rewrite of shootout-reverse-complement.rs
This version is inspired by the best version in C by Mr Ledrug, but without the parallelisation.
This commit is contained in:
Guillaume Pinot
parent
69186efc19
commit
e76e83cb10
@ -1,151 +1,79 @@
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// xfail-pretty
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// xfail-test
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// Copyright 2013 The Rust Project Developers. See the COPYRIGHT
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// file at the top-level directory of this distribution and at
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// http://rust-lang.org/COPYRIGHT.
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//
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// Licensed under the Apache License, Version 2.0 <LICENSE-APACHE or
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// http://www.apache.org/licenses/LICENSE-2.0> or the MIT license
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// <LICENSE-MIT or http://opensource.org/licenses/MIT>, at your
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// option. This file may not be copied, modified, or distributed
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// except according to those terms.
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use std::cast::transmute;
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use std::libc::{STDOUT_FILENO, c_int, fdopen, fgets, fopen, fputc, fwrite};
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use std::libc::{size_t};
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use std::ptr::null;
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use std::iter::range_step;
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use std::io::{stdin, stdout, File};
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static LINE_LEN: u32 = 80;
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static LINE_LEN: uint = 60;
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static COMPLEMENTS: [u8, ..256] = [
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0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
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0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
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0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
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0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
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0,
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'T' as u8,
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'V' as u8,
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'G' as u8,
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'H' as u8,
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0,
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0,
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'C' as u8,
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'D' as u8,
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0,
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0,
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'M' as u8,
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0,
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'K' as u8,
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'N' as u8,
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0,
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0,
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0,
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'Y' as u8,
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'S' as u8,
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'A' as u8,
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'A' as u8,
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'B' as u8,
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'W' as u8,
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0,
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'R' as u8,
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0,
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0,
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0,
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0,
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0,
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0,
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0,
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'T' as u8,
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'V' as u8,
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'G' as u8,
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'H' as u8,
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0,
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0,
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'C' as u8,
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'D' as u8,
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0,
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0,
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'M' as u8,
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0,
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'K' as u8,
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'N' as u8,
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0,
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0,
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0,
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'Y' as u8,
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'S' as u8,
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'A' as u8,
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'A' as u8,
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'B' as u8,
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'W' as u8,
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0,
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'R' as u8,
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0,
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0,
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0,
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0,
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0,
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0,
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0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
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0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
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0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
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0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
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0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
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0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
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0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
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0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
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];
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fn make_complements() -> [u8, ..256] {
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let transforms = [
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('A', 'T'), ('C', 'G'), ('G', 'C'), ('T', 'A'),
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('U', 'A'), ('M', 'K'), ('R', 'Y'), ('W', 'W'),
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('S', 'S'), ('Y', 'R'), ('K', 'M'), ('V', 'B'),
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('H', 'D'), ('D', 'H'), ('B', 'V'), ('N', 'N'),
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('\n', '\n')];
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let mut complements: [u8, ..256] = [0, ..256];
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for (i, c) in complements.mut_iter().enumerate() {
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*c = i as u8;
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}
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let lower = 'A' as u8 - 'a' as u8;
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for &(from, to) in transforms.iter() {
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complements[from as u8] = to as u8;
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complements[from as u8 - lower] = to as u8;
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}
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complements
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}
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fn main() {
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unsafe {
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let mode = "r";
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//let stdin = fdopen(STDIN_FILENO as c_int, transmute(&mode[0]));
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let path = "reversecomplement-input.txt";
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let stdin = fopen(transmute(&path[0]), transmute(&mode[0]));
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let mode = "w";
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let stdout = fdopen(STDOUT_FILENO as c_int, transmute(&mode[0]));
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let complements = make_complements();
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let mut data = if std::os::getenv("RUST_BENCH").is_some() {
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File::open(&Path::init("shootout-k-nucleotide.data")).read_to_end()
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} else {
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stdin().read_to_end()
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};
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let mut out: ~[u8] = ~[];
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out.reserve(12777888);
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let mut pos = 0;
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for seq in data.mut_split(|c| *c == '>' as u8) {
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// skip header and last \n
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let begin = match seq.iter().position(|c| *c == '\n' as u8) {
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None => continue,
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Some(c) => c
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};
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let len = seq.len();
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let seq = seq.mut_slice(begin + 1, len - 1);
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loop {
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let needed = pos + (LINE_LEN as uint) + 1;
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if out.capacity() < needed {
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out.reserve_at_least(needed);
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// arrange line breaks
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let len = seq.len();
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let off = LINE_LEN - len % (LINE_LEN + 1);
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for i in range_step(LINE_LEN, len, LINE_LEN + 1) {
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for j in std::iter::count(i, -1).take(off) {
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seq[j] = seq[j - 1];
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}
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let mut ptr = out.unsafe_mut_ref(pos);
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if fgets(transmute(ptr), LINE_LEN as c_int, stdin) == null() {
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break;
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}
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// Don't change lines that begin with '>' or ';'.
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let first = *ptr;
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if first == ('>' as u8) {
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while *ptr != 0 {
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ptr = ptr.offset(1);
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}
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*ptr = '\n' as u8;
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pos = (ptr as uint) - (out.unsafe_ref(0) as uint);
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fwrite(transmute(out.unsafe_ref(0)),
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1,
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pos as size_t,
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stdout);
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pos = 0;
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continue;
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}
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// Complement other lines.
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loop {
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let ch = *ptr;
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if ch == 0 {
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break;
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}
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*ptr = COMPLEMENTS.unsafe_get(ch as uint);
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ptr = ptr.offset(1);
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}
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*ptr = '\n' as u8;
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pos = (ptr as uint) - (out.unsafe_ref(0) as uint);
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seq[i - off] = '\n' as u8;
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}
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fwrite(transmute(out.unsafe_ref(0)), 1, pos as size_t, stdout);
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// reverse complement, as
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// seq.reverse(); for c in seq.mut_iter() {*c = complements[*c]}
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// but faster:
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let mut it = seq.mut_iter();
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loop {
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match (it.next(), it.next_back()) {
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(Some(front), Some(back)) => {
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let tmp = complements[*front];
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*front = complements[*back];
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*back = tmp;
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}
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_ => break // vector exhausted.
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}
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}
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}
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stdout().write(data);
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}
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