[DAS2] Sequence retrieval proposal
suzi at fruitfly.org
Mon Dec 19 18:18:13 UTC 2005
yikes, i lost track of the time. i had planned on being on the call.
sorry about that.
On Dec 19, 2005, at 9:10 AM, Lincoln Stein wrote:
> Just CVS updated the spec today in anticipation of the telecon, and I
> see any changes to the feature or region requests. Didn't we agree to
> On Monday 12 December 2005 04:33 pm, Steve Chervitz wrote:
>> On Sun, 11 Dec 2005 Andrew Dalke wrote:
>>>> I am also somewhat loath to add yet another sequence file format to
>>>> world. Seems reasonable to state that a DAS/2 server can supply
>>>> sequence in
>>>> an alternative format via requests such as:
>>> 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"
>>> "If the server implements one or more of these sequence formats
>>> 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
>> alternative feature formats:
>>> 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
>>>> proper fasta format. I put in a little bit of description of a
>>>> DAS-acceptable fasta format here in the retrieval spec:
>>> 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
>> 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
>> info, and there are so many variations out there, we might consider
>> that clients are free to ignore the header. Then if we do this, why
>> 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,
>> Does anyone know how DAS/1 clients make use of these from the seq
>>> The wikiepedia entry for FASTA is pretty good.
>> Interesting. That more-than-one-header business seems evil. They give
>> good link for alternative sequence formats.
>> DAS2 mailing list
>> DAS2 at portal.open-bio.org
> Lincoln D. Stein
> Cold Spring Harbor Laboratory
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