[DAS] Locations between bases

[Thomas Down]

Well, that's a separate debate, and I don't really want to open it at the
moment.

However, right now I *am* thinking quite specifically of visualization
issues.  Once you're zoomed in to base-pair resolution, there is a
meaningful distinction between "on a base" and "between a base".

Andy: what I'm trying to model is insertion sites.  I guess that's the main
use for this kind of thing.

               Thomas.



On Mon, Mar 7, 2011 at 3:26 PM, Ewan Birney <birney at ebi.ac.uk> wrote:

>
> I also note that this is stretching DAS's mindset away from
>
>   "DAS is to support visualisation of data on clients for human users to
> read"
>
> to
>
>   "DAS semantically represents things accurately for programmatic
> decisions"
>
>
> I think one is better off keeping these things separate.
>
>
>
> On 7 Mar 2011, at 15:21, Andy Jenkinson wrote:
>
>  Oh Thomas, why do you do it to us?
>>
>> May I ask what the specific application is? Depending on what you need, an
>> insertion can be modelled with a feature covering both bases with a specific
>> glyph (or type).
>>
>> I think what you propose is a common approach, but it is very likely going
>> to break things for some clients (or at least give undefined results). Some
>> additional element would be more compatible.
>>
>> On 7 Mar 2011, at 14:41, Thomas Down wrote:
>>
>>  The day has come when I find I need to be able to distinguish between a
>>> feature which actually *covers* one or a small number of bases (e.g. a
>>> SNP)
>>> and a feature which refers to a point between two bases (e.g. an
>>> insertion).  Have any other DAS folk dealt with this before, and if so
>>> how?
>>> One possible approach would be something like:
>>>
>>>       <START>30000000</START>
>>>       <STOP>29999999</STOP>
>>>
>>> ...as a way to reference the position between the 29999999th and
>>> 30000000th
>>> bases in a sequence... but is this going to break lots of existing client
>>> code?
>>>
>>> (I also rather dislike it because there's currently sanity-checking code
>>> in
>>> Dazzle to stop you doing stuff like this...)
>>>
>>> Any better ideas?
>>>
>>>          Thomas.
>>>
>>> PS. Yes, I'm aware this is a solved problem in DAS/2.  Afraid I need a
>>> DAS/1
>>> solution, though.
>>> _______________________________________________
>>> DAS mailing list
>>> DAS at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/das
>>>
>>
>>
>> _______________________________________________
>> DAS mailing list
>> DAS at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/das
>>
>
>