It sounds like you need something like this:

my ( $fasta, $valid, $invalid );
while ( <STDIN> ) {
    tr/ATCGatcg//cd;
    next unless /[ATCGatcg]/;
    if ( length % 3 ) {
        $invalid++;
        next;
        }
    $valid++;
    $fasta .= $_;
    }

print LOGFILE "Found ", $valid + $invalid, " blocks, joined $valid of 
+them and left out $invalid.\n";
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