[Gmod-help] RE: [Gmod-gbrowse] Drop data from one track only and reload

Tue May 25 19:02:05 EDT 2010

Thanks for the link Dave, 

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:

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. 

I know that the regions are served by the Render.pm script somewhere
around line 180. 

"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.. 

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

[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

[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

[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: 
http://rgddev.mcw.edu/cgi-bin/gbrowse/yeast/?source=yeast

But nothing more than that...

Would you know if anybody else has also had a similar problem..? 

Pushkala Jayaraman

Programmer/Analyst

Rat Genome Database

Human and Molecular Genetics Center

Medical College of Wisconsin

Email: pjayaraman at mcw.edu

Work: 414-955-2229

www.rgd.mcw.edu

From: gmodhelp at googlemail.com [mailto:gmodhelp at googlemail.com] On Behalf
Of Dave Clements, GMOD Help Desk
Sent: Tuesday, May 25, 2010 5:26 PM
To: Jayaraman, Pushkala
Cc: gmod-gbrowse at lists.sourceforge.net
Subject: Re: [Gmod-gbrowse] Drop data from one track only and reload

Hi Pushkala,

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:

http://old.nabble.com/load-unload-a-track-%28only%29--td19926340.html#a1
9926340

Dave C.

PS: I assume that since you are using Bio::DB::GFF that your files are
GFF2 and not GFF3?

On Fri, May 21, 2010 at 7:48 AM, Jayaraman, Pushkala <
pjayaraman at mcw.edu> wrote:

Hello, 

I am currently using the Bio::DB::GFF schema on the older version 1.7 of
gbrowse. 

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?

Thanks,

Pushkala Jayaraman

Programmer/Analyst

Rat Genome Database

Human and Molecular Genetics Center

Medical College of Wisconsin

Email: pjayaraman at mcw.edu

Work: 414-955-2229

www.rgd.mcw.edu

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