[Gmod-help] GFF3 file uploads

[Rohan Bansal]

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 
> <mailto:bansal at princeton.edu>> wrote:
>
>     To The Help Desk,
>
>
>        I am a user that creates simple gff3 files and uploads them to
>     plasmodb.org <http://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 <mailto:bansal at princeton.edu>
>
>
>
>
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