Looking at the sample, you want the reverse complement of the second line, plus four, plus four... You can use $. which keeps the line number and the modulus operator %: 
use feature 'say';
while (<>) {
    chomp;
    if ($. % 4 == 2 ) {
        $_ = reverse;
        y/ACTG/TGAC/;
    }
    say;
}

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In reply to Re: find reverse complement of every 2nd line by choroba
in thread find reverse complement of every 2nd line by bingalee

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