Re: Different rendering for wiggle tracks

Hi Steve,

Sadly the default "stdev2" default is still in the Bio::Graphics
distribution! I swear I removed it, but perhaps I failed to commit the code.
I am working on another bug in Bio::Graphics and will submit a new version
to CPAN.

Unfortunately the stdev2 filtering occurs at LOAD time, which means you have
to reload all wiggle files. Making stdev2 the default was a bad mistake and
I regret the inconvenience.

Lincoln

On Fri, May 29, 2009 at 11:01 AM, Steve Taylor
<stephen.taylor@...>wrote:

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@... <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

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