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Computer Language Benchmarks Game      [[ Play ]]

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 performance measurements

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

N	CPU secs	Elapsed secs	Memory KB	Code B	≈ CPU Load
50,000	0.06	0.06	?	477	0% 0% 0% 100%
500,000	0.47	0.47	11,760	477	2% 0% 4% 100%
5,000,000	4.60	4.61	189,608	477	1% 0% 0% 100%

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

Read regex-dna benchmark to see what this program should do.

 notes

This is perl 5, version 18, subversion 0 (v5.18.0) built for i686-linux

Compile-time options: HAS_TIMES PERLIO_LAYERS PERL_DONT_CREATE_GVSV
                        PERL_HASH_FUNC_ONE_AT_A_TIME_HARD PERL_MALLOC_WRAP
                        PERL_PRESERVE_IVUV PERL_SAWAMPERSAND USE_LARGE_FILES
                        USE_LOCALE USE_LOCALE_COLLATE USE_LOCALE_CTYPE
                        USE_LOCALE_NUMERIC USE_PERLIO USE_PERL_ATOF

Don't split pattern at |

 regex-dna Perl #6 program source code

# The Computer Language Benchmarks Game
# http://benchmarksgame.alioth.debian.org/
# contributed by Danny Sauer
# modified by Mirco Wahab
# modified by Steffen Mueller
# modified by Kuang-che Wu

use strict;
use warnings;

my $content =  do { local $/; <STDIN> };
my $l_file  =  length $content;
$content =~ s/^>.*$//mg;
$content =~ s/\n//g;
my $l_code  =  length $content;

my @seq = ( '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' );

my @cnt = (0) x @seq;
for (0..$#seq) {
  my ($l, $r) = map {qr/$_/} split /\|/, $seq[$_];
  $cnt[$_] += (() = ($content=~/$l/gi, $content=~/$r/gi));
  print $seq[$_], ' ', $cnt[$_], "\n";
}

my %iub = (         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)' );

my $findiub = '(['.(join '', keys %iub).'])';

$content =~ s/$findiub/$iub{$1}/g;
print "\n", $l_file, "\n", $l_code, "\n", length($content), "\n";

 make, command-line, and program output logs

Tue, 21 May 2013 20:37:18 GMT

COMMAND LINE:
/usr/local/src/perl-5.18.0_no_ithreads_no_multi/bin/perl regexdna.perl-6.perl 0 < regexdna-input5000000.txt

PROGRAM OUTPUT:
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
66800214

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