use warnings;
use strict;
use Benchmark qw( timethese cmpthese );

my $sample = ">gi|5524211|gb|AAD44166.1| cytochrome b [Elephas maximus maximus]
LCLYTHIGRNIYYGSYLYSETWNTGIMLLLITMATAFMGYVLPWGQMSFWGATVITNLFSAIPYIGTNLV
EWIWGGFSVDKATLNRFFAFHFILPFTMVALAGVHLTFLHETGSNNPLGLTSDSDKIPFHPYYTIKDFLG
LLILILLLLLLALLSPDMLGDPDNHMPADPLNTPLHIKPEWYFLFAYAILRSVPNKLGGVLALFLSIVIL
GLMPFLHTSKHRSMMLRPLSQALFWTLTMDLLTLTWIGSQPVEYPYTIIGQMASILYFSIILAFLPIAGX
IENY
>SEQUENCE_1
MTEITAAMVKELRESTGAGMMDCKNALSETNGDFDKAVQLLREKGLGKAAKKADRLAAEG
LVSVKVSDDFTIAAMRPSYLSYEDLDMTFVENEYKALVAELEKENEERRRLKDPNKPEHK
IPQFASRKQLSDAILKEAEEKIKEELKAQGKPEKIWDNIIPGKMNSFIADNSQLDSKLTL
MGQFYVMDDKKTVEQVIAEKEKEFGGKIKIVEFICFEVGEGLEKKTEDFAAEVAAQL
";

foreach(1..10){
    $sample .= $sample;
}
my @sample_array = split "\n", $sample;

sub tr1_count_ar {
    return $sample =~ tr/>//;
}
sub tr2_count_ar {
    my $c;
    foreach(@sample_array) {
        $c += $_ =~ tr/>//;
    }
    return $c;
}
sub s1_count_ar {
    my $c;
    foreach(@sample_array) {
        $c += $_ =~ s/^>/>/g;
    }
    return $c;
}
sub s2_count_ar {
    return $sample =~ s/>/>/g;
}
sub m1_count_ar {
    my $c;
    $c += () = $sample =~ m/>/g;
    return $c;
}
sub m2_count_ar {
    my $c;
    foreach(@sample_array) {
        $c += () = $_ =~ m/^>/;
    }
    return $c;
}
sub m3_count_ar {
    my $c;
    foreach(@sample_array) {
        $c++ if $_ =~ m/^>/;
    }
    return $c;
}
sub g_count_ar {
    my $c;
    $c = scalar grep /^>/, @sample_array;
    return $c;
}

print "tr1: ", tr1_count_ar( ) ,"\n";
print "tr2: ", tr2_count_ar( ) ,"\n";
print "s1: ",  s1_count_ar( ) ,"\n";
print "s2: ",  s2_count_ar( ) ,"\n";
print "m1: ",  m1_count_ar( ) ,"\n";
print "m2: ",  m2_count_ar( ) ,"\n";
print "m3: ",  m3_count_ar( ) ,"\n";
print "g:  ",  g_count_ar( )  ,"\n";

print '-'x80,"\n";
print join "\n", @sample_array[0..6];
print "\n",'-'x80,"\n";

my $results = timethese (
    -10,
    {
        'tr1'  => 'tr1_count_ar',
        'tr2'  => 'tr2_count_ar',
        's1'   => 's1_count_ar',
        's2'   => 's2_count_ar',
        'm1'   => 'm1_count_ar',
        'm2'   => 'm2_count_ar',
        'm3'   => 'm3_count_ar',
        'grep' => 'g_count_ar'
    }
);
cmpthese($results);

##</code><code>##

tr1: 2048
tr2: 2048
s1: 2048
s2: 2048
m1: 2048
m2: 2048
m3: 2048
g:  2048
--------------------------------------------------------------------------------
>gi|5524211|gb|AAD44166.1| cytochrome b [Elephas maximus maximus]
LCLYTHIGRNIYYGSYLYSETWNTGIMLLLITMATAFMGYVLPWGQMSFWGATVITNLFSAIPYIGTNLV
EWIWGGFSVDKATLNRFFAFHFILPFTMVALAGVHLTFLHETGSNNPLGLTSDSDKIPFHPYYTIKDFLG
LLILILLLLLLALLSPDMLGDPDNHMPADPLNTPLHIKPEWYFLFAYAILRSVPNKLGGVLALFLSIVIL
GLMPFLHTSKHRSMMLRPLSQALFWTLTMDLLTLTWIGSQPVEYPYTIIGQMASILYFSIILAFLPIAGX
IENY
>SEQUENCE_1
--------------------------------------------------------------------------------
Benchmark: running grep, m1, m2, m3, s1, s2, tr1, tr2 for at least 10 CPU seconds...
      grep: 11 wallclock secs (10.25 usr +  0.00 sys = 10.25 CPU) @ 894.04/s (n=9163)
        m1: 11 wallclock secs (10.81 usr +  0.00 sys = 10.81 CPU) @ 728.89/s (n=7880)
        m2: 10 wallclock secs (10.58 usr +  0.00 sys = 10.58 CPU) @ 385.18/s (n=4074)
        m3: 11 wallclock secs (10.47 usr +  0.00 sys = 10.47 CPU) @ 599.25/s (n=6273)
        s1: 11 wallclock secs (10.44 usr +  0.00 sys = 10.44 CPU) @ 432.16/s (n=4510)
        s2: 11 wallclock secs (10.39 usr +  0.00 sys = 10.39 CPU) @ 926.56/s (n=9626)
       tr1: 10 wallclock secs (10.52 usr +  0.00 sys = 10.52 CPU) @ 2473.89/s (n=26013)
       tr2: 11 wallclock secs (10.64 usr +  0.00 sys = 10.64 CPU) @ 581.26/s (n=6184)
       Rate   m2   s1  tr2   m3   m1 grep   s2  tr1
m2    385/s   -- -11% -34% -36% -47% -57% -58% -84%
s1    432/s  12%   -- -26% -28% -41% -52% -53% -83%
tr2   581/s  51%  35%   --  -3% -20% -35% -37% -77%
m3    599/s  56%  39%   3%   -- -18% -33% -35% -76%
m1    729/s  89%  69%  25%  22%   -- -18% -21% -71%
grep  894/s 132% 107%  54%  49%  23%   --  -4% -64%
s2    927/s 141% 114%  59%  55%  27%   4%   -- -63%
tr1  2474/s 542% 472% 326% 313% 239% 177% 167%   --