use strict;
use warnings;
use Benchmark qw(:all) ;

    my $x = $ARGV[0];
    my $r = timethese( 5, {
        a => sub{
        open (BOUT, "<", $x) ||  die "Ther were some problems with opening BLAST output : $!";
        $/ = ">#W#";   
        my $count = 0 ;
        while(<BOUT>){ 
        $count++ if (m/>/g)  ;
        }              
        $/="\n";
        close BOUT;
        #print "$count \n";
        },
        b => sub{
        open (BOUT, "<", $x) ||  die "Ther were some problems with opening BLAST output : $!";
        my $count = 0 ; 
        while(<BOUT>){  
        $count++ if (m/>/g);       
        }               
        close BOUT;
        #print "$count \n";
        
        
        },
    } );
    cmpthese $r;


Benchmark: timing 5 iterations of a, b...
         a: 43 wallclock secs (23.06 usr +  1.86 sys = 24.92 CPU) @  0.20/s (n=5)
         b: 169 wallclock secs (160.39 usr +  1.34 sys = 161.74 CPU) @  0.03/s (n=5)
  s/iter    b    a
b   32.3   -- -85%
a   4.98 549%   --





##</code><code>##

$/ = ">#W#";   
        my $count = 0 ;
        while(<BOUT>){ 
        $count++ if (m/>/g)  ;
        
        $/="\n";

          while(){}
        $/=">#W#";


        }              
        $/="\n";