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mirror of https://github.com/golang/go synced 2024-11-24 15:20:03 -07:00

regex-dna

R=rsc
DELTA=243  (242 added, 0 deleted, 1 changed)
OCL=32786
CL=32791
This commit is contained in:
Rob Pike 2009-08-05 13:03:46 -07:00
parent 6adadeb3ab
commit d9a0bc9b58
5 changed files with 301 additions and 1 deletions

154
test/bench/regex-dna.c Normal file
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/*
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
* 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
CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
POSSIBILITY OF SUCH DAMAGE.
*/
/*
** The Computer Language Shootout
** http://shootout.alioth.debian.org/
** contributed by Mike Pall
**
** regex-dna benchmark using PCRE
**
** compile with:
** gcc -O3 -fomit-frame-pointer -o regexdna regexdna.c -lpcre
*/
#define __USE_STRING_INLINES
#include <stdio.h>
#include <string.h>
#include <stdlib.h>
#include <pcre.h>
typedef struct fbuf {
char *buf;
size_t size, len;
} fbuf_t;
static void fb_init(fbuf_t *b)
{
b->buf = NULL;
b->len = b->size = 0;
}
static char *fb_need(fbuf_t *b, size_t need)
{
need += b->len;
if (need > b->size) {
if (b->size == 0) b->size = need;
else while (need > b->size) b->size += b->size;
if (!(b->buf = realloc(b->buf, b->size))) exit(1);
}
return b->buf+b->len;
}
#define FB_MINREAD (3<<16)
/* Read all of a stdio stream into dst buffer. */
static size_t fb_readall(fbuf_t *dst, FILE *fp)
{
char *dp;
int n;
for (dp = fb_need(dst, FB_MINREAD);
(n = fread(dp, 1, dst->size-dst->len, fp)) > 0;
dp = fb_need(dst, FB_MINREAD)) dst->len += n;
if (ferror(fp)) exit(1);
return dst->len;
}
/* Substitute pattern p with replacement r, copying from src to dst buffer. */
static size_t fb_subst(fbuf_t *dst, fbuf_t *src, const char *p, const char *r)
{
pcre *re;
pcre_extra *re_ex;
const char *re_e;
char *dp;
int re_eo, m[3], pos, rlen, clen;
if (!(re = pcre_compile(p, PCRE_CASELESS, &re_e, &re_eo, NULL))) exit(1);
re_ex = pcre_study(re, 0, &re_e);
for (dst->len = 0, rlen = strlen(r), pos = 0;
pcre_exec(re, re_ex, src->buf, src->len, pos, 0, m, 3) >= 0;
pos = m[1]) {
clen = m[0]-pos;
dp = fb_need(dst, clen+rlen);
dst->len += clen+rlen;
memcpy(dp, src->buf+pos, clen);
memcpy(dp+clen, r, rlen);
}
clen = src->len-pos;
dp = fb_need(dst, clen);
dst->len += clen;
memcpy(dp, src->buf+pos, clen);
return dst->len;
}
/* Count all matches with pattern p in src buffer. */
static int fb_countmatches(fbuf_t *src, const char *p)
{
pcre *re;
pcre_extra *re_ex;
const char *re_e;
int re_eo, m[3], pos, count;
if (!(re = pcre_compile(p, PCRE_CASELESS, &re_e, &re_eo, NULL))) exit(1);
re_ex = pcre_study(re, 0, &re_e);
for (count = 0, pos = 0;
pcre_exec(re, re_ex, src->buf, src->len, pos, 0, m, 3) >= 0;
pos = m[1]) count++;
return count;
}
static const char *variants[] = {
"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", NULL
};
static const char *subst[] = {
"B", "(c|g|t)", "D", "(a|g|t)", "H", "(a|c|t)", "K", "(g|t)",
"M", "(a|c)", "N", "(a|c|g|t)", "R", "(a|g)", "S", "(c|g)",
"V", "(a|c|g)", "W", "(a|t)", "Y", "(c|t)", NULL
};
int main(int argc, char **argv)
{
fbuf_t seq[2];
const char **pp;
size_t ilen, clen, slen;
int flip;
fb_init(&seq[0]);
fb_init(&seq[1]);
ilen = fb_readall(&seq[0], stdin);
clen = fb_subst(&seq[1], &seq[0], ">.*|\n", "");
for (pp = variants; *pp; pp++)
printf("%s %d\n", *pp, fb_countmatches(&seq[1], *pp));
for (slen = 0, flip = 1, pp = subst; *pp; pp += 2, flip = 1-flip)
slen = fb_subst(&seq[1-flip], &seq[flip], *pp, pp[1]);
printf("\n%zu\n%zu\n%zu\n", ilen, clen, slen);
return 0;
}

117
test/bench/regex-dna.go Normal file
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/*
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
* 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
CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
POSSIBILITY OF SUCH DAMAGE.
*/
/* The Computer Language Benchmarks Game
* http://shootout.alioth.debian.org/
*
* contributed by The Go Authors.
*/
package main
import (
"fmt";
"io";
"os";
"regexp";
)
func compile(s string) *regexp.Regexp {
r, err := regexp.Compile(s);
if err != nil {
fmt.Fprintf(os.Stderr, "can't compile pattern %q: %s\n", s, err);
os.Exit(2);
}
return r;
}
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 {"B", "(c|g|t)"},
Subst {"D", "(a|g|t)"},
Subst {"H", "(a|c|t)"},
Subst {"K", "(g|t)"},
Subst {"M", "(a|c)"},
Subst {"N", "(a|c|g|t)"},
Subst {"R", "(a|g)"},
Subst {"S", "(c|g)"},
Subst {"V", "(a|c|g)"},
Subst {"W", "(a|t)"},
Subst {"Y", "(c|t)"},
}
func countMatches(pat, str string) int {
re := compile(pat);
n := 0;
pos := 0;
for {
e := re.Execute(str);
if len(e) == 0 {
break;
}
n++;
str = str[e[1]:len(str)];
}
return n;
}
func main() {
bytes, err := io.ReadFile("/dev/stdin");
if err != nil {
fmt.Fprintf(os.Stderr, "can't read input: %s\n", err);
os.Exit(2);
}
str := string(bytes);
ilen := len(str);
// Delete the comment lines and newlines
str = compile("(>[^\n]+)?\n").ReplaceAll(str, "");
clen := len(str);
for i, s := range variants {
fmt.Printf("%s %d\n", s, countMatches(s, str));
}
for i, sub := range substs {
str = compile(sub.pat).ReplaceAll(str, sub.repl);
}
fmt.Printf("\n%d\n%d\n%d\n", ilen, clen, len(str));
}

13
test/bench/regex-dna.txt Normal file
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agggtaaa|tttaccct 0
[cgt]gggtaaa|tttaccc[acg] 3
a[act]ggtaaa|tttacc[agt]t 9
ag[act]gtaaa|tttac[agt]ct 8
agg[act]taaa|ttta[agt]cct 10
aggg[acg]aaa|ttt[cgt]ccct 3
agggt[cgt]aa|tt[acg]accct 4
agggta[cgt]a|t[acg]taccct 3
agggtaa[cgt]|[acg]ttaccct 5
101745
100000
133640

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@ -53,3 +53,8 @@ fannkuch 12
gccgo -O2 fannkuch.go 64.89u 0.00s 64.92r
gc fannkuch 124.59u 0.00s 124.67r
gc_B fannkuch 91.14u 0.00s 91.16r
regex-dna 100000
gcc -O2 regex-dna.c -lpcre 0.92u 0.00s 0.99r
gc regexp-dna 26.94u 0.18s 28.75r
gc_B regexp-dna 26.51u 0.09s 26.75r

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@ -65,9 +65,20 @@ fannkuch() {
run 'gc_B fannkuch' $O.out -n 12
}
regexdna() {
gcc -O2 fasta.c
a.out 100000 > x
echo 'regex-dna 100000'
run 'gcc -O2 regex-dna.c -lpcre' a.out <x
# run 'gccgo -O2 regex-dna.go' a.out <x # pages badly; don't run
run 'gc regex-dna' $O.out <x
run 'gc_B regex-dna' $O.out <x
rm x
}
case $# in
0)
run="fasta revcom nbody binarytree fannkuch"
run="fasta revcom nbody binarytree fannkuch regexdna"
;;
*)
run=$*