[DAS] Restricting the range of an alignment query.

Thomas Down thomas.a.down at gmail.com
Thu Aug 12 11:06:19 UTC 2010

On Thu, Aug 12, 2010 at 10:41 AM, Andy Jenkinson
<andy.jenkinson at ebi.ac.uk>wrote:
> OK so you're a lot further along, sounds good. A while back we were aiming
> to get compara alignments as DAS too (which necessitated the cols
> parameter).

By "compara alignments", you're talking about the MySQL ensembl-compara
database, right?

Is there still any interest in this on the Ensembl side?  It's something I'm
going to be needing soon, too (my current chain-file-based server doesn't
handle all the cases I'm interested in).

> > As regards to what would be necessary to do what you want, I don't think
> we can change the subject parameter unless the existing alignment servers
> and clients using it can be changed, i.e. Pfam (not sure if there are
> others). I can't really think of another way to do it off the top of my head
> - the 'query' parameter has space for start/end positions and can be a
> sequence identifier, but this is more like 'get all alignments containing
> this sequence' which is not quite the same thing. It would also be a bit
> clunky to describe - what would "?query=alignment42:30,40" do?
> >
> > Any suggestions?
> >
> > Well, the obvious thing is to couple the coordinate restrictions to the
> sequence to which they apply.
> >
> > Simplest solution I can think of would be to add:
> >
> >            ?segment=seqName[:start,end]
> >
> > ...where:
> >
> >            ?segment=P12345
> >
> > ...is synonymous with:
> >
> >            ?subject=P12345        (which would still be supported),
> >
> > ...but...
> >
> >            ?segment=22:30000000,30200000
> >
> > ...does what I want.   Maybe not the cleanest solution, but I don't think
> it's going to horribly break anything (unless there are subtleties I'm
> missing here?)
> >
> >                      Thomas.
> I think you're right in that it is going to need another parameter to make
> it work. Any objections from anyone? What would happen if you specified
> multiple segments which did not correspond to the same section? Return
> multiple blocks representing multiple horizontal sections?

That's the idea.

Use case for this: user is viewing 22:30000000,30200000, then zooms out.
 Trigger a fetch for:


...then merge the results into the working set.


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