[DAS] LDAS + Ensembl

[Tony Cox]

On Wed, 27 Mar 2002 lstein@formaggio.cshl.org wrote:

Licoln,

could you put Jim's test SNP data source on the end of a URL please so that I
can load it up and test it URL-for-URL against your source?

thanks

Tony



+>Hi,
+>
+>I've tracked down the problem with Jim's features not displaying on
+>Ensembl contigview.  I've got it fixed and working now with my
+>server.  To see:
+>
+>	 1) go to http://www.ensembl.org/perl/contigview?contig=Z96810.1.99682
+>	 2) add the das server http://brie2.cshl.org:8081/db/misc/das
+>	    DSN "freeman"
+>	 3) zoom way way in -- there are a LOT of features in the test
+>		 file -- at low mag it looks like a solid line (I was
+>		 going crazy trying to debug this "bug")
+>
+>There were a couple of issues that needed to be fixed.  I'll start
+>with the most important ones:
+>
+>     1) SOFTWARE VERSION SKEW (For Tony's attention!)
+>	The Bio-Das2 library on Ensembl needs to be updated.  A few
+>	weeks ago I added a new tag to the XML and updated Bio-Das2
+>	to accomodate it -- Thomas updated Dazzle.  You need Bio-Das2
+>	version 0.6 or higher.  This is available in the FTP directory
+>	at www.biodas.org, or via CVS (don't worry; only two lines
+>	changed).
+>
+>	If Tony can't make this change because of release schedules,
+>	etc., there's a quick workaround with the LDAS server.  See
+>	below.
+>
+>     2) LOAD PROBLEMS AT JIM'S END
+>        The load file must have the suffix .das (or .das.gz, .das.Z,
+>	.das.bz2 for compressed files).  Otherwise the loader assumes
+>	that it is a GFF-format file.  The sample file Jim sent me 
+>	ended in .txt!  This is a bit anal so I'm going to eliminate
+>	this restriction in the next version of the loader.
+>
+>     3) REDUNDANT DATA IN JIM'S FILE
+>	The same variations were annotated on multiple coordinate
+>	systems. I suppose this a reflection of frustration, but it
+>	isn't necessary.  A cleaned up load file that works is
+>	attached.
+>	
+>     4) CONFIGURATION FILE
+>	This was basically fine, but Jim might want to exclude
+>	features of type "Component" from the features dump.
+>	Otherwise it might show up in the Ensembl display (actually
+>	it doesn't seem to, probably because Tony filters it out).
+>	A slightly modified configuration file with the exclude=
+>	option is  attached.
+>
+>WORKAROUND TO MAKE LDAS WORK WITH ENSEMBL CONTIGVIEW (AS OF 3/27/02):
+>
+>   1) find the CGI script named "das"
+>   2) find the subroutine named error_segment() and comment it out
+>   3) replace the subroutine with a dummy error_segment() that does
+>      nothing:
+>
+>	sub error_segment { }
+>
+>Sorry for the delay in figuring all this out,
+>
+>Lincoln
+>
+>-- 
+>
+>

******************************************************
Tony Cox			Email:avc@sanger.ac.uk
Sanger Institute		WWW:www.sanger.ac.uk
Wellcome Trust Genome Campus	Webmaster
Hinxton				Tel: +44 1223 834244
Cambs. CB10 1SA			Fax: +44 1223 494919
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