[DAS2] Getting individual features in DAS/1

[Helt,Gregg]

We need to discuss at today's meeting.  I don't think the original DAS
list should be closed, but rather continue to serve as a list to discuss
the DAS/1 protocol and implementations, and the DAS2 mailing list should
focus on DAS/2.  If we mix DAS/1 and DAS/2 discussions in the same
mailing list I think it's going to lead to a lot of confusion.

	gregg

> -----Original Message-----
> From: das2-bounces at portal.open-bio.org
[mailto:das2-bounces at portal.open-
> bio.org] On Behalf Of Andrew Dalke
> Sent: Monday, November 21, 2005 9:09 AM
> To: DAS/2
> Subject: Re: [DAS2] Getting individual features in DAS/1
> 
> 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
> 
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