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# The Computer Language Benchmarks Game
# http://shootout.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;
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