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use strict;
use warnings;
...
    print "$line\n";
    $flag = 1;
}

C:\Users\user\Perl>perl test.pl
GO:0002366       False
...
#Chunk 3
GO:0055065       False
GO:0055080       True

use strict;
use warnings;
...
    }
    print "$line\n";
}

C:\Users\user\Perl>perl test.pl

...
GO:0055080       True

C:\Users\user\Perl>