Use the $. global variable.

while (<>) {
     my_sub() if $. > $allowedlines;
     print;  # do the rest of your stuff
}
[download]

As an alternative, you can set a variable yourself, for example if you need to reset the counter.

my $count =0;
while (<>) {
     if ($count++ > $allowedlines) {
        my_sub();
        $count =0;
     }
     print;  # do the rest of your stuff
}
[download]

See perldoc perlvar for more info on $.