mirror of
https://github.com/golang/go
synced 2024-11-25 03:07:56 -07:00
k-nucleotide
R=rsc DELTA=367 (366 added, 0 deleted, 1 changed) OCL=32832 CL=32836
This commit is contained in:
Rob Pike
parent
5876cb0e63
commit
ae3939cb78
228
test/bench/k-nucleotide.c
Normal file
228
test/bench/k-nucleotide.c
Normal file
@ -0,0 +1,228 @@
|
||||
/*
|
||||
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.
|
||||
*/
|
||||
|
||||
#include <stdio.h>
|
||||
#include <string.h>
|
||||
#include <ctype.h>
|
||||
#include <stdlib.h>
|
||||
#include <glib.h>
|
||||
|
||||
typedef struct stat_s stat_t;
|
||||
struct stat_s
|
||||
{
|
||||
const gchar *key;
|
||||
long stat;
|
||||
};
|
||||
|
||||
#define MAX_ELM (8192 / sizeof (stat_t))
|
||||
|
||||
static int
|
||||
generate_frequencies (int fl, char *buffer, long buflen,
|
||||
GHashTable *ht, GTrashStack **ts, GPtrArray *roots, GStringChunk *sc)
|
||||
{
|
||||
gchar *key;
|
||||
long i;
|
||||
|
||||
if (fl > buflen) return 0;
|
||||
if (fl == 0) return 0;
|
||||
|
||||
for (i = 0; i < buflen - fl + 1; ++i)
|
||||
{
|
||||
char nulled;
|
||||
stat_t *stat;
|
||||
|
||||
nulled = buffer[i + fl];
|
||||
buffer[i + fl] = '\0';
|
||||
|
||||
key = g_string_chunk_insert_const(sc, buffer + i);
|
||||
|
||||
stat = g_hash_table_lookup(ht, key);
|
||||
if (!stat)
|
||||
{
|
||||
stat = g_trash_stack_pop(ts);
|
||||
if (!stat)
|
||||
{
|
||||
int j;
|
||||
|
||||
stat = malloc(sizeof (stat_t) * MAX_ELM);
|
||||
g_ptr_array_add(roots, stat);
|
||||
|
||||
for (j = 1; j < MAX_ELM; ++j)
|
||||
g_trash_stack_push(ts, stat + j);
|
||||
}
|
||||
stat->stat = 1;
|
||||
stat->key = key;
|
||||
|
||||
g_hash_table_insert(ht, key, stat);
|
||||
}
|
||||
else
|
||||
stat->stat++;
|
||||
|
||||
buffer[i + fl] = nulled;
|
||||
}
|
||||
|
||||
return buflen - fl + 1;
|
||||
}
|
||||
|
||||
static int
|
||||
cmp_func(gconstpointer a, gconstpointer b)
|
||||
{
|
||||
const stat_t *left = a;
|
||||
const stat_t *right = b;
|
||||
|
||||
return right->stat - left->stat;
|
||||
}
|
||||
|
||||
static void
|
||||
sorted_list(gpointer key, gpointer value, gpointer user_data)
|
||||
{
|
||||
stat_t *data = value;
|
||||
GList **lst = user_data;
|
||||
|
||||
*lst = g_list_insert_sorted(*lst, data, cmp_func);
|
||||
}
|
||||
|
||||
static void
|
||||
display_stat(gpointer data, gpointer user_data)
|
||||
{
|
||||
long *total = user_data;
|
||||
stat_t *st = data;
|
||||
|
||||
printf("%s %.3f\n", st->key, 100 * (float) st->stat / *total);
|
||||
}
|
||||
|
||||
void
|
||||
write_frequencies (int fl, char *buffer, long buflen, GTrashStack **ts, GPtrArray *roots)
|
||||
{
|
||||
GStringChunk *sc;
|
||||
GHashTable *ht;
|
||||
GList *lst;
|
||||
long total;
|
||||
|
||||
ht = g_hash_table_new_full(g_str_hash, g_str_equal, NULL /* free key */, NULL /* free value */);
|
||||
sc = g_string_chunk_new(buflen);
|
||||
lst = NULL;
|
||||
|
||||
total = generate_frequencies (fl, buffer, buflen, ht, ts, roots, sc);
|
||||
|
||||
if (!total) goto on_error;
|
||||
|
||||
g_hash_table_foreach(ht, sorted_list, &lst);
|
||||
g_list_foreach(lst, display_stat, &total);
|
||||
g_list_free(lst);
|
||||
|
||||
on_error:
|
||||
g_hash_table_destroy(ht);
|
||||
g_string_chunk_free(sc);
|
||||
}
|
||||
|
||||
void
|
||||
write_count (char *searchFor, char *buffer, long buflen, GTrashStack **ts, GPtrArray *roots)
|
||||
{
|
||||
GStringChunk *sc;
|
||||
GHashTable *ht;
|
||||
stat_t *result;
|
||||
GList *lst;
|
||||
long total;
|
||||
long fl;
|
||||
|
||||
fl = strlen(searchFor);
|
||||
|
||||
ht = g_hash_table_new_full(g_str_hash, g_str_equal, NULL /* free key */, NULL /* free value */);
|
||||
sc = g_string_chunk_new(buflen);
|
||||
lst = NULL;
|
||||
result = NULL;
|
||||
|
||||
total = generate_frequencies (fl, buffer, buflen, ht, ts, roots, sc);
|
||||
|
||||
if (!total) goto on_error;
|
||||
|
||||
result = g_hash_table_lookup(ht, searchFor);
|
||||
|
||||
on_error:
|
||||
printf("%ld\t%s\n", result ? result->stat : 0, searchFor);
|
||||
|
||||
g_hash_table_destroy(ht);
|
||||
g_string_chunk_free(sc);
|
||||
}
|
||||
|
||||
int
|
||||
main ()
|
||||
{
|
||||
char buffer[4096];
|
||||
GTrashStack *ts;
|
||||
GPtrArray *roots;
|
||||
GString *stuff;
|
||||
gchar *s;
|
||||
int len;
|
||||
|
||||
roots = g_ptr_array_new();
|
||||
ts = NULL;
|
||||
|
||||
while (fgets(buffer, sizeof (buffer), stdin))
|
||||
if (strncmp(buffer, ">THREE", 6) == 0)
|
||||
break;
|
||||
|
||||
stuff = g_string_new(NULL);
|
||||
|
||||
while (fgets(buffer, sizeof (buffer), stdin))
|
||||
{
|
||||
size_t sz;
|
||||
|
||||
if (buffer[0] == '>')
|
||||
break;
|
||||
|
||||
sz = strlen(buffer);
|
||||
if (buffer[sz - 1] == '\n')
|
||||
--sz;
|
||||
|
||||
stuff = g_string_append_len(stuff, buffer, sz);
|
||||
}
|
||||
|
||||
stuff = g_string_ascii_up(stuff);
|
||||
len = stuff->len;
|
||||
s = g_string_free(stuff, FALSE);
|
||||
|
||||
write_frequencies(1, s, len, &ts, roots);
|
||||
printf("\n");
|
||||
write_frequencies(2, s, len, &ts, roots);
|
||||
printf("\n");
|
||||
write_count("GGT", s, len, &ts, roots);
|
||||
write_count("GGTA", s, len, &ts, roots);
|
||||
write_count("GGTATT", s, len, &ts, roots);
|
||||
write_count("GGTATTTTAATT", s, len, &ts, roots);
|
||||
write_count("GGTATTTTAATTTATAGT", s, len, &ts, roots);
|
||||
|
||||
free(s);
|
||||
|
||||
g_ptr_array_foreach(roots, free, NULL);
|
||||
g_ptr_array_free(roots, TRUE);
|
||||
|
||||
return 0;
|
||||
}
|
||||
151
test/bench/k-nucleotide.go
Normal file
151
test/bench/k-nucleotide.go
Normal file
@ -0,0 +1,151 @@
|
||||
/*
|
||||
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 (
|
||||
"bufio";
|
||||
"bytes";
|
||||
"fmt";
|
||||
"io";
|
||||
"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);
|
||||
buf := new(bytes.Buffer);
|
||||
three := strings.Bytes(">THREE ");
|
||||
for {
|
||||
line, err := in.ReadLineSlice('\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 := io.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);
|
||||
}
|
||||
}
|
||||
27
test/bench/k-nucleotide.txt
Normal file
27
test/bench/k-nucleotide.txt
Normal file
@ -0,0 +1,27 @@
|
||||
A 30.284
|
||||
T 29.796
|
||||
C 20.312
|
||||
G 19.608
|
||||
|
||||
AA 9.212
|
||||
AT 8.950
|
||||
TT 8.948
|
||||
TA 8.936
|
||||
CA 6.166
|
||||
CT 6.100
|
||||
AC 6.086
|
||||
TC 6.042
|
||||
AG 6.036
|
||||
GA 5.968
|
||||
TG 5.868
|
||||
GT 5.798
|
||||
CC 4.140
|
||||
GC 4.044
|
||||
CG 3.906
|
||||
GG 3.798
|
||||
|
||||
562 GGT
|
||||
152 GGTA
|
||||
15 GGTATT
|
||||
0 GGTATTTTAATT
|
||||
0 GGTATTTTAATTTATAGT
|
||||
@ -66,3 +66,10 @@ spectral-norm 5500
|
||||
gc_B spectral-norm 49.69u 0.01s 49.83r
|
||||
gc spectral-norm-parallel 24.47u 0.03s 11.05r # has shift >>1 not div /2
|
||||
[using >>1 instead of /2 : gc gives 24.33u 0.00s 24.33r]
|
||||
|
||||
August 6, 2009
|
||||
|
||||
k-nucleotide 5000000
|
||||
gcc -O2 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include k-nucleotide.c -lglib-2.0 k-nucleotide.c: 10.72u 0.01s 10.74r
|
||||
gccgo -O2 k-nucleotide.go 22.69u 0.85s 24.09r
|
||||
gc k-nucleotide 15.63u 0.26s 16.41r
|
||||
|
||||
@ -84,9 +84,19 @@ spectralnorm() {
|
||||
run 'gc_B spectral-norm' $O.out -n 5500
|
||||
}
|
||||
|
||||
knucleotide() {
|
||||
gcc -O2 fasta.c
|
||||
a.out 1000000 > x # should be using 25000000
|
||||
echo 'k-nucleotide 1000000'
|
||||
run 'gcc -O2 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include k-nucleotide.c -lglib-2.0' a.out <x
|
||||
run 'gccgo -O2 k-nucleotide.go' a.out <x # warning: pages badly!
|
||||
run 'gc k-nucleotide' $O.out <x
|
||||
rm x
|
||||
}
|
||||
|
||||
case $# in
|
||||
0)
|
||||
run="fasta revcom nbody binarytree fannkuch regexdna spectralnorm"
|
||||
run="fasta revcom nbody binarytree fannkuch regexdna spectralnorm knucleotide"
|
||||
;;
|
||||
*)
|
||||
run=$*
|
||||
|
||||
Loading…
Reference in New Issue
Block a user