[Bioperl-l] SeqFetcherI (fwd)

[Ewan Birney]

On Thu, 17 May 2001, Elia Stupka wrote:

> I am forwarding an e-mail from Val Curwen over here at EnsEMBL about our
> new SeqFetcherI interface. Basically a tiny tiny interface with one method
> called fetch_Seq_by_dbname_accession, which we are going to use to fetch
> sequences from a bioperl-db database as well as using efetch,getz,etc.
> within the EnsEMBL Pipeline. 
> 
> One could envisage simple implementantions in bioperl-db such as a
> Bio::SeqIO loop that return a Seq when it finds the right one, and we
> already have one over here using the bioperl indexer. 
> 
> Is everybody cool with this complex and clever piece of code? ;)

Why is Bio::DB::RandomAccessI not ok with

  $db->get_Seq_by_acc();

and

  $db->get_Seq_by_id();

(you can implement only one if you wish).


Ewan - hoping that wheel reinvention wont have to occur ;)