go/test/bench/fasta.go

/*
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    * Redistributions of source code must retain the above copyright
    notice, this list of conditions and the following disclaimer.

    * Redistributions in binary form must reproduce the above copyright
    notice, this list of conditions and the following disclaimer in the
    documentation and/or other materials provided with the distribution.

    * Neither the name of "The Computer Language Benchmarks Game" nor the
    name of "The Computer Language Shootout Benchmarks" nor the names of
    its contributors may be used to endorse or promote products derived
    from this software without specific prior written permission.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
ARE DISCLAIMED.  IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
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ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
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*/

/* The Computer Language Benchmarks Game
 * http://shootout.alioth.debian.org/
 *
 * contributed by The Go Authors.
 * Based on C program by Joern Inge Vestgaarden
 * and Jorge Peixoto de Morais Neto.
 */

package main

import (
	"bufio"
	"flag"
	"os"
)

var out *bufio.Writer

var n = flag.Int("n", 1000, "length of result")

const WIDTH = 60 // Fold lines after WIDTH bytes

func min(a, b int) int {
	if a < b {
		return a
	}
	return b
}

type AminoAcid struct {
	p float
	c byte
}

func AccumulateProbabilities(genelist []AminoAcid) {
	for i := 1; i < len(genelist); i++ {
		genelist[i].p += genelist[i-1].p
	}
}

// RepeatFasta prints the characters of the byte slice s. When it
// reaches the end of the slice, it goes back to the beginning.
// It stops after generating count characters.
// After each WIDTH characters it prints a newline.
// It assumes that WIDTH <= len(s) + 1.
func RepeatFasta(s []byte, count int) {
	pos := 0
	s2 := make([]byte, len(s)+WIDTH)
	copy(s2, s)
	copy(s2[len(s):], s)
	for count > 0 {
		line := min(WIDTH, count)
		out.Write(s2[pos : pos+line])
		out.WriteByte('\n')
		pos += line
		if pos >= len(s) {
			pos -= len(s)
		}
		count -= line
	}
}

var lastrandom uint32 = 42

const (
	IM = 139968
	IA = 3877
	IC = 29573
)

// Each element of genelist is a struct with a character and
// a floating point number p between 0 and 1.
// RandomFasta generates a random float r and
// finds the first element such that p >= r.
// This is a weighted random selection.
// RandomFasta then prints the character of the array element.
// This sequence is repeated count times.
// Between each WIDTH consecutive characters, the function prints a newline.
func RandomFasta(genelist []AminoAcid, count int) {
	buf := make([]byte, WIDTH+1)
	for count > 0 {
		line := min(WIDTH, count)
		for pos := 0; pos < line; pos++ {
			lastrandom = (lastrandom*IA + IC) % IM
			// Integer to float conversions are faster if the integer is signed.
			r := float(int32(lastrandom)) / IM
			for _, v := range genelist {
				if v.p >= r {
					buf[pos] = v.c
					break
				}
			}
		}
		buf[line] = '\n'
		out.Write(buf[0 : line+1])
		count -= line
	}
}

func main() {
	out = bufio.NewWriter(os.Stdout)
	defer out.Flush()

	flag.Parse()

	iub := []AminoAcid{
		AminoAcid{0.27, 'a'},
		AminoAcid{0.12, 'c'},
		AminoAcid{0.12, 'g'},
		AminoAcid{0.27, 't'},
		AminoAcid{0.02, 'B'},
		AminoAcid{0.02, 'D'},
		AminoAcid{0.02, 'H'},
		AminoAcid{0.02, 'K'},
		AminoAcid{0.02, 'M'},
		AminoAcid{0.02, 'N'},
		AminoAcid{0.02, 'R'},
		AminoAcid{0.02, 'S'},
		AminoAcid{0.02, 'V'},
		AminoAcid{0.02, 'W'},
		AminoAcid{0.02, 'Y'},
	}

	homosapiens := []AminoAcid{
		AminoAcid{0.3029549426680, 'a'},
		AminoAcid{0.1979883004921, 'c'},
		AminoAcid{0.1975473066391, 'g'},
		AminoAcid{0.3015094502008, 't'},
	}

	AccumulateProbabilities(iub)
	AccumulateProbabilities(homosapiens)

	alu := []byte(
		"GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGG" +
			"GAGGCCGAGGCGGGCGGATCACCTGAGGTCAGGAGTTCGAGA" +
			"CCAGCCTGGCCAACATGGTGAAACCCCGTCTCTACTAAAAAT" +
			"ACAAAAATTAGCCGGGCGTGGTGGCGCGCGCCTGTAATCCCA" +
			"GCTACTCGGGAGGCTGAGGCAGGAGAATCGCTTGAACCCGGG" +
			"AGGCGGAGGTTGCAGTGAGCCGAGATCGCGCCACTGCACTCC" +
			"AGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAA")

	out.WriteString(">ONE Homo sapiens alu\n")
	RepeatFasta(alu, 2**n)
	out.WriteString(">TWO IUB ambiguity codes\n")
	RandomFasta(iub, 3**n)
	out.WriteString(">THREE Homo sapiens frequency\n")
	RandomFasta(homosapiens, 5**n)
}