Re: [Gmod-gbrowse] [Gmod-help] Change bgcolor using notes

[Scott C. <sc...@sc...>]

Hi Wilfried,

Please keep the GBrowse mailing list cc'ed.

OK, a few more things:

1. Images are cached on the server, so if you change the track and
then just reload the page, you will not see a change until that cached
image expires (usually set for an hour).  You can make the server
redraw by zooming or panning.

2. One thing I do with debugging in-conf callbacks is to have what I
am testing also go in the label, like this:

label   = sub {
               my $f = shift;
               my ($note) = $f->notes;
               return $note;
     }

If that doesn't turn up anything useful, you can also put debugging
"warn" statements in the code of the callback which will print content
to the apache error log.

Scott


On Wed, Sep 7, 2011 at 5:35 PM, Wilfried Guiblet
<wil...@up...> wrote:
> Thank you for answering so fast. I cc here my conf file
>
>
> [GENERAL]
> db_adaptor    = Bio::DB::SeqFeature::Store
> db_args       = -adaptor memory
>                 -dir '/var/lib/gbrowse2/databases/taino'
>
> plugins = TrackDumper
>
> default features = ExampleFeatures
>
> region segment = 50000000
>
> initial landmark = chr1
>
>
>
> ########################
> # Default glyph settings
> ########################
>
> [TRACK DEFAULTS]
> glyph         = generic
> height        = 10
> bgcolor       = red
> fgcolor       =
> font2color    =
> label density = 25
> bump density  = 100
> # where to link to when user clicks in detailed view
> link          = AUTO
>
> ################## TRACK CONFIGURATION ####################
> # the remainder of the sections configure individual tracks
> ###########################################################
>
> [ExampleFeatures]
> feature      = Ancestry_Calls
> glyph        = generic
> stranded     = 1
> bgcolor      = sub {
>                 my ($feature,$option_name,$part_no,$total_parts,$glyph) =
> @_;
>                 my ($ref, $name, $notes);
>                 ($notes) = $feature->attributes('Note');
>                 if ($notes) =~ /CEU/) {
>                 return 'blue';
>                 } else {
>                 return 'green';
>                 }
>         }
> height       = 10
> key          = Example Features
>
>
>
> I think I let a tab before the   }   if this is what you meant.
>
> If it is not in the perl function, where could I've done a mistake?
>
> Again, thanks.
>
> Wilfried
>
>
>
>
> On Wed, Sep 7, 2011 at 5:27 PM, Scott Cain <sc...@sc...> wrote:
>>
>> Hi Wilfried,
>>
>> I'm cc'ing this to the gbrowse mailing list and trimming out the help
>> mailing list.
>>
>> Could you please send your full configuration file?  There is nothing
>> obviously wrong with the code your wrote.  One thing that some times
>> trips people up (including me!) is that the last curly brace of the
>> sub cannot be the first character in the line (there must be at least
>> one space before it).
>>
>> Scott
>>
>>
>> On Wed, Sep 7, 2011 at 5:07 PM, Wilfried Guiblet
>> <wil...@up...> wrote:
>> > Hello,
>> >
>> > I am currently trying to custom my GBrowser in order to display
>> > different
>> > ancestry on the same track, by the use of generic glyph.
>> >
>> > Here is one line from my gff3 :
>> >
>> >
>> >
>> > chr1    example    Ancestry_Calls    752566    1089699    0.997862    .
>> > .    Name=HG00551_2;Note=CEU
>> >
>> >
>> >
>> > I would like to be able to change the bgcolor in the Track Configuration
>> > using a Perl function. So far, reading on different subjects, I wrote
>> > this
>> > one:
>> >
>> >
>> >
>> > sub {
>> >         my ($feature,$option_name,$part_no,$total_parts,$glyph) = @_;
>> >         my ($ref, $name, $notes);
>> >         ($notes) = $feature->attributes('Note');
>> >         if ($notes) =~ /CEU/) {
>> >         return 'red';
>> >         } else {
>> >         return 'orange';
>> >         }
>> >     }
>> >
>> >
>> >
>> > But I can't make it work. It keeps displaying me another color than the
>> > ones
>> > I set up in the function, so I guess something is wrong inside my
>> > coding.
>> >
>> > I hope you would be able to point what is my mistake,
>> >
>> > Thank you,
>> >
>> > Wilfried Guiblet
>> > Graduate Student
>> > University of Puerto Rico Mayaguez
>> >
>>
>>
>>
>> --
>> ------------------------------------------------------------------------
>> Scott Cain, Ph. D.                                   scott at scottcain
>> dot net
>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> Ontario Institute for Cancer Research
>
>



-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research