[Open-bio-l] GAME -> BioSQL?

[David Huen]

On Friday 07 Jun 2002 10:59 am, Matthew Pocock wrote:
> Hilmar Lapp wrote:
> > The subject basically says it all. Does anyone have a GAME loader for
> > BioSQL?
> >
> > Bioperl has a GAME SeqIO parser (what about BioJava?). Supposedly,
> > bioperl-db can load Bio::Seq objects into BioSQL (correct?). Is some of
> > the information originally contained in the GAME input lost along the
> > way? I.e., if I wanted to, could I round-trip GAME through BioSQL
> > (assuming that Bioperl GAME SeqIO could write GAME which I think it
> > can't)?
> >
> > 	-hilmar
>
> Hi Hilmar,
>
> We definitely have a GAME reader. I don't know if we have a GAME writer
> though. I've had reasonable success round-tripping stuff with the
> biojava BioSQL driver. Your script would look something like
> frankenstein's child of game.TestGAME and biosql.UploadFlat both under
> the biojava-live/demos directory.
>
We do have a GAME reader (and I have another that will do more than the 
original one but not in the same way) but not a GAME writer.  The mapping 
between the Biojava object model and GAME in sufficiently fraught when 
going from Biojava/BioSQL that I cannot devise a writer that will write 
GAME in a form that any GAME user could use.  The problem is that GAME as 
used by Gadfly has a gene model that is rather more concrete than the 
Biojava semantic free model and interpretation is need to determine which 
Biojava feature types should be translated into what GAME features.  As 
GAME is in spec-free mode right now (the spec for me is my interpretation 
of what I infer from Gadfly data - I think they are the major remaining 
user of GAME), it's not easy to figure out general solutions.

Be warned that the GAME reader as it stands uses GAME-1.001 coordinates 
while at least some data out there from Gadfly is in GAME-1.2 coordinates 
which have a different basis!  I do have stuff that does 1.2 coordinates 
too but not in any clean form (ie. suitable for internal use or by a 
determined hacker only).

Regards,
David Huen


Cambridge, CB2 3UH
U.K.