Re: Different rendering for wiggle tracks

Hi Lincoln/Jason,

The wiggle code was recently moved out of GBrowse and into a separate Bio::Graphics distribution. At the same time we removed the default smoothing to better render the raw data. Could you try to download the CPAN version of Bio::Graphics and install it on *top* of the GBrowse-CVS version? If the data continues to look wrong, I will fix it.

We tried it with Bio::Graphics 1.94 and no difference...at least when I just reloaded the page...

Jason, the code you pointed out

  my $trim      = $self->current_track->{display_options}{trim} || 'stdev2';

seems to fly in the face of the docs
       
http://gmod.org/wiki/Gbrowse/Uploading_Wiggle_Tracks#Wiggle_Track_Options_Supported_by_GBrowse

 trim              stdev|stdev2|stdevn          # default is none

So would it be better to change it to

  my $trim      = $self->current_track->{display_options}{trim} || 'none';

?

What I am not 100% clear on is do we have regenerate all the wig binaries to see an effect or just reload the page after these fixes (assuming mod_perl is off!)?

Thanks,

Steve

Lincoln

On Thu, May 28, 2009 at 11:06 AM, Steve Taylor <stephen.taylor@... <mailto:stephen.taylor@...>> wrote:

   Hi,

   We have two installations of gbrowse for our production and test
   environment.

   (1) The gbrowse production server was from the 1.69 tar ball using
   ActivePerl-5.8.8.822, and run with bioperl-live as on 2008-09-04
   (2) On the gbrowse development server we installed GBrowse-CVS as on
   2009-03-19 using netinstall to see if this would fix some problems

   However, on (2) we noticed there is a difference in the way wiggle
   tracks are rendering. The (2) version looks smoothed and wrong
   compared with the raw data.
   Was this type of rendering desired? We notice the wiggle_xyplot.pm

   <http://wiggle_xyplot.pm> code is completely different.

   To see what I mean have a look at:

   (1) http://sara.molbiol.ox.ac.uk/userweb/staylor/gbrowse/gbrowse.jpg
   (2) http://sara.molbiol.ox.ac.uk/userweb/staylor/gbrowse/gbrowsedev.jpg

   The age old question :-) do we wait for 1.7 to fix this or is this
   type of rendering likely to stay?

   Kind regards and thanks,

   Steve
   ------------------------------------------------------------------
   Medical Sciences Division
   Weatherall Institute of Molecular Medicine/Sir William Dunn School
   Oxford University

   ------------------------------------------------------------------------------
   Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT
   is a gathering of tech-side developers & brand creativity
   professionals. Meet
   the minds behind Google Creative Lab, Visual Complexity, Processing, &
   iPhoneDevCamp as they present alongside digital heavyweights like
   Barbarian
   Group, R/GA, & Big Spaceship. http://p.sf.net/sfu/creativitycat-com
   _______________________________________________
   Gmod-gbrowse mailing list
   Gmod-gbrowse@...

   <mailto:Gmod-gbrowse@...>

   https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse




--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514

Assistant: Renata Musa <Renata.Musa@... <mailto:Renata.Musa@...>>


------------------------------------------------------------------------

------------------------------------------------------------------------------
Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT is a gathering of tech-side developers & brand creativity professionals. Meet
the minds behind Google Creative Lab, Visual Complexity, Processing, & iPhoneDevCamp as they present alongside digital heavyweights like Barbarian Group, R/GA, & Big Spaceship. http://p.sf.net/sfu/creativitycat-com

------------------------------------------------------------------------

_______________________________________________
Gmod-gbrowse mailing list
Gmod-gbrowse@...
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse