[Bioperl-l] SeqFetcherI (fwd)

[Jonathan Epstein]

[Hi, Lincoln et al]

I, too, would especially welcome the opportunity to fetch by GI.

This is particularly an issue when parsing blast results derived from searching against the human genome.  For some reason, retrieving by accessions (on the web or via BioPerl) frequently fails while retrieving by GIs works (on the web).  If we could retrieve by GI this would be a great help.

-Jonathan

At 11:43 AM 5/21/2001 , Lincoln Stein wrote:
>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 ;)
>  > 
>  > 
>  > 
>  >  
>  > 
>  > 
>  > _______________________________________________
>  > Bioperl-l mailing list
>  > Bioperl-l@bioperl.org
>  > http://bioperl.org/mailman/listinfo/bioperl-l
>
>-- 
>========================================================================
>Lincoln D. Stein                           Cold Spring Harbor Laboratory
>lstein@cshl.org                                   Cold Spring Harbor, NY
>
>NOW HIRING BIOINFORMATICS POSTDOCTORAL FELLOWS AND PROGRAMMERS. 
>PLEASE WRITE FOR DETAILS.
>========================================================================
>_______________________________________________
>Bioperl-l mailing list
>Bioperl-l@bioperl.org
>http://bioperl.org/mailman/listinfo/bioperl-l



Jonathan Epstein                                Jonathan_Epstein@nih.gov
Head, Unit on Biologic Computation              (301)402-4563
Office of the Scientific Director               Bldg 31, Room 2A47
Nat. Inst. of Child Health & Human Development  31 Center Drive
National Institutes of Health                   Bethesda, MD 20892