[Bioperl-l] write protein sequence by Bio::SeqIO

[suhoiy]

Hello all,

I am sorry to bother you. There is a problem in my code. I want to write a protein
sequence in genbank format, but the code change it to nucleic acid sequence. For
example:

========
my $in   = Bio::SeqIO->new(  '-format' => 'genbank', 
                                             '-file'   => 'sample.genpept',
		             );
my $out  = Bio::SeqIO->new('-format' => 'genbank',
                                            '-file' => '>sampleout.genpept',
                                          );
my $seq = $in->next_seq;
$out->write_seq($seq);
========

the locus line of origin sequence is:
LOCUS       108_LYCES                102 aa            linear   PLN 15-JUL-1999

while the locus line of the output sequence is:
LOCUS       108_LYCES                102 bp    linear  linear   PLN 15-JUL-1999

I use bioperl 1.0.2. there are these lines in the write_seq method in Bio::SeqIO::genbank:

========
    if( !$seq->can('molecule') || ! defined ($mol = $seq->molecule()) ) {
	$mol = $seq->alphabet || 'DNA';
    }
========

many thanks for your help!

suhoiy