[Bioperl-l] Bio::DB::GenBank question
Jason Stajich
jason.stajich at gmail.com
Sat Jul 24 16:41:30 UTC 2010
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
>
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