[DAS] DAS spec clarifications

[Ewan Birney]

On Fri, 19 Jul 2002, Steve Chervitz wrote:

> Some issues came up in our internal discussion at Affymetrix about DAS that I'd
> like clarification on:
> 
> * Should the server perform a logical AND or an OR when a feature command
> specifies both type and category?
> 
> * It would be nice if the feature command permitted method specification in
> addition to type and category. This would enhance the usefulness of the method
> information you get back from the types command.
> 
> * Does a server have to deal in 1-based sequence coordinates to be
> DAS1-compliant? I'm assuming yes, but it would be good to state so explicitly
> in the spec. This is relevant to a recent thread on the Bioperl list: 


Yes.

> 
> http://bioperl.org/pipermail/bioperl-l/2002-July/008318.html
> 
> Internally, we make much use of 0-based half-open intervals (or "inter-base"
> coordinates as we call them, where the numbers refer to the positions
> in-between the bases). It would be great if a server could specify the
> coordinate system it uses. It would then be up to the client to do the
> appropriate conversion if necessary. Perhaps something for DAS2?
> 

I would vote against DAS coordinates changing - pick one, and stick to
it. In the broader public arena we have 20 years of legacy in one base,
inclusive coordinates. start = internal_start+1 is not a hard thing to put
in server side....





> Steve
> 
> =====
> Steve Chervitz
> sac@bioperl.org
> 
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Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
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