<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Dave<div><br></div><div>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. </div><div><br></div><div>Thanks</div><div><br></div><div>Scooter</div><div><br><div><div>On Jul 20, 2010, at 4:02 PM, Dave Clements, GMOD Help Desk wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">Hi Scooter,<div><br></div><div>There hasn't been serious work done on this plugin for almost 4 years.</div><div><br></div><div>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:</div>
<div><br></div><div> <a href="http://gmod.svn.sourceforge.net/viewvc/gmod/Generic-Genome-Browser/trunk/conf/plugins/ProteinDumper.pm?revision=23571&view=markup">http://gmod.svn.sourceforge.net/viewvc/gmod/Generic-Genome-Browser/trunk/conf/plugins/ProteinDumper.pm?revision=23571&view=markup</a></div>
<div><br></div><div>Thanks,</div><div><br></div><div>Dave C<br><br><div class="gmail_quote">On Thu, Jul 15, 2010 at 7:57 AM, Scooter Willis <span dir="ltr"><<a href="mailto:HWillis@scripps.edu">HWillis@scripps.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">Scott<br>
<br>
Any thoughts on how to get the ProteinDumper plugin working again?<br>
<br>
Thanks<br>
<br>
Scooter<br>
<br>
________________________________________<br>
From: Scott Cain [<a href="mailto:scott@scottcain.net">scott@scottcain.net</a>]<br>
Sent: Thursday, July 08, 2010 9:55 AM<br>
To: Scooter Willis<br>
<div class="im">Cc: <a href="mailto:gmod-devel@lists.sourceforge.net">gmod-devel@lists.sourceforge.net</a><br>
</div>Subject: Re: [GMOD-devel] ProteinDumper<br>
<div class="im"><br>
Hi Scooter,<br>
<br>
What GBrowse version are you using, what database adaptor, and do you get any useful information from the apache error_log?<br>
<br>
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.<br>
<br>
Scott<br>
<br>
<br>
</div><div class="im">On Thu, Jul 8, 2010 at 8:42 AM, Scooter Willis <<a href="mailto:HWillis@scripps.edu">HWillis@scripps.edu</a><mailto:<a href="mailto:HWillis@scripps.edu">HWillis@scripps.edu</a>>> wrote:<br>
<br>
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.<br>
<br>
Thanks<br>
<br>
Scooter<br>
<br>
<!DOCTYPE html<br>
PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"<br>
"<a href="http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd" target="_blank">http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd</a>"><br>
<html xmlns="<a href="http://www.w3.org/1999/xhtml" target="_blank">http://www.w3.org/1999/xhtml</a>" lang="en-US" xml:lang="en-US"><br>
<head><br>
<title>scaffold00071:2589833..2591388</title><br>
<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" /><br>
</head><br>
<body><br>
<h1>scaffold00071:2589833..2591388</h1><pre></pre><br>
</body><br>
</html><br>
<br>
<br>
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