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

[Heikki Lehvaslaiho]

Ewan Birney wrote:
> 
> On Wed, 4 Apr 2001, Heikki Lehvaslaiho wrote:
> 
> > Hi,
> >
> > The new version of emblfetch cgi script went live today here at EBI.
> > It is now possible to retrieve raw text files without HTML tags which
> > makes entries a lot easier to parse.
> >
> > I've just committed Bio::DB::EMBL which has four methods for
> > retrieving entries:
> >
> > get_Seq_by_id()
> > get_Seq_by_acc()
> > get_Seq_by_version()
> > get_Stream_by_batch()
> >
> >
> > Design issues:
> >
> > The get_Seq_by_version() is a new method and should probably be added
> > into
> >
> > get_Stream_by_batch() is in Bio::DB::NCBIHelper but I rather not
> > inherit from it. ;-) Bio::DB::WebDBSeqI again?
> 
> I'm cool with Bio::DB::WebDBSeqI changes...
> 
>    get_Stream_by_batch()
> 
> and
> 
>    get_Seq_by_version (should this be get_Seq_by_acc_version?)

Not in my opinion. Version implies accession. The version number
itself is not a useful identifier.

EMBL docs:
---------------------------------------
3.4.3 The SV Line

The SV (Sequence Version)  line  contains  the  new  format  of  the 
nucleotide sequence identifier. 

An example of a Sequence Version line is shown below: 

        SV   X56734.1

The new nucleotide sequence identifier is of  the  form  of 
'Accession.Version' where  the  accession  number  part  will be
stable, but the version part will be incremented when the sequence
changes. 
---------------------------------------

	-Heikki

> Jason?
> 
> >
> >
> > BTW, from the servers point of view it is exactly the same which
> > method you use, it takes in up to 50 identifiers and returns the
> > corresponding unique entries.
> >
> > Have fun,
> >
> >       -Heikki
> >
> > --
> > ______ _/      _/_____________________________________________________
> >       _/      _/                      http://www.ebi.ac.uk/mutations/
> >      _/  _/  _/  Heikki Lehvaslaiho          heikki@ebi.ac.uk
> >     _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
> >    _/  _/  _/  Wellcome Trust Genome Campus, Hinxton
> >   _/  _/  _/  Cambs. CB10 1SD, United Kingdom
> >      _/      Phone: +44 (0)1223 494 644   FAX: +44 (0)1223 494 468
> > ___ _/_/_/_/_/________________________________________________________
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> >
> 
> -----------------------------------------------------------------
> Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
> <birney@ebi.ac.uk>.
> -----------------------------------------------------------------

-- 
______ _/      _/_____________________________________________________
      _/      _/                      http://www.ebi.ac.uk/mutations/
     _/  _/  _/  Heikki Lehvaslaiho          heikki@ebi.ac.uk
    _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
   _/  _/  _/  Wellcome Trust Genome Campus, Hinxton
  _/  _/  _/  Cambs. CB10 1SD, United Kingdom
     _/      Phone: +44 (0)1223 494 644   FAX: +44 (0)1223 494 468
___ _/_/_/_/_/________________________________________________________