[Bioperl-l] Bio::SeqIO::game

[Bradley Marshall]

--- Ewan Birney <birney@ebi.ac.uk> wrote:
> On Fri, 1 Dec 2000, Bradley Marshall wrote:
> 
> > 
> > How about this as a solution?
> > 
> > We'll add a top level attribute and/or tag
> describing
> > whether or not the document is "chunkable".  Chris
> > suggested we have a top level <flavor> element. 
> This
> > can specify whether or not the document is
> chunkable. 
> > A chunkable document would have this structure:
> > 
> 
> ;). 
> 
> I think all useful documents will be chunkable. 

I agree that this is the case for large data transfer
jobs like you're talking about.  A question we have is
whether or not you're planning on transfering only
genomic seqs w/ features or if you're doing mixed
files - with genomic seqs' features forming mRNA and
AA sequences.  It is this second case in which keeping
things "chunkable" becomes difficult.  

But this flexibilty is also a major advantage of the
GAME format. And even if a document is NOT chunkable,
parsing performance is pretty gude for non-huge
documents.  We still need to deal with the file-handle
issue....


Brad


> I'd
> claim that were just
> letting ourselves into trouble if we allow badly
> compacted XML to be
> "valid"
> 
> This solution is ok, but I would argue that it is
> better to be strict
> about these things otherwise implementations either
> will have to throw
> exceptions on non chunkable documents or have other
> poorly defined
> criteria....
> 
>  
> 
> > <game>
> > <flavor>chunkable</flavor>
> > <seq1/>
> > < all features pertaining to seq1 />
> > <seq2/>
> > < all features pertaining to seq2 />
> > <seq3/>
> > < all features pertaining to seq3 />
> > </game>
> > 
> > If a document is chunkable, we will read into
> memory a
> > string from the first <seq> to the next <seq> and
> > parse that in one pass when next_seq is called. 
> Then
> > we'll move on to the next chunk.
> > 
> > If the document is not chunkable, we'll continue
> to
> > parse it as we have been.  This allows us to keep
> GAME
> > flexible and yet still be useful in the SeqIO
> system.
> > 
> > Brad
> > 
> > 
> > 
> > 
> > __________________________________________________
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> 
>
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> Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44
> 1223 494420
> <birney@ebi.ac.uk>. 
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