Re^4: Question about speeding a regexp count

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Re^5: Question about speeding a regexp count by BrowserUk (Patriarch) on Oct 15, 2005 at 05:36 UTC
my bug report stands. My (described) two-line bugfix applied. No dramatic difference to the performance of the algorithm #! perl -slw use strict; use Time::HiRes qw[ time ]; use List::Util qw[sum];; my $sequence = join'', map{ ( qw[ A C G T ] )[ rand 4 ] } 1 .. 600_000 +; my $start = time; my( %one, %two, %three ); $one{ $_ }++ for unpack '(A1)', $sequence; $two{ $_ }++ for unpack '(A2X)', $sequence; delete @two{ (qw'A C G T') };; $three{ $_ }++ for unpack '(A3XX)*', $sequence; delete @three{ (qw'AA AC AG AT CA CC CG CT GA GC GG GT TA TC TG TT') } +; printf "Elapsed: %3f seconds\n", time - $start; print sum values %one; print sum values %two; print sum values %three; __END__ P:\test>junk Elapsed: 3.390625 seconds 600000 599999 599998 [download] Examine what is said, not who speaks -- Silence betokens consent -- Love the truth but pardon error. Lingua non convalesco, consenesco et abolesco. -- Rule 1 has a caveat! -- Who broke the cabal? "Science is about questioning the status quo. Questioning authority". The "good enough" maybe good enough for the now, and perfection maybe unobtainable, but that should not preclude us from striving for perfection, when time, circumstance or desire allow.	[reply] [d/l]

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Re^5: Question about speeding a regexp count
by BrowserUk (Patriarch) on Oct 15, 2005 at 05:36 UTC

my bug report stands.

My (described) two-line bugfix applied. No dramatic difference to the performance of the algorithm

#! perl -slw
use strict;
use Time::HiRes qw[ time ];
use List::Util qw[sum];;

my $sequence = join'', map{ ( qw[ A C G T ] )[ rand 4 ] } 1 .. 600_000
+;

my $start = time;
my( %one, %two, %three );
$one{ $_ }++ for unpack '(A1)*', $sequence;
$two{ $_ }++ for unpack '(A2X)*', $sequence;
delete @two{ (qw'A C G T') };;
$three{ $_ }++ for unpack '(A3XX)*', $sequence;
delete @three{ (qw'AA AC AG AT CA CC CG CT GA GC GG GT TA TC TG TT') }
+;

printf "Elapsed: %3f seconds\n", time - $start;

print sum values %one;
print sum values %two;
print sum values %three;

__END__
P:\test>junk
Elapsed: 3.390625 seconds
600000
599999
599998
[download]

Examine what is said, not who speaks -- Silence betokens consent -- Love the truth but pardon error.

Lingua non convalesco, consenesco et abolesco. -- Rule 1 has a caveat! -- Who broke the cabal?

"Science is about questioning the status quo. Questioning authority".

The "good enough" maybe good enough for the now, and perfection maybe unobtainable, but that should not preclude us from striving for perfection, when time, circumstance or desire allow.

[reply]
[d/l]