It looks like it's using "-complete" to represent the stop codon. As is usually the case, for simple string manipulation it's easier and faster to take BioPerl out of the equation. All you need is a substitution and a lookup table: 
my %prot = (
'TCA'=>'S','TCC'=>'S','TCG'=>'S','TCT'=>'S',
'TTC'=>'F','TTT'=>'F',
'TTA'=>'L','TTG'=>'L',
'TAC'=>'Y','TAT'=>'Y',
'TAA'=>'_','TAG'=>'_','TGA'=>'_',
'TGC'=>'C','TGT'=>'C',
'TGG'=>'W',
'CTA'=>'L','CTC'=>'L','CTG'=>'L','CTT'=>'L',
'CCA'=>'P','CCC'=>'P','CCG'=>'P','CCT'=>'P',
'CAC'=>'H','CAT'=>'H',
'CAA'=>'Q','CAG'=>'Q',
'CGA'=>'R','CGC'=>'R','CGG'=>'R','CGT'=>'R',
'ATA'=>'I','ATC'=>'I','ATT'=>'I',
'ATG'=>'M',
'ACA'=>'T','ACC'=>'T','ACG'=>'T','ACT'=>'T',
'AAC'=>'N','AAT'=>'N',
'AAA'=>'K','AAG'=>'K',
'AGC'=>'S','AGT'=>'S',
'AGA'=>'R','AGG'=>'R',
'GTA'=>'V','GTC'=>'V','GTG'=>'V','GTT'=>'V',
'GCA'=>'A','GCC'=>'A','GCG'=>'A','GCT'=>'A',
'GAC'=>'D','GAT'=>'D',
'GAA'=>'E','GAG'=>'E',
'GGA'=>'G','GGC'=>'G','GGG'=>'G','GGT'=>'G');

sub dna2prot
{
    my $dna = uc shift;
    $dna =~ y/ACGT//cd;
    map {
        s/(...)/$prot{$1}||'?'/eg; $_
    } $dna, ''.substr($dna,1), ''.substr($dna,2);
}

print "$_\n" for dna2prot($sequence)

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In reply to Re: BioPerl translate sequence by educated_foo
in thread BioPerl translate sequence by RobertCraven

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