[DAS2] Sequence retrieval proposal

[Lincoln Stein]

Hi,

Just CVS updated the spec today in anticipation of the telecon, and I don't 
see any changes to the feature or region requests. Didn't we agree to drop 
region?

Lincoln

On Monday 12 December 2005 04:33 pm, Steve Chervitz wrote:
> On Sun, 11 Dec 2005 Andrew Dalke wrote:
> > Steve:
> >> I am also somewhat loath to add yet another sequence file format to the
> >> world. Seems reasonable to state that a DAS/2 server can supply
> >> sequence in
> >> an alternative format via requests such as:
> >>
> >>   http://www.wormbase.org/das/genome/volvox/1/sequence?format=GAME
> >
> > That makes good sense to me.
> >
> >> Here's a brief tour of some possibly extensible candidates:
> >
> > Do you want to say this as:
> >    "The server must implement these sequence formats"
> > or
> >    "If the server implements one or more of these sequence formats then
> >      it must use the corresponding id and content-type."
> > ?
> >
> > Or say nothing and wait until several different servers implement
> > this then standardize on what they do?
> >
> > I don't think anyone here seriously wants the first. :)
> >
> > The last is my favorite, then the middle one.
>
> The last is fine with me. This is the approach we use for type-specific
> alternative feature formats:
> http://biodas.org/documents/das2/das2_get.html#types
>
> > My stronger preference is to get a complete 2.0 spec out.  Do
> > you or other users need checksum validation of the sequence and/or
> > alternate sequence formats in 2.0?  What prevents you from extending
> > existing HTTP headers or experimenting with extensions then
> > submitting your experience for inclusion in future versions of
> > the spec?
> >
> > My sense is that this can wait.
>
> Yep. Especially in light of this morning's teleconf (notes for which are on
> the way). This seems like a good place to invoke YAGNI (
> http://keithdevens.com/quotes/YAGNI ).
>
> >> We might consider proscribing some conventions for what DAS considers
> >> proper fasta format. I put in a little bit of description of a
> >> DAS-acceptable fasta format here in the retrieval spec:
> >> http://biodas.org/documents/das2/das2_get.html#sequence
> >
> > Do current DAS clients even use the header?
> >
> > Will future ones use it?  If so, why?  Shouldn't all the information
> > in a header be available as an annotation?
>
> Don't know. Seems like it should be left to the client implementation to
> decide what to do with the header. The aim of the sequence request (soon to
> be 'residues') is to get sequence data, not annotations.
>
> If we're not saying what DAS/2 clients are supposed to do with the header
> info, and there are so many variations out there, we might consider stating
> that clients are free to ignore the header. Then if we do this, why use
> fasta format instead of raw sequence?
>
> Btw, DAS/1 used an XML formatted response for sequence data. The DAS/1
> sequence element has these attributes: id, start, stop, moltype, version.
> Does anyone know how DAS/1 clients make use of these from the seq response?
>
> > The wikiepedia entry for FASTA is pretty good.
> >    http://en.wikipedia.org/wiki/Fasta_format
>
> Interesting. That more-than-one-header business seems evil. They give a
> good link for alternative sequence formats.
>
> Steve
>
>
>
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-- 
Lincoln D. Stein
Cold Spring Harbor Laboratory
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