From: Dave C. G. H. D. <he...@gm...> - 2010-07-20 20:03:00
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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 <HW...@sc...> wrote: > Scott > > Any thoughts on how to get the ProteinDumper plugin working again? > > Thanks > > Scooter > > ________________________________________ > From: Scott Cain [sc...@sc...] > Sent: Thursday, July 08, 2010 9:55 AM > To: Scooter Willis > Cc: gmo...@li... > 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 <HW...@sc... > <mailto:HW...@sc...>> 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> > > > > ------------------------------------------------------------------------------ > This SF.net email is sponsored by Sprint > What will you do first with EVO, the first 4G phone? > Visit sprint.com/first<http://sprint.com/first> -- > http://p.sf.net/sfu/sprint-com-first > _______________________________________________ > Gmod-devel mailing list > Gmo...@li...<mailto:Gmo...@li...> > https://lists.sourceforge.net/lists/listinfo/gmod-devel > > > > > -- > ------------------------------------------------------------------------ > Scott Cain, Ph. D. scott at scottcain dot > net > GMOD Coordinator (http://gmod.org/) 216-392-3087 > Ontario Institute for Cancer Research > > > ------------------------------------------------------------------------------ > This SF.net email is sponsored by Sprint > What will you do first with EVO, the first 4G phone? > Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first > _______________________________________________ > Gmod-devel mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-devel > -- ===> PLEASE KEEP RESPONSES ON THE LIST <=== http://gmod.org/wiki/GMOD_News http://gmod.org/wiki/Calendar http://gmod.org/wiki/Help_Desk_Feedback |