[Gmod-help] Re: [Gmod-gbrowse] how to specify glyph type in "add" URL

[David M. Goodstein]

I remember reading a single line in one of the older versions of the  
Gbrowse tutorial that mentioned using the "add" URL to add a single  
feature to your session. It creates a  file called "Custom_Track" in  
the "uploaded file" subdir of the Gbrowse tmp/org/ session_id  
directory, e.g.,

[daveg at privatezome ~]$ more /var/tmp/www/frog2/uploaded_file/ 
ffd3c2a45a7235f72fa77e1fd61b539f/Custom_Track

reference=scaffold_44
"UserBlast"	"your.query_scaffold_44_s1_0"	 
2659025..2659622,2658639..2659027

reference=scaffold_44
"UserBlast"	"your.query_scaffold_44_s1_1"	1588629..1589714

reference=scaffold_44
"UserBlast"	"your.query_scaffold_44_s1_2"	3505485..3506576

reference=scaffold_44
"UserBlast"	"your.query_scaffold_44_s1_3"	3344284..3345379

reference=scaffold_44
"UserBlast"	"your.query_scaffold_44_s1_4"	2934732..2935830

reference=scaffold_44
"UserBlast"	"your.query_scaffold_44_s1_5"	1424834..1424922



It looks like this URL is getting parsed in  the handle_quickie  
subroutine of gbrowse (using parse_feature_str) into a  
Bio::Graphics::Feature object, and then written out in the  
write_auto.  It builds a Bio::Graphics::Feature object from the  
URL,and uses the type to define the track name (UserBlast in my  
case).   No opportunity to specify a more typical "type" (e.g., gapped  
alignment, transcript, etc.) and it doesn't look for a "strand" param.

-David




On  11, 2009, at 8:51 PM, "Dave Clements, GMOD Help Desk" <gmodhelp at googlemail.com 
 > wrote:

> Hi David,
>
> Thanks for reposting your question.  Unfortunately, I haven't been
> able to find a way to do what you are asking, and I'm guessing from
> the lack of response that no one else does either.
>
> I couldn't even find documentation describing on how to do what you
> are already doing.  Do you remember where that doc is or how you
> figured it out?  I'd like to make this feature more prominent.
>
> With apologies,
>
> Dave C
>
> On Fri, May 29, 2009 at 2:58 PM, David  
> Goodstein<dmgoodstein at lbl.gov> wrote:
>> giving this question another try....
>>
>> On May 21, 2009, at 11:41 PM, David Goodstein wrote:
>>
>>> I have a URL of this form (generated from parsing the HSPs of a
>>> blast hit):
>>>
>>>  /cgi-bin/gbrowse/bradi/?add=Bd1 UserBlast "your.query_Bd1_s1_0"
>>> 6313667..6314801,6315973..6317067,6314988..6315691,6317153..6317756,6312807..6313002,6312373..6312548,6311260..6311395,6313420..6313535,6315783..6315888,6311051..6311140,6310888..6310960,6313082..6313150,6311480..6311538,6310320..6310377&name=Bd1:6310320..6317756
>>>
>>> which nicely adds the BLAST feature to the UserBlast track on my
>>> gbrowse detail view.
>>>
>>>
>>> <pastedGraphic.tiff>
>>>
>>>
>>> However, I was wondering if there is a way to specify the strand of
>>> the feature I'm adding, as well as the glyph type, so it can be
>>> drawn with an arrowed glyph to indicate the strand?
>>>
>>> thx,
>>> -David
>>>
>>>
>>>
>>> David M. Goodstein
>>> Joint Genome Institute / Lawrence Berkeley National Laboratory
>>>
>>>
>>>
>>>
>>>
>>
>>
>> ------------------------------------------------------------------------------
>> 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 at lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>
>
>
>
> -- 
> Was this helpful?  Let us know at http://gmod.org/wiki/Help_Desk_Feedback
>
> Learn more about GMOD at:
> AGA Next Gen Seq in Non-Models: http://www.regonline.com/ 
> Nextgeneration
> Galaxy Workshop at NBIC: http://www.nbic.nl/nbic/newsevents/Galaxy/