[Bioperl-l] Re: Seq or SeqIO to BSML

[Nathan O. Siemers]

So if we generate an ensembl embl format dump and then load it into
bioperl via seqio, that will be equivalent for our purposes to using
the original ensembl Seq(IO) object?  That's fine with me, but I
thought you had voiced a reservation to doing it this way in
Copenhagen. Perhaps I misunderstood.  The eventual point will be to
create a piece of code that will work with ensembl's native tongue
(SeqIO I assume) and send out a stream of xml/bsml from the ensembl
site.

nathan


Ewan Birney <birney@ebi.ac.uk> writes:

> On Fri, 3 Aug 2001, Nathan O. Siemers wrote:
> 
> > 
> > Hello Ewan,
> > 
> >         As mentioned, we have volunteered to write a BSML output
> >         module for Seq or SeqIO objects, initially for use with
> >         ensembl but of course to be designed to be generally useful.  
> 
> 
> Basically go for SeqIO system and from there we can put in additional
> hooks.
> 
> > 
> >         Could you provide a data dumper output of a fairly small but
> >         richly annotated area of the genome from ensembl?  We can eval
> >         it up locally and use it as our starting point.
> > 
> 
> It is easy to generate -> go to ensembl -> find a gene rich region ->
> click on export -> click on generate flat file
> 
> 
> 
> >         Finally, I would welcome discussion as to where this code
> >         should eventually be placed (how tightly integrated?)  in the
> >         bioperl structure.
> > 
> 
> 
> It should be a SeqIO module, working off RichSeq definitions like
> embl/genbank but able to cope with Bio::SeqI stuff. I'll handle any
> necessary ensembl extensions first off as it will probably confuse you ;)
> 
> 
> 
> >         Thanks,
> > 
> > 
> >         nathan
> > 
> >         
> > 
> >         
> > 
> > -- 
> > Nathan Siemers, Group Leader, Bioinformatics-Applied Genomics
> > Bristol-Myers Squibb Pharmaceutical Research Institute, Hopewell 3-0.07
> > P.O. Box 5400, Princeton, NJ 08543-5400, (609)818-6568
> > nathan.siemers@bms.com
> > 
> 
> -----------------------------------------------------------------
> Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
> <birney@ebi.ac.uk>. 
> -----------------------------------------------------------------
> 
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-- 
Nathan Siemers, Group Leader, Bioinformatics-Applied Genomics
Bristol-Myers Squibb Pharmaceutical Research Institute, Hopewell 3-0.07
P.O. Box 5400, Princeton, NJ 08543-5400, (609)818-6568
nathan.siemers@bms.com