#!/usr/bin/perl -w
use strict;
use warnings;

my $readfile = "C:/Documents and Settings/mydir/Desktop/TARGETING.gb";
my $writefile = "C:/Documents and Settings/mydir/Desktop/TARGET.gb";

open my $in, "<", $readfile or die "couldn't open $readfile: $!";
open my $out, ">", $writefile or die "couldn't open $writefile: $!";

my $state;
while(my $line =<$in>){    
    if ($line=~/^([A-Z]+)/) {
        $state=$1;        
    }
    print $out $line unless $state eq "COMMENT";
}
close $in;
close $out