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

[Scott Cain]

Hi Farbia,

There aren't configuration options to do that, though it might not prove too
difficult to do it yourself.  It isn't documented, but as I said before, the
details page isn't terribly complicated either.

Scott


On Sat, Aug 28, 2010 at 12:59 AM, Fariba M <fariba_mahdavifard at yahoo.com>wrote:

> Hi,
>
> Thanks for your answers.
> But in fact, for the gbrowse details page, I would like to have:
>
> 1.  the spliced coding sequence (i.e. the CDS).  For example, for g2928,
> each of the exons appears as a pink box.  We would like to join (splice) the
> text from the pink boxes, end to end, removing the non-pink (intron)
> sequence in between each exon and print out a string on the report called
> the CDS.
> 2. the translation of the CDS from RNA into protein (single-letter amino
> acid code).
>
> I don't know how GBrowse should be configured to do these. I would be
> so grateful if you can help me.
>
> Thanks,
> Fariba
>
>
>
> --- On *Wed, 8/25/10, Scott Cain <scott at scottcain.net>* wrote:
>
>
> From: Scott Cain <scott at scottcain.net>
> Subject: Re: [Gmod-gbrowse] Question about Linking and how
> "gbrowse_details" works
> To: "Dave Clements, GMOD Help Desk" <help at gmod.org>
> Cc: "Fariba M" <fariba_mahdavifard at yahoo.com>,
> gmod-gbrowse at lists.sourceforge.net
> Date: Wednesday, August 25, 2010, 7:00 PM
>
>
> 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 <http://mc/compose?to=help@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<http://mc/compose?to=fariba_mahdavifard@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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> --
> ------------------------------------------------------------------------
> 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
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