regex-dna

R=rsc
DELTA=243  (242 added, 0 deleted, 1 changed)
OCL=32786
CL=32791

test/bench/regex-dna.c

+/*
+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;
+}

test/bench/regex-dna.go

+/*
+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));
+}

test/bench/regex-dna.txt

+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

test/bench/timing.log

@@ -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

test/bench/timing.sh

@@ -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 $# in
 0)
-	run="fasta revcom nbody binarytree fannkuch"
+	run="fasta revcom nbody binarytree fannkuch regexdna"
 	;;
 *)
 	run=$*