performance measurements

Each table row shows performance measurements for this Go program with a particular command-line input value N.

 N  CPU secs Elapsed secs Memory KB Code B ≈ CPU Load
250,0001.481.4837,7361531  0% 1% 2% 100%
2,500,00013.5213.5357,8641531  0% 1% 1% 100%
25,000,000133.32133.41277,1121531  0% 1% 1% 100%

Read the ↓ make, command line, and program output logs to see how this program was run.

Read k-nucleotide benchmark to see what this program should do.

 notes

go version go1.4 linux/386

 k-nucleotide Go #2 program source code

/* The Computer Language Benchmarks Game
 * http://benchmarksgame.alioth.debian.org/
 *
 * contributed by Tylor Arndt
 */

package main

import (
   "bufio"
   "bytes"
   "fmt"
   "io/ioutil"
   "log"
   "os"
   "runtime"
   "sort"
   "sync"
)

func main() {
   runtime.GOMAXPROCS(4)
   dna := readEncDNA()
   var wgs [7]*sync.WaitGroup
   for i := 0; i < 7; i++ {
      wgs[i] = new(sync.WaitGroup)
   }
   report(dna, 1, nil, wgs[0])
   report(dna, 2, wgs[0], wgs[1])
   report(dna, 3, wgs[1], wgs[2])
   report(dna, 4, wgs[2], wgs[3])
   report(dna, 6, wgs[3], wgs[4])
   report(dna, 12, wgs[4], wgs[5])
   report(dna, 18, wgs[5], wgs[6])
   wgs[6].Wait()
}

func readEncDNA() []byte {
   in, startTok := bufio.NewReader(os.Stdin), []byte(">THREE ")
   for line, err := in.ReadSlice('\n'); !bytes.HasPrefix(line, startTok); line, err = in.ReadSlice('\n') {
      if err != nil {
         log.Panicf("Error: Could not read input from stdin; Details: %s", err)
      }
   }
   ascii, err := ioutil.ReadAll(in)
   if err != nil {
      log.Panicf("Error: Could not read input from stdin; Details: %s", err)
   }
   j := 0
   for i, c, asciic := 0, byte(0), len(ascii); i < asciic; i++ {
      c = ascii[i]
      switch c {
      case 'a', 'A':
         c = 0
      case 't', 'T':
         c = 1
      case 'g', 'G':
         c = 2
      case 'c', 'C':
         c = 3
      case '\n':
         continue
      default:
         log.Fatalf("Error: Invalid nucleotide value: '%c'", ascii[i])
      }
      ascii[j] = c
      j++
   }
   return ascii[:j+1]
}

var targSeqs = []string{3: "GGT", 4: "GGTA", 6: "GGTATT", 12: "GGTATTTTAATT", 18: "GGTATTTTAATTTATAGT"}

func report(dna []byte, n int, prev, done *sync.WaitGroup) {
   done.Add(1)
   go func() {
      tbl, output := count(dna, n), ""
      switch n {
      case 1, 2:
         output = freqReport(tbl, n)
      default:
         targ := targSeqs[n]
         output = fmt.Sprintf("%d\t%s\n", tbl[compStr(targ)], targ)
      }
      if prev != nil {
         prev.Wait()
      }
      fmt.Print(output)
      done.Done()
   }()
}

func count(dna []byte, n int) map[uint64]uint64 {
   tbl := make(map[uint64]uint64, (2<<16)+1)
   for i, end := 0, len(dna)-n; i < end; i++ {
      tbl[compress(dna[i:i+n])]++
   }
   return tbl
}

func compress(dna []byte) uint64 {
   var val uint64
   for i, dnac := 0, len(dna); i < dnac; i++ {
      val = (val << 2) | uint64(dna[i])
   }
   return val
}

func compStr(dna string) uint64 {
   raw := []byte(dna)
   for i, rawc, c := 0, len(raw), byte(0); i < rawc; i++ {
      c = raw[i]
      switch c {
      case 'A':
         c = 0
      case 'T':
         c = 1
      case 'G':
         c = 2
      case 'C':
         c = 3
      }
      raw[i] = c
   }
   return compress(raw)
}

func decompToBytes(compDNA uint64, n int) []byte {
   buf := bytes.NewBuffer(make([]byte, 0, n))
   var c byte
   for i := 0; i < n; i++ {
      switch compDNA & 3 {
      case 0:
         c = 'A'
      case 1:
         c = 'T'
      case 2:
         c = 'G'
      case 3:
         c = 'C'
      }
      buf.WriteByte(c)
      compDNA = compDNA >> 2
   }
   if n > 1 {
      return reverse(buf.Bytes())
   }
   return buf.Bytes()
}

func reverse(s []byte) []byte {
   for i, j := 0, len(s)-1; i < j; i, j = i+1, j-1 {
      s[i], s[j] = s[j], s[i]
   }
   return s
}

func freqReport(tbl map[uint64]uint64, n int) string {
   seqs := make(seqSlice, 0, len(tbl))
   var val, count, sum uint64
   for val, count = range tbl {
      seqs = append(seqs, seq{nuc: decompToBytes(val, n), n: count})
      sum += count
   }
   sort.Sort(seqs)
   var buf bytes.Buffer
   sumFloat, entry := float64(sum), seq{}
   for _, entry = range seqs {
      fmt.Fprintf(&buf, "%s %.3f\n", entry.nuc, (100*float64(entry.n))/sumFloat)
   }
   buf.WriteByte('\n')
   return buf.String()
}

type seq struct {
   nuc []byte
   n   uint64
}

type seqSlice []seq

func (seq seqSlice) Len() int      { return len(seq) }
func (seq seqSlice) Swap(i, j int) { seq[i], seq[j] = seq[j], seq[i] }
func (seq seqSlice) Less(i, j int) bool {
   if seq[i].n == seq[j].n {
      return bytes.Compare(seq[i].nuc, seq[j].nuc) < 0
   }
   return seq[i].n > seq[j].n
}

 make, command-line, and program output logs

Fri, 12 Dec 2014 03:20:17 GMT

MAKE:
/usr/local/src/go/bin/go build -o knucleotide.go-2.go_run
0.34s to complete and log all make actions

COMMAND LINE:
./knucleotide.go-2.go_run 0 < knucleotide-input25000000.txt

PROGRAM OUTPUT:
A 30.295
T 30.151
C 19.800
G 19.754

AA 9.177
TA 9.132
AT 9.131
TT 9.091
CA 6.002
AC 6.001
AG 5.987
GA 5.984
CT 5.971
TC 5.971
GT 5.957
TG 5.956
CC 3.917
GC 3.911
CG 3.909
GG 3.902

1471758	GGT
446535	GGTA
47336	GGTATT
893	GGTATTTTAATT
893	GGTATTTTAATTTATAGT

Revised BSD license

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