[Bioperl-l] Bio::DB::WebDBSeqI

[Jason Stajich]

Checked in new modules Bio::DB::WebDBSeqI, Bio::DB::NCBIHelper
which provide common functionality for connecting to Webbased Sequence
databases. 

Bio::DB::GenBank, Bio::DB::GenPept, Bio::DB::SwissProt, t/DB.t were all
updated to migrate to this new code.

The interface to the original modules has not changed, however, more
options are supported and LWP is fully supported for those behind
firewalls.  For example;

use Bio::DB::GenBank;
my $db = new Bio::DB::GenBank;
$db->ua->proxy('protocol', 'hostname');

my $seq = $db->get_Seq_by_acc($accession);

Realize, as always, NCBI Entrez does not distinguish queries for unique
identifiers (genbankid) and accession numbers so the routines
get_Seq_by_id() or get_Seq_by_acc() are identitical in this
implementation.

Bio::DB::SwissProt talks to expasy right now, but other swissprot
providers could be added.


Also, about temporary files.  I am using File::Temp, which behaves
wonderfully on my solaris machines.  I'd appreciate those with different
architectures testing out and letting me know if we are having any
problems.

I have also updated Bio::Seq::LargePrimarySeq to use File::Temp as well
and find it behaves nicely.  

Jason Stajich
jason@chg.mc.duke.edu
Center for Human Genetics
Duke University Medical Center 
http://www.chg.duke.edu/