sub translate {<\/div>
<\/div>
# Translate the input file from dna to protein, replacing the<\/div>
# original file. Sequences that are already protein remain<\/div>
# untouched.<\/div>
<\/div>
my ( $filename, $fullpath ) = @_;<\/div>
<\/div>
# Input sequence stream.<\/div>
my $seqI = Bio::SeqIO->new( -file => $fullpath );<\/div>
<\/div>
# Output sequence stream.<\/div>
my $tempfile = File::Temp->new( SUFFIX => \'.fasta\' )->filename;<\/div>
my $seqO = Bio::SeqIO->new(<\/div>
-file => ">$tempfile",<\/div>
-format => \'fasta\'<\/div>
);<\/div>
<\/div>
# Translate dna sequences and write to temp file.<\/div>
while ( my $seq = $seqI->next_seq ) {<\/div>
if ( $seq->alphabet eq \'dna\' ) {<\/div>
$seq = $seq->translate;<\/div>
}<\/div>
$seqO->write_seq($seq);<\/div>
}<\/div>
<\/div>
$_->close for ( $seqI, $seqO );<\/div>
<\/div>
# Replace the original file with the temporary one with the<\/div>
# translated sequences.<\/div>
move( $tempfile, $fullpath );<\/div>
<\/div>
}<\/div><\/pre><\/div>\n \n <\/div>\n\n