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rewrite of shootout-reverse-complement.rs #10799

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Merged
merged 1 commit into from
Dec 5, 2013
Merged

rewrite of shootout-reverse-complement.rs #10799

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212 changes: 70 additions & 142 deletions src/test/bench/shootout-reverse-complement.rs
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Original file line number Diff line number Diff line change
@@ -1,151 +1,79 @@
// xfail-pretty
// xfail-test

use std::cast::transmute;
use std::libc::{STDOUT_FILENO, c_int, fdopen, fgets, fopen, fputc, fwrite};
use std::libc::{size_t};
use std::ptr::null;

static LINE_LEN: u32 = 80;

static COMPLEMENTS: [u8, ..256] = [
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,

0,
'T' as u8,
'V' as u8,
'G' as u8,
'H' as u8,
0,
0,
'C' as u8,
'D' as u8,
0,
0,
'M' as u8,
0,
'K' as u8,
'N' as u8,
0,
0,
0,
'Y' as u8,
'S' as u8,
'A' as u8,
'A' as u8,
'B' as u8,
'W' as u8,
0,
'R' as u8,
0,
0,
0,
0,
0,
0,

0,
'T' as u8,
'V' as u8,
'G' as u8,
'H' as u8,
0,
0,
'C' as u8,
'D' as u8,
0,
0,
'M' as u8,
0,
'K' as u8,
'N' as u8,
0,
0,
0,
'Y' as u8,
'S' as u8,
'A' as u8,
'A' as u8,
'B' as u8,
'W' as u8,
0,
'R' as u8,
0,
0,
0,
0,
0,
0,

0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
];
// Copyright 2013 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.

use std::iter::range_step;
use std::io::{stdin, stdout, File};

static LINE_LEN: uint = 60;

fn make_complements() -> [u8, ..256] {
let transforms = [
('A', 'T'), ('C', 'G'), ('G', 'C'), ('T', 'A'),
('U', 'A'), ('M', 'K'), ('R', 'Y'), ('W', 'W'),
('S', 'S'), ('Y', 'R'), ('K', 'M'), ('V', 'B'),
('H', 'D'), ('D', 'H'), ('B', 'V'), ('N', 'N'),
('\n', '\n')];
let mut complements: [u8, ..256] = [0, ..256];
for (i, c) in complements.mut_iter().enumerate() {
*c = i as u8;
}
let lower = 'A' as u8 - 'a' as u8;
for &(from, to) in transforms.iter() {
complements[from as u8] = to as u8;
complements[from as u8 - lower] = to as u8;
}
complements
}

fn main() {
unsafe {
let mode = "r";
//let stdin = fdopen(STDIN_FILENO as c_int, transmute(&mode[0]));
let path = "reversecomplement-input.txt";
let stdin = fopen(transmute(&path[0]), transmute(&mode[0]));
let mode = "w";
let stdout = fdopen(STDOUT_FILENO as c_int, transmute(&mode[0]));

let mut out: ~[u8] = ~[];
out.reserve(12777888);
let mut pos = 0;

loop {
let needed = pos + (LINE_LEN as uint) + 1;
if out.capacity() < needed {
out.reserve_at_least(needed);
}

let mut ptr = out.unsafe_mut_ref(pos);
if fgets(transmute(ptr), LINE_LEN as c_int, stdin) == null() {
break;
}

// Don't change lines that begin with '>' or ';'.
let first = *ptr;
if first == ('>' as u8) {
while *ptr != 0 {
ptr = ptr.offset(1);
}
*ptr = '\n' as u8;

pos = (ptr as uint) - (out.unsafe_ref(0) as uint);
fwrite(transmute(out.unsafe_ref(0)),
1,
pos as size_t,
stdout);

pos = 0;
continue;
let complements = make_complements();
let mut data = if std::os::getenv("RUST_BENCH").is_some() {
File::open(&Path::init("shootout-k-nucleotide.data")).read_to_end()
} else {
stdin().read_to_end()
};

for seq in data.mut_split(|c| *c == '>' as u8) {
// skip header and last \n
let begin = match seq.iter().position(|c| *c == '\n' as u8) {
None => continue,
Some(c) => c
};
let len = seq.len();
let seq = seq.mut_slice(begin + 1, len - 1);

// arrange line breaks
let len = seq.len();
let off = LINE_LEN - len % (LINE_LEN + 1);
for i in range_step(LINE_LEN, len, LINE_LEN + 1) {
for j in std::iter::count(i, -1).take(off) {
seq[j] = seq[j - 1];
}
seq[i - off] = '\n' as u8;
}

// Complement other lines.
loop {
let ch = *ptr;
if ch == 0 {
break;
// reverse complement, as
// seq.reverse(); for c in seq.mut_iter() {*c = complements[*c]}
// but faster:
let mut it = seq.mut_iter();
loop {
match (it.next(), it.next_back()) {
(Some(front), Some(back)) => {
let tmp = complements[*front];
*front = complements[*back];
*back = tmp;
}
*ptr = COMPLEMENTS.unsafe_get(ch as uint);
ptr = ptr.offset(1);
_ => break // vector exhausted.
}
*ptr = '\n' as u8;

pos = (ptr as uint) - (out.unsafe_ref(0) as uint);
}

fwrite(transmute(out.unsafe_ref(0)), 1, pos as size_t, stdout);
}

stdout().write(data);
}