[Bioperl-l] SeqFetcherI (fwd)

[Lincoln Stein]

Can't one have a Bio::DB::RandomAccessI connected to a meta database
that accepts compound accessions and then dispatches to the correct
database?  Or is "gb|A12345" just too ugly for words?

Lincoln

Ewan Birney writes:
 > 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 ;)
 > 
 > 
 > 
 >  
 > 
 > 
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Lincoln D. Stein                           Cold Spring Harbor Laboratory
lstein@cshl.org			                  Cold Spring Harbor, NY

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