From ilari.scheinin at helsinki.fi  Tue Dec  6 05:01:36 2005
From: ilari.scheinin at helsinki.fi (Ilari Scheinin)
Date: Tue Dec  6 05:24:21 2005
Subject: [DAS] Getting individual features
Message-ID: <1133863296.439561807fad7@www1.helsinki.fi>

I am setting up a DAS server that serves CGH data from a database to  
a visualization software (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 be done simply 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. I wonder if this is a limitation of the generic seqfeature  
plugin, or a limitation of Dazzle?

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