[DAS] LDAS + Ensembl
Tony Cox
avc@sanger.ac.uk
Thu, 28 Mar 2002 17:07:39 +0000 (GMT)
On Thu, 28 Mar 2002, Lincoln Stein wrote:
+>Hi Tony,
+>
+>You'll need to incorporate the Das2 version into the current online version
+>of Ensembl in order for the contigviewer not to crash on new LDAS sources.
+>You're planning to do this, right?
right.
+>
+>I'm pretty sure that I incorporated James's changes -- at least there is a
+>dsn() call now. Just to be absolutely sure you should do a diff of your
+>version against the latest version (should be in CVS and on FTP). Or send me
+>a tar file of what you're using now and I'll make sure that we are in synch.
righto - thanks
Tony
+>
+>Lincoln
+>
+>On Thursday 28 March 2002 05:16, Tony Cox wrote:
+>> On Wed, 27 Mar 2002 lstein@formaggio.cshl.org wrote:
+>>
+>> Hi Lincoln,
+>>
+>> Thanks for tracking this down. I'll make the code fix for now but include
+>> the updated Das2 version in the next code release - which should be for the
+>> mouse release now that the assembly is all but "blessed".
+>>
+>> I also noticed the file extension thing after getting burned by it when
+>> implementing the data upload scripts. One question: is bz2 a sensible
+>> supported default format? - while lots of (linux) clients may be able to
+>> produce the files it is not a default install on many unix servers like our
+>> Tru64 boxes. If you can use bz2, you can use gz, and I believe the
+>> difference in compression to be relatively small. All in the name of
+>> simplicity and maintainability. It is up there with automatically assuming
+>> that everybodys tar supports the -z option.
+>>
+>> Did you incorporate the changes that James made here, and sent you, to add
+>> back the "sources" call? If we update the Das2 code and this is missing our
+>> upload code will break. For that reason I'll roll your changes below into
+>> our code ASAP and let you know. I'll check out a new copy of Das2 on our
+>> dev server and test it out.
+>>
+>> thanks
+>>
+>> Tony
+>>
+>> PS: yes, we do indeed filter out Component features. We also rely on the
+>> feature type IDs containing either "transcript" or "exon" to enable drawing
+>> of the "humpy/bumpy" introns, rather than simply boxing the features up
+>> (naturally the feature ID has to be the same as well!).
+>>
+>>
+>> +>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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+>
******************************************************
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
******************************************************