 2.0 <LICENSE-APACHE or
// http://www.apache.org/licenses/LICENSE-2.0> or the MIT license
// <LICENSE-MIT or http://opensource.org/licenses/MIT>, at your
// option. This file may not be copied, modified, or distributed
// except according to those terms.
// FIXME(#13725) windows needs fixing.
// ignore-win32
// ignore-stage1
// ignore-cross-compile #12102
#![feature(macro_rules, phase)]
extern crate regex;
#[phase(syntax)]extern crate regex_macros;
extern crate sync;
use std::io;
use regex::{NoExpand, Regex};
use sync::Arc;
fn count_matches(seq: &str, variant: &Regex) -> int {
let mut n = 0;
for _ in variant.find_iter(seq) {
n += 1;
}
n
}
fn main() {
let mut rdr = if std::os::getenv("RUST_BENCH").is_some() {
let fd = io::File::open(&Path::new("shootout-k-nucleotide.data"));
~io::BufferedReader::new(fd) as ~io::Reader
} else {
~io::stdin() as ~io::Reader
};
let mut seq = StrBuf::from_str(rdr.read_to_str().unwrap());
let ilen = seq.len();
seq = regex!(">[^\n]*\n|\n").replace_all(seq.as_slice(), NoExpand(""));
let seq_arc = Arc::new(seq.clone()); // copy before it moves
let clen = seq.len();
let mut seqlen = sync::Future::spawn(proc() {
let substs = ~[
(regex!("B"), "(c|g|t)"),
(regex!("D"), "(a|g|t)"),
(regex!("H"), "(a|c|t)"),
(regex!("K"), "(g|t)"),
(regex!("M"), "(a|c)"),
(regex!("N"), "(a|c|g|t)"),
(regex!("R"), "(a|g)"),
(regex!("S"), "(c|g)"),
(regex!("V"), "(a|c|g)"),
(regex!("W"), "(a|t)"),
(regex!("Y"), "(c|t)"),
];
let mut seq = seq;
for (re, replacement) in substs.move_iter() {
seq = re.replace_all(seq.as_slice(), NoExpand(replacement));
}
seq.len()
});
let variants = ~[
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 variant_strs, mut counts) = (vec!(), vec!());
for variant in variants.move_iter() {
let seq_arc_copy = seq_arc.clone();
variant_strs.push(variant.to_str().to_owned());
counts.push(sync::Future::spawn(proc() {
count_matches(seq_arc_copy.as_slice(), &variant)
}));
}
for (i, variant) in variant_strs.iter().enumerate() {
println!("{} {}", variant, counts.get_mut(i).get());
}
println!("");
println!("{}", ilen);
println!("{}", clen);
println!("{}", seqlen.get());
}
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