[DAS2] Sequence retrieval proposal

[Suzanna Lewis]

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:

> 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
> 1 Bungtown Road
> Cold Spring Harbor, NY 11724
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