test/bench/k-nucleotide.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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POSSIBILITY OF SUCH DAMAGE.
*/

/* The Computer Language Benchmarks Game
 * http://shootout.alioth.debian.org/
 *
 * contributed by The Go Authors.
 */

package main

import (
	"bufio"
	"bytes"
	"fmt"
	"io/ioutil"
	"os"
	"sort"
	"strings"
)

var in *bufio.Reader

func count(data string, n int) map[string]int {
	counts := make(map[string]int)
	top := len(data) - n
	for i := 0; i <= top; i++ {
		s := data[i : i+n]
		if k, ok := counts[s]; ok {
			counts[s] = k + 1
		} else {
			counts[s] = 1
		}
	}
	return counts
}

func countOne(data string, s string) int {
	counts := count(data, len(s))
	if i, ok := counts[s]; ok {
		return i
	}
	return 0
}


type kNuc struct {
	name  string
	count int
}

type kNucArray []kNuc

func (kn kNucArray) Len() int      { return len(kn) }
func (kn kNucArray) Swap(i, j int) { kn[i], kn[j] = kn[j], kn[i] }
func (kn kNucArray) Less(i, j int) bool {
	if kn[i].count == kn[j].count {
		return kn[i].name > kn[j].name // sort down
	}
	return kn[i].count > kn[j].count
}

func sortedArray(m map[string]int) kNucArray {
	kn := make(kNucArray, len(m))
	i := 0
	for k, v := range m {
		kn[i].name = k
		kn[i].count = v
		i++
	}
	sort.Sort(kn)
	return kn
}

func print(m map[string]int) {
	a := sortedArray(m)
	sum := 0
	for _, kn := range a {
		sum += kn.count
	}
	for _, kn := range a {
		fmt.Printf("%s %.3f\n", kn.name, 100*float64(kn.count)/float64(sum))
	}
}

func main() {
	in = bufio.NewReader(os.Stdin)
	three := strings.Bytes(">THREE ")
	for {
		line, err := in.ReadSlice('\n')
		if err != nil {
			fmt.Fprintln(os.Stderr, "ReadLine err:", err)
			os.Exit(2)
		}
		if line[0] == '>' && bytes.Equal(line[0:len(three)], three) {
			break
		}
	}
	data, err := ioutil.ReadAll(in)
	if err != nil {
		fmt.Fprintln(os.Stderr, "ReadAll err:", err)
		os.Exit(2)
	}
	// delete the newlines and convert to upper case
	j := 0
	for i := 0; i < len(data); i++ {
		if data[i] != '\n' {
			data[j] = data[i] &^ ' ' // upper case
			j++
		}
	}
	str := string(data[0:j])

	print(count(str, 1))
	fmt.Print("\n")

	print(count(str, 2))
	fmt.Print("\n")

	interests := []string{"GGT", "GGTA", "GGTATT", "GGTATTTTAATT", "GGTATTTTAATTTATAGT"}
	for _, s := range interests {
		fmt.Printf("%d %s\n", countOne(str, s), s)
	}
}