How To Get Genbank File Using Bioperl

Question

[shilpy]

I currently have the following:

use Bio::SeqIO;

$seqio_obj = Bio::SeqIO->new(-file => "J01673.gb", -format => "genbank" );
$seq_obj = $seqio_obj->next_seq;

I am not able to get output using above code.

[Neilfws]

That's because none of that code generates any output.

[Peter]

Have you already downloaded the file J01673.gb or are you trying to get BioPerl to download it for you? See Hernan's reply below.

Answer 1

[Hernán]

May be something like:

use Bio::DB::GenBank;
$gb = new Bio::DB::GenBank(-retrievaltype => 'tempfile' , -format => 'gb');
$seqio_object = $gb->get_Stream_by_id(['J00522']);
while( my $seq = $seqio_object->next_seq ) {
    $seqio_object->write_seq($seq);}