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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	0.74	0.74	3,024	440	0% 0% 3% 100%
500,000	7.47	7.48	11,884	440	0% 0% 0% 100%
5,000,000	73.34	73.37	188,720	440	0% 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

 regex-dna Perl #4 program source code

# The Computer Language Benchmarks Game

# http://benchmarksgame.alioth.debian.org/

# contributed by Danny Sauer

# completely rewritten and

# cleaned up for speed and fun by Mirco Wahab

# improved STDIN read, regex clean up by Jake Berner


use strict;
use warnings;

my $l_file  = -s STDIN;
my $content; read STDIN, $content, $l_file;
# this is significantly faster than using <> in this case


my $dispose =  qr/(^>.*)?\n/m; # slight performance gain here

   $content =~ s/$dispose//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 my $k (0..$#seq) {
  ++$cnt[$k] while $content=~/$seq[$k]/gi;
  printf "$seq[$k] $cnt[$k]\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)' );

# using $& and no submatch marginally improves the

# speed here, but mentioning $& causes perl to 

# define that value for the @seq patterns too, which

# slows those down considerably. No change.


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

$content =~ s/$findiub/$iub{$1}/g;

printf "\n%d\n%d\n%d\n", $l_file, $l_code, length $content;

 make, command-line, and program output logs

Tue, 21 May 2013 20:38:22 GMT

COMMAND LINE:
/usr/local/src/perl-5.18.0_no_ithreads_no_multi/bin/perl regexdna.perl-4.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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