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<div class=Section1>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Thanks for the link Dave, <o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>My files are gff3.. I use the –gff3_munge option when I
use the Bio::DB::GFF option. Would you also know how this happens:<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><img width=1280 height=480 id="Picture_x0020_1"
src="cid:image003.jpg@01CAFC34.6284CDD0"></span><span style='font-size:11.0pt;
font-family:"Calibri","sans-serif";color:#1F497D'><o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>The left screen shows the sample in-memory database with the
yeast(basic) config file. The right window shows the development server with
the data source being a mysql database. They are both served by the same Gbrowse.conf
and have different datasource.conf files(since they are running gbrowse2). But there
is a whole chunk of section missing in the right screen. <o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>I know that the regions are served by the Render.pm script
somewhere around line 180. <o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>“action=show_hide_section;show=details_panel at
/usr/local/lib/perl5/site_perl/5.8.8/sun4-solaris/Bio/Graphics/Browser2/Render.pm
line 180”… this is the debug message when I try to hide the
panels.. <o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>RUN(): POST: http://rgddev.mcw.edu/cgi-bin/gbrowse/yeast/
action=show_hide_section;show=details_panel at
/usr/local/lib/perl5/site_perl/5.8.8/sun4-solaris/Bio/Graphics/Browser2/Render.pm
line 180., referer: http://rgddev.mcw.edu/cgi-bin/gbrowse/yeast/?source=yeast<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>[Tue May 25 17:57:33 2010] [error] [client 141.106.161.52]
[22840] add_user_tracks() at
/usr/local/lib/perl5/site_perl/5.8.8/sun4-solaris/Bio/Graphics/Browser2/Render.pm
line 187., referer: http://rgddev.mcw.edu/cgi-bin/gbrowse/yeast/?source=yeast<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>[Tue May 25 17:57:33 2010] [error] [client 141.106.161.52]
[22840] testing for asynchronous event() at
/usr/local/lib/perl5/site_perl/5.8.8/sun4-solaris/Bio/Graphics/Browser2/Render.pm
line 198., referer: http://rgddev.mcw.edu/cgi-bin/gbrowse/yeast/?source=yeast<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>[Tue May 25 17:57:33 2010] [error] [client 141.106.161.52]
[22840] asynchronous exit at
/usr/local/lib/perl5/site_perl/5.8.8/sun4-solaris/Bio/Graphics/Browser2/Render.pm
line 200., referer: <a
href="http://rgddev.mcw.edu/cgi-bin/gbrowse/yeast/?source=yeast">http://rgddev.mcw.edu/cgi-bin/gbrowse/yeast/?source=yeast</a><o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>But nothing more than that...<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Would you know if anybody else has also had a similar problem..?
<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Baskerville Old Face","serif";
color:#1F497D'>Pushkala Jayaraman<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Baskerville Old Face","serif";
color:#1F497D'>Programmer/Analyst<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Baskerville Old Face","serif";
color:#1F497D'>Rat Genome Database<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Baskerville Old Face","serif";
color:#1F497D'>Human and Molecular Genetics Center<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Baskerville Old Face","serif";
color:#1F497D'>Medical College of Wisconsin</span><span style='font-size:11.0pt;
font-family:"Baskerville Old Face","serif";color:#1F497D'><o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Baskerville Old Face","serif";
color:#1F497D'>Email: pjayaraman@mcw.edu<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Baskerville Old Face","serif";
color:#1F497D'>Work: 414-955-2229</span><span style='font-family:"Baskerville Old Face","serif";
color:#1F497D'><o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Baskerville Old Face","serif";
color:#1F497D'>www.rgd.mcw.edu<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<div style='border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0in 0in 0in'>
<p class=MsoNormal><b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>From:</span></b><span
style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>
gmodhelp@googlemail.com [mailto:gmodhelp@googlemail.com] <b>On Behalf Of </b>Dave
Clements, GMOD Help Desk<br>
<b>Sent:</b> Tuesday, May 25, 2010 5:26 PM<br>
<b>To:</b> Jayaraman, Pushkala<br>
<b>Cc:</b> gmod-gbrowse@lists.sourceforge.net<br>
<b>Subject:</b> Re: [Gmod-gbrowse] Drop data from one track only and reload<o:p></o:p></span></p>
</div>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>Hi Pushkala,<o:p></o:p></p>
<div>
<p class=MsoNormal><o:p> </o:p></p>
</div>
<div>
<p class=MsoNormal>I believe there is a script to do this, but I can't find it.
I did find a thread from 18 months ago that addresses this:<o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><o:p> </o:p></p>
</div>
<div>
<p class=MsoNormal style='margin-bottom:12.0pt'> <a
href="http://old.nabble.com/load-unload-a-track-%28only%29--td19926340.html#a19926340">http://old.nabble.com/load-unload-a-track-%28only%29--td19926340.html#a19926340</a><o:p></o:p></p>
</div>
<div>
<p class=MsoNormal>Dave C.<o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><o:p> </o:p></p>
</div>
<div>
<p class=MsoNormal>PS: I assume that since you are using Bio::DB::GFF that
your files are GFF2 and not GFF3?<o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><o:p> </o:p></p>
<div>
<p class=MsoNormal>On Fri, May 21, 2010 at 7:48 AM, Jayaraman, Pushkala <<a
href="mailto:pjayaraman@mcw.edu">pjayaraman@mcw.edu</a>> wrote:<o:p></o:p></p>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>Hello,
<o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>I
am currently using the Bio::DB::GFF schema on the older version 1.7 of gbrowse.
<o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>I
would like to reload just one track, i.e delete from database the old gff3
files for “gene” track and load the updated gff3 files for the
genes track while keeping all the other data as is in the database. What
BioPerl script could I use to ensure that no other data is affected except the
data that I want?<o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>Thanks,<o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span
style='font-family:"Baskerville Old Face","serif"'>Pushkala Jayaraman</span><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span
style='font-family:"Baskerville Old Face","serif"'>Programmer/Analyst</span><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span
style='font-family:"Baskerville Old Face","serif"'>Rat Genome Database</span><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span
style='font-size:10.0pt;font-family:"Baskerville Old Face","serif"'>Human and
Molecular Genetics Center</span><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span
style='font-size:10.0pt;font-family:"Baskerville Old Face","serif"'>Medical
College of Wisconsin</span><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span
style='font-family:"Baskerville Old Face","serif"'>Email: <a
href="mailto:pjayaraman@mcw.edu" target="_blank">pjayaraman@mcw.edu</a></span><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span
style='font-family:"Baskerville Old Face","serif"'>Work: 414-955-2229</span><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span
style='font-family:"Baskerville Old Face","serif"'><a
href="http://www.rgd.mcw.edu" target="_blank">www.rgd.mcw.edu</a></span><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <o:p></o:p></p>
</div>
</div>
<p class=MsoNormal style='margin-bottom:12.0pt'><br>
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