main.go

/* The Computer Language Benchmarks Game
 * https://salsa.debian.org/benchmarksgame-team/benchmarksgame/
 *
 * regex-redux program contributed by BurntSushi.
 */

package main

import (
	"fmt"
	"io/ioutil"
	"os"
	"runtime"

	"github.com/BurntSushi/rure-go"
)

var variants = []string{
	"agggtaaa|tttaccct",
	"[cgt]gggtaaa|tttaccc[acg]",
	"a[act]ggtaaa|tttacc[agt]t",
	"ag[act]gtaaa|tttac[agt]ct",
	"agg[act]taaa|ttta[agt]cct",
	"aggg[acg]aaa|ttt[cgt]ccct",
	"agggt[cgt]aa|tt[acg]accct",
	"agggta[cgt]a|t[acg]taccct",
	"agggtaa[cgt]|[acg]ttaccct",
}

type Subst struct {
	pat, repl string
}

var substs = []Subst{
	Subst{"tHa[Nt]", "<4>"},
	Subst{"aND|caN|Ha[DS]|WaS", "<3>"},
	Subst{"a[NSt]|BY", "<2>"},
	Subst{"<[^>]*>", "|"},
	Subst{"\\|[^|][^|]*\\|", "-"},
}

func countMatches(pat string, bytes []byte) int {
	n := 0
	for it := rure.MustCompile(pat).IterBytes(bytes); it.Next(nil); {
		n++
	}
	return n
}

func replaceAll(re *rure.Regex, src []byte, repl []byte) []byte {
	dst := make([]byte, 0, len(src))
	lastMatch := 0
	for it := re.IterBytes(src); it.Next(nil); {
		start, end := it.Match()
		dst = append(dst, src[lastMatch:start]...)
		lastMatch = end
		dst = append(dst, repl...)
	}
	return append(dst, src[lastMatch:]...)
}

func main() {
	runtime.GOMAXPROCS(runtime.NumCPU())
	bytes, err := ioutil.ReadFile("/dev/stdin")
	if err != nil {
		fmt.Fprintf(os.Stderr, "can't read input: %s\n", err)
		os.Exit(2)
	}
	ilen := len(bytes)
	// Delete the comment lines and newlines
	bytes = replaceAll(rure.MustCompile("(>[^\n]+)?\n"), bytes, []byte{})
	clen := len(bytes)

	mresults := make([]chan int, len(variants))
	for i, s := range variants {
		ch := make(chan int)
		mresults[i] = ch
		go func(ss string) {
			ch <- countMatches(ss, bytes)
		}(s)
	}

	lenresult := make(chan int)
	bb := bytes
	go func() {
		for _, sub := range substs {
			bb = replaceAll(rure.MustCompile(sub.pat), bb, []byte(sub.repl))
		}
		lenresult <- len(bb)
	}()

	for i, s := range variants {
		fmt.Printf("%s %d\n", s, <-mresults[i])
	}
	fmt.Printf("\n%d\n%d\n%d\n", ilen, clen, <-lenresult)
}

results

[andrew@Cheetah benchgame] time bench-native < /tmp/input5000000.txt
agggtaaa|tttaccct 356
[cgt]gggtaaa|tttaccc[acg] 1250
a[act]ggtaaa|tttacc[agt]t 4252
ag[act]gtaaa|tttac[agt]ct 2894
agg[act]taaa|ttta[agt]cct 5435
aggg[acg]aaa|ttt[cgt]ccct 1537
agggt[cgt]aa|tt[acg]accct 1431
agggta[cgt]a|t[acg]taccct 1608
agggtaa[cgt]|[acg]ttaccct 2178

50833411
50000000
27388361

real    0m20.709s
user    1m19.839s
sys     0m0.183s


[andrew@Cheetah benchgame] time bench-pcre < /tmp/input5000000.txt
agggtaaa|tttaccct 356
[cgt]gggtaaa|tttaccc[acg] 1250
a[act]ggtaaa|tttacc[agt]t 4252
ag[act]gtaaa|tttac[agt]ct 2894
agg[act]taaa|ttta[agt]cct 5435
aggg[acg]aaa|ttt[cgt]ccct 1537
agggt[cgt]aa|tt[acg]accct 1431
agggta[cgt]a|t[acg]taccct 1608
agggtaa[cgt]|[acg]ttaccct 2178

50833411
50000000
27388361

real    0m10.510s
user    0m35.362s
sys     0m0.211s


[andrew@Cheetah benchgame] time bench-rust < /tmp/input5000000.txt
agggtaaa|tttaccct 356
[cgt]gggtaaa|tttaccc[acg] 1250
a[act]ggtaaa|tttacc[agt]t 4252
ag[act]gtaaa|tttac[agt]ct 2894
agg[act]taaa|ttta[agt]cct 5435
aggg[acg]aaa|ttt[cgt]ccct 1537
agggt[cgt]aa|tt[acg]accct 1431
agggta[cgt]a|t[acg]taccct 1608
agggtaa[cgt]|[acg]ttaccct 2178

50833411
50000000
27388361

real    0m2.235s
user    0m3.410s
sys     0m0.157s