Drop data from one track only and reload

classic Classic list List threaded Threaded
4 messages Options
Reply | Threaded
Open this post in threaded view
|

Drop data from one track only and reload

Jayaraman, Pushkala

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: [hidden email]

Work: 414-955-2229

www.rgd.mcw.edu

 


------------------------------------------------------------------------------


_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
Reply | Threaded
Open this post in threaded view
|

Re: Drop data from one track only and reload

Dave Clements, GMOD Help Desk-3
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:

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 <[hidden email]> 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: [hidden email]

Work: 414-955-2229

www.rgd.mcw.edu

 


------------------------------------------------------------------------------


_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse




--
===> PLEASE KEEP RESPONSES ON THE LIST <===
http://gmod.org/wiki/GMOD_News
http://gmod.org/wiki/Calendar
http://gmod.org/wiki/Help_Desk_Feedback


------------------------------------------------------------------------------


_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
Reply | Threaded
Open this post in threaded view
|

Re: Drop data from one track only and reload

Jayaraman, Pushkala

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: [hidden email]

Work: 414-955-2229

www.rgd.mcw.edu

 

From: [hidden email] [mailto:[hidden email]] On Behalf Of Dave Clements, GMOD Help Desk
Sent: Tuesday, May 25, 2010 5:26 PM
To: Jayaraman, Pushkala
Cc: [hidden email]
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:

 

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 <[hidden email]> 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: [hidden email]

Work: 414-955-2229

www.rgd.mcw.edu

 


------------------------------------------------------------------------------


_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse




--
===> PLEASE KEEP RESPONSES ON THE LIST <===
http://gmod.org/wiki/GMOD_News
http://gmod.org/wiki/Calendar
http://gmod.org/wiki/Help_Desk_Feedback


------------------------------------------------------------------------------


_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
Reply | Threaded
Open this post in threaded view
|

Re: Drop data from one track only and reload

Lincoln Stein
In reply to this post by Jayaraman, Pushkala
Hi,

I don't recall if there is a Bio::DB::GFF script to do this. There is a script used with Bio::DB::SeqFeature::Store, however. For Bio::DB::GFF you need to write a little script like this one:

use Bio::DB::GFF;
my $db = Bio::DB::GFF->new(@args_to_connect_to_db);
my $iterator = $db->get_seq_stream(-type=>'gene');
my @ids_to_delete;
while (my $f = $iterator->next_seq) {
   push @ids_to_delete,$f->gid;
}
my $count = $db->delete_groups(@ids_to_delete);
print "$count groups deleted\n";

You might want to backup your database before you do this.

Lincoln

On Fri, May 21, 2010 at 7:48 AM, Jayaraman, Pushkala <[hidden email]> 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: [hidden email]

Work: 414-955-2229

www.rgd.mcw.edu

 


------------------------------------------------------------------------------


_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse




--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <[hidden email]>

------------------------------------------------------------------------------


_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse