G'day perlance,

Reading the entire file contents into a string, and then reading all of that data again to parse it, is not very efficent: instead, parse the data as you're reading it (once). I also think you're completely on the wrong track with '... split(/($pattern)/ ...'; to be honest, I'm not really sure what you were hoping to achieve with that.

All you probably need is something simple like this:

#!/usr/bin/env perl

use strict;
use warnings;

my $chunk = -1;

while (<DATA>) {
    if ((split)[1] eq 'False') {
        ++$chunk;
        print "#Chunk $chunk:\n";
    }

    print;
}

__DATA__
GO:0002366   False
GO:0002446   True
GO:0002275   True
GO:0043312   True
GO:0006733   False
GO:0019674   False
GO:0043588   False
GO:0055065   False
GO:0055080   True
[download]

Output:

#Chunk 0:
GO:0002366       False
GO:0002446       True
GO:0002275       True
GO:0043312       True
#Chunk 1:
GO:0006733       False
#Chunk 2:
GO:0019674       False
#Chunk 3:
GO:0043588       False
#Chunk 4:
GO:0055065       False
GO:0055080       True
[download]