Another thing worth to mention is that, Perl actually counts input line numbers separately for each file handler. $. is just an alias for the input line number of the last accessed handler.

In case, you can not determine which file handler is the last accessed, or such a determination is not easy to make, you have to use input_line_number against a particular file handler.

A piece of code to demo those mentioned:

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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