It's easier when you work *with* Perl rather than against it:

sub reverse_complement {
    local $_ = shift;
    y/ACGT/TGCA/;
    reverse;
}
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As for the OP's question, FASTA is a pretty simple format other than the various stuff people put in the sequence labels. So your code will probably look something like this:

while (<FASTA>) {
    chomp;
    if (/^>\s*(.*)/) {
        # it's a sequence label
        $name = $1;
    } else {
        # it's sequence data
    }
}
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