117 lines
3.9 KiB
Rust
117 lines
3.9 KiB
Rust
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/* -*- mode: rust; indent-tabs-mode: nil -*-
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* Implementation of 'fasta' benchmark from
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* Computer Language Benchmarks Game
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* http://shootout.alioth.debian.org/
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*/
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use std;
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import vec;
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import uint;
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import int;
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import str;
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import io::writer_util;
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fn LINE_LENGTH() -> uint { ret 60u; }
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type myrandom = @{mut last: u32};
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fn myrandom_next(r: myrandom, mx: u32) -> u32 {
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r.last = (r.last * 3877u32 + 29573u32) % 139968u32;
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mx * r.last / 139968u32
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}
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type aminoacids = {ch: char, prob: u32};
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fn make_cumulative(aa: ~[aminoacids]) -> ~[aminoacids] {
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let mut cp: u32 = 0u32;
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let mut ans: ~[aminoacids] = ~[];
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for aa.each {|a| cp += a.prob; ans += ~[{ch: a.ch, prob: cp}]; }
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ret ans;
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}
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fn select_random(r: u32, genelist: ~[aminoacids]) -> char {
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if r < genelist[0].prob { ret genelist[0].ch; }
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fn bisect(v: ~[aminoacids], lo: uint, hi: uint, target: u32) -> char {
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if hi > lo + 1u {
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let mid: uint = lo + (hi - lo) / 2u;
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if target < v[mid].prob {
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ret bisect(v, lo, mid, target);
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} else { ret bisect(v, mid, hi, target); }
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} else { ret v[hi].ch; }
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}
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ret bisect(genelist, 0u, vec::len::<aminoacids>(genelist) - 1u, r);
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}
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fn make_random_fasta(wr: io::writer, id: str, desc: str, genelist: ~[aminoacids], n: int) {
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wr.write_line(">" + id + " " + desc);
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let rng = @{mut last: std::rand::rng().next()};
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let mut op: str = "";
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for uint::range(0u, n as uint) {|_i|
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str::push_char(op, select_random(myrandom_next(rng, 100u32),
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genelist));
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if str::len(op) >= LINE_LENGTH() {
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wr.write_line(op);
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op = "";
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}
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}
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if str::len(op) > 0u { wr.write_line(op); }
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}
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fn make_repeat_fasta(wr: io::writer, id: str, desc: str, s: str, n: int) unsafe {
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wr.write_line(">" + id + " " + desc);
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let mut op: str = "";
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let sl: uint = str::len(s);
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for uint::range(0u, n as uint) {|i|
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str::unsafe::push_byte(op, s[i % sl]);
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if str::len(op) >= LINE_LENGTH() {
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wr.write_line(op);
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op = "";
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}
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}
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if str::len(op) > 0u { wr.write_line(op); }
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}
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fn acid(ch: char, prob: u32) -> aminoacids { ret {ch: ch, prob: prob}; }
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fn main(args: ~[str]) {
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let args = if os::getenv("RUST_BENCH").is_some() {
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// alioth tests k-nucleotide with this data at 25,000,000
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~["", "5000000"]
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} else if args.len() <= 1u {
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~["", "1000"]
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} else {
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args
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};
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let writer = if os::getenv("RUST_BENCH").is_some() {
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result::get(io::file_writer("./shootout-fasta.data", ~[io::truncate, io::create]))
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} else {
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io::stdout()
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};
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let n = int::from_str(args[1]).get();
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let iub: ~[aminoacids] =
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make_cumulative(~[acid('a', 27u32), acid('c', 12u32), acid('g', 12u32),
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acid('t', 27u32), acid('B', 2u32), acid('D', 2u32),
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acid('H', 2u32), acid('K', 2u32), acid('M', 2u32),
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acid('N', 2u32), acid('R', 2u32), acid('S', 2u32),
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acid('V', 2u32), acid('W', 2u32), acid('Y', 2u32)]);
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let homosapiens: ~[aminoacids] =
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make_cumulative(~[acid('a', 30u32), acid('c', 20u32), acid('g', 20u32),
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acid('t', 30u32)]);
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let alu: str =
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"GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGG" +
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"GAGGCCGAGGCGGGCGGATCACCTGAGGTCAGGAGTTCGAGA" +
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"CCAGCCTGGCCAACATGGTGAAACCCCGTCTCTACTAAAAAT" +
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"ACAAAAATTAGCCGGGCGTGGTGGCGCGCGCCTGTAATCCCA" +
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"GCTACTCGGGAGGCTGAGGCAGGAGAATCGCTTGAACCCGGG" +
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"AGGCGGAGGTTGCAGTGAGCCGAGATCGCGCCACTGCACTCC" +
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"AGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAA";
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make_repeat_fasta(writer, "ONE", "Homo sapiens alu", alu, n * 2);
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make_random_fasta(writer, "TWO", "IUB ambiguity codes", iub, n * 3);
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make_random_fasta(writer, "THREE",
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"Homo sapiens frequency", homosapiens, n * 5);
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}
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