[DAS2] Getting individual features in DAS/1

[Andrew Dalke]

Has anyone answered Ilari's question?

I never used DAS/1 enough to answer it myself.

If the normal DAS list is closed, is this the right place for DAS/1 
questions?


On Nov 18, 2005, at 4:22 PM, Ilari Scheinin wrote:

> This mail is not really about DAS/2, but the web site says the 
> original DAS mailing list is now closed.
>
> I am setting up a DAS server that serves CGH data from my database to 
> a visualization software, which in my case is gbrowse. I've already 
> set up Dazzle that serves the reference data from a local copy of 
> Ensembl. I need to be able to select individual CGH experiments to be 
> visualized, and as the measurements from a single CGH experiment cover 
> the entire genome, this cannot of course be done by specifying a 
> segment along with the features command.
>
> I noticed that there is a feature_id option for getting the features 
> in DAS/1.5, but on a closer look, it seems to work by getting the 
> segment that the specified feature corresponds to, and then getting 
> all features from that segment. My next approach was to use the 
> feature type to distinguish between different CGH experiments. As all 
> my data is of the type CGH, I thought that I could use spare this 
> piece of information for identifying purposes.
>
> First I tried the generic seqfeature plugin. I created a database for 
> it with some test data. However, getting features by type does not 
> seem to work. I always get all the features from the segment in 
> question.
>
> Next I tried the LDAS plugin. Again I created a compatible database 
> with some test data. I must have done something wrong the the data 
> file I imported to the database, because getting the features does not 
> work. I can get the feature types, but trying to get the features 
> gives me an ERRORSEGMENT error.
>
> I thought that before I go further, it might be useful to ask whether 
> my approach seems reasonable, or is there a better way to achieve what 
> I am trying to do? What should I do to be able to visualize individual 
> CGH profiles?
>
> I'm grateful for any advice,
> Ilari

					Andrew
					dalke at dalkescientific.com