my $start_time = time(); # remember when we started
my $progress;

while (<$input_file>) {
    ...
    if (time - $start_time > 2) { # 2 seconds have passed
        $progress = create_progress_dialog();
        Tk->update(); # I don't know if there is such a thing or whether Tk needs it
    };
};

undef $progress; # hide progress dialog if we have one