By the way, there was no need to use $counter at all. Perl has a variable $. which tracks the counter of the last accessed file handler. Have more than one file open? okay, then use FOO->input_line_number(). Play with the following code (save this piece of code as test.pl):

use IO::Handle;
open(MYSELF1, "<", "test.pl");
open(MYSELF2, "<", "test.pl");
while (<MYSELF1>) {
    print "after reading from myself1: $.\n";
    if ($. % 2) {
        <MYSELF2>;
        print "after reading from myself2: $.\n";
    }
    print "returned values from input_line_number: (";
    print MYSELF1->input_line_number(), ", ";
    print MYSELF2->input_line_number(), ")\n";
}
close(MYSELF1);
close(MYSELF2);
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