« Return to Thread: Different rendering for wiggle tracks
Re: Different rendering for wiggle tracks
by Stephen Taylor-5
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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
------------------------------------------------------------------------------
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
>
> 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
------------------------------------------------------------------------------
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
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