[ensembl-dev] Protein feature DAS track

Liu, Mingyi Mingyi.Liu at bms.com
Tue Jun 5 20:56:22 BST 2012


I've sent this email about adding protein DAS track a couple weeks ago but haven't seen a reply (I hope I didn't miss any).  Would anyone experienced with adding custom protein tracks in protview please take a look at this?  Thanks!

I've been try to figure out how to display some protein features using custom DAS tracks.  There are rather patchy documentation about this. In the end, here's what I've got:

In Homo_sapiens.ini, I have:
protfeat = 1
dsn = protfeat
state = off
url = http://...
label = Protein Features
caption = Protein Features
col = purple
description = Protein Features
on = [transview protview]
type = ensembl_peptide

In proserver.ini, I have:

In proserver's sourceAdaptor directory I have the protfeat.pm properly defined and tested with the http://.../protfeat/features?segment=ENSP..., the returned features were correct.

The problem is that I could attach the DAS to the protein summary for the transview, but the DAS track won't display. If I check the DAS track for the 'External Data' section for transview, clicking on this new external source display the correct number of result with a message like:

There were 29 non-text annotations. To view these, enable the DAS source on a graphical view.

Ensembl doc on this (http://useast.ensembl.org/info/data/ensembl_das.html) seems to indicate the protview is no longer available? Which graphical view is still available? I tried Protein Summary but it didn't seem to display custom DAS tracks, despite that you can attach.

BTW, I'd like to display the protein features in Protein Summary. I had success adding DAS for contigview using genomic coords, but this is not an option for the protein features.  Is there any way to display the features in a graphical view using protein coordinates?



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