[Gmod-help] GFF3 file uploads

[Scott Cain]

Hi Rohan,

The variables you are using ($name, $description, etc) are special
"built in" variables that GBrowse makes use of; to do more complicated
things, you need to write a little perl subroutine called a callback.
When you are using a callback, you can have complete control over how
each glyph gets displayed and access to all of the data in the ninth
column.  The only problem is that most GBrowse instances are
configured to not allow callbacks to execute from uploaded GFF files,
because it presents a security hole big enough to drive a truck
through.

It might be possible to get an image in a popup menu through clever
use of the "Note" attribute in the ninth column.  Notes are what go in
the $description variable, so if you put fully formed html that would
cause an image to be displayed, and then put $note in your balloon
configuration, it might display an image.  I say might because you
might have to experiment with character encoding, since some html
characters might be modified during the upload process.

Scott


On Thu, Jun 24, 2010 at 9:31 AM, Rohan Bansal <bansal at princeton.edu> wrote:
> Thank you!
>
>     One more question regarding uploading files that are readable by gbrowse
> instances.  I am creating a balloon that appears on hover, and I do see that
> I can refer to individual features names, start sites, end sites, landmark,
> and the source by using variables such as $name, $start, $end, $class, and
> $source.  However, I am unable to refer to self-created attributes in the
> ninth column of the gff3 file.  For example, if in the ninth column I have
>
> Sequence=ATCGAT
>
> and I put $sequence into the display part of balloon hover, then it just
> displays "$sequence".  Is there any way to work around this and display self
> created attributes?
>
> Also, is it  possible to embed an image into the balloon itself?
>
> I also want to make sure you keep in mind that these are just gff3 files
> that I am uploading to a plasmodb gbrowse - I am not hosting the gbrowse
> myself.
>
> Thanks again,
>
> Rohan Bansal
>
> On 6/23/2010 12:20 AM, Dave Clements, GMOD Help Desk wrote:
>
> Hi Rohan,
> You should be able to control the display by including GBrowse stanza
> definitions in your uploaded file.
> See http://wormbase.org/gbrowse2/annotation_help.html#customize.  Try:
> label = 0
> description = 0
> You can also strip optional attributes from column 9 before loading the
> file.
> Dave C.
>
> On Tue, Jun 22, 2010 at 5:52 PM, Rohan Bansal <bansal at princeton.edu> wrote:
>>
>> To The Help Desk,
>>
>>
>>    I am a user that creates simple gff3 files and uploads them to
>> plasmodb.org, which hosts an instance of gbrowse online.
>>
>>    While creating the gff3 file, I do not want the Name, Note, and ID etc.
>> as defined in column 9 (the attributes) to show on the track (i.e. I would
>> like to hide them).  Is this at all possible to specify within the gff3
>> file?
>>
>>
>> Thank you,
>>
>> Rohan Bansal
>>
>> bansal at princeton.edu
>
>
>
> --
> ===> PLEASE KEEP RESPONSES ON THE LIST <===
> http://gmod.org/wiki/GMOD_News
> http://gmod.org/wiki/Calendar
> http://gmod.org/wiki/Help_Desk_Feedback
>
>



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