[Bioperl-l] Bio::DB::GenBank question

[Jason Stajich]

Hi. You should ask questions to the list. There are many who can  
answer your question there.

In the older versions you can put the retrieve statement in an eval  
block. I think newer behavior may be only to issue a warning and keep  
going.

You may be able to also set verbose to -1 (-verbose => -1) in the  
initialization of the db obj and see whether it skips or fails on  
missing ID.
  -Jason.
Sent from my iPod

On Jul 23, 2010, at 6:48, Hongseok Tae <htae at vbi.vt.edu> wrote:

> Hi Jason Stajich,
>
> I am using Bioperl and it is very useful. I have a question about  
> Bio::DB::GenBank.
> This is a simple code.
>
> --------------------------
>
> $db = Bio::DB::GenBank->new();
> @ids = ("LOC441435", "X78121");
> foreach $id (@ids){
> $seqobj = $db->get_Seq_by_id($id);
> $seqstr   = $seqobj->seq();
> print "$>id\n$seqstr\n";
> }
>
> --------------------------
>
> If there is no entry for an ID, I would like to skip it and to get  
> next one. But this code stops running when an ID does not exist in  
> genbank.
> How can I solve this problem?
>
> Thanks.
> Hongseok Tae
>