[Gmod-help] Re: [Gmod-gbrowse] Question about Linking and how "gbrowse_details" works

[Scott Cain]

Hi Fariba,

I suspect you are referring to the extracted sequence for the feature that
appears at the bottom of the gbrowse_details page.  The script is just using
the reference sequence in the database and the start and stop data for the
feature (and child features if present) and extracting the sequence from the
database (via bioperl).  I agree with Dave that you should look into using
the config file to modify how the details page looks before hacking away at
the script (though the details page script isn't terribly complicated).

Scott


On Tue, Aug 24, 2010 at 7:25 PM, Dave Clements, GMOD Help Desk <
help at gmod.org> wrote:

> Hi Fariba,
>
> You can control some things on the gbrowse_details page using the methods
> listed at:
>
>
> http://gmod.org/wiki/GBrowse_Configuration_HOWTO#Controlling_the_gbrowse_details_page
>
> Other than looking at the code (available online at
> http://gmod.svn.sourceforge.net/viewvc/gmod/Generic-Genome-Browser/trunk/cgi-bin/gbrowse_details),
> I don't know how to figure out how it infers things.
>
> What specifically are you seeing that is inferred?  What does the relevant
> GFF3 look like?
>
> Dave C.
>
> On Thu, Aug 19, 2010 at 11:02 AM, Fariba M <fariba_mahdavifard at yahoo.com>wrote:
>
>> Hi Scott,
>>
>> I have a question about Gbrowse, I would be grateful if you can help me.
>>
>> The tutorial says that when we use a  "Link = AUTO" in [TRACK DEFAULTS]
>> section,  an automatic link to a helper script named "gbrowse_details"
>> will be generated.
>>
>> I was wondering how this link is generated, because in the details page I
>> can see info about gene sequences that are not even in my data file. I mean
>> they are probably inferred from my data file, but I'd like to know how they
>> are inferred.
>> I'd like to know that, because I want to modify this details page a little
>> bit and also use this inferred data as well.
>> I think it should be possible to modify the details page, isn't it?
>>
>> Thanks,
>> Fariba
>>
>>
>>
>>
>>
>>
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>
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-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot
net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research
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