[Gmod-help] Re: [GMOD-devel] ProteinDumper

Thu Aug 26 13:54:30 EDT 2010

Dave

I wanted to see if you had any response or discussions about getting ProteinDumper plugin fixed? I would imagine it should be fairly straight forward for an experienced GBrowse/Perl developer to figure out what has changed. From Scott's email below using Chado he gets a malformed sql query and in the memory adaptor just a blank page.

Thanks

Scooter

On Jul 20, 2010, at 4:02 PM, Dave Clements, GMOD Help Desk wrote:

Hi Scooter,

There hasn't been serious work done on this plugin for almost 4 years.

Is there anyone out there who is knowledgeable about GBrowse plugins who can take a look at this?  The plugin is less than 300 lines of perl:

  http://gmod.svn.sourceforge.net/viewvc/gmod/Generic-Genome-Browser/trunk/conf/plugins/ProteinDumper.pm?revision=23571&view=markup

Thanks,

Dave C

On Thu, Jul 15, 2010 at 7:57 AM, Scooter Willis <HWillis at scripps.edu<mailto:HWillis at scripps.edu>> wrote:
Scott

Any thoughts on how to get the ProteinDumper plugin working again?

Thanks

Scooter

________________________________________
From: Scott Cain [scott at scottcain.net<mailto:scott at scottcain.net>]
Sent: Thursday, July 08, 2010 9:55 AM
To: Scooter Willis
Cc: gmod-devel at lists.sourceforge.net<mailto:gmod-devel at lists.sourceforge.net>
Subject: Re: [GMOD-devel] ProteinDumper

Hi Scooter,

What GBrowse version are you using, what database adaptor, and do you get any useful information from the apache error_log?

When I tried this dumper with the Chado adaptor on GBrowse2, I got a helpful message in the error log (a malformed sql query--it must be doing something I didn't expect).  However, when I do this with the Bio::DB::SeqFeature::Store memory adaptor and GBrowse2, I got what it looks like you got and no error message (making life a little more difficult).  My guess is you're the first person to try this dumper in a while.

Scott

On Thu, Jul 8, 2010 at 8:42 AM, Scooter Willis <HWillis at scripps.edu<mailto:HWillis at scripps.edu><mailto:HWillis at scripps.edu<mailto:HWillis at scripps.edu>>> wrote:

I added in ProteinDumper plugin and when selected I get a new browser window with a selected gene but no protein sequence. Any suggestions on what would result in an empty page. In HTML mode I do get the scaffold/range with the following HTML. I have the glyph type as gene and wonder if a specific feature type is required for ProteinDumper to recognize the CDS/Exon region.

Thanks

Scooter

       <!DOCTYPE html
       PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
       "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
       <html xmlns="http://www.w3.org/1999/xhtml" lang="en-US" xml:lang="en-US">
       <head>
       <title>scaffold00071:2589833..2591388</title>
       <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
       </head>
       <body>
       <h1>scaffold00071:2589833..2591388</h1><pre></pre>
       </body>
       </html>

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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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