7956a11df6
In the "reverse-complement" loop, if there is an odd number of element, we forget to complement the element in the middle. For example, if the input is "ggg", the result before the fix is "CgC" instead of "CCC". This is because of this bug that the official shootout says that the rust version is in "Bad Output". This commit should fix this error.
85 lines
2.7 KiB
Rust
85 lines
2.7 KiB
Rust
// Copyright 2013-2014 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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// ignore-android doesn't terminate?
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// ignore-pretty
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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: uint = 60;
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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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let complements = make_complements();
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let data = if std::os::getenv("RUST_BENCH").is_some() {
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File::open(&Path::new("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 data = data.unwrap();
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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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// 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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seq[i - off] = '\n' as u8;
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}
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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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(Some(last), None) => *last = complements[*last], // last element
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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).unwrap();
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}
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