Gbrowse2 tracks not visible..possible bug?

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Gbrowse2 tracks not visible..possible bug?

Jayaraman, Pushkala

Hello,

I seem to be having problems with Gbrowse showing tracks on screen. This is slightly complicated:

1.       I have set up a fully functional gbrowse2 v2.03 on my Virtual Box with saved snapshots.

2.       I upgraded to Gbrowse 2.08 from SVN stable branch last month and set up that on my virtual Box. That seemed to be working too.

3.       I then had Gbrowse2 installed on our development server. This is where problems began,

When I tried to load the exact data that I had displaying successfully on my Virtual Box(lets call it Gbrowse_vbox), onto the gbrowse on the server (lets call it Gbrowse_serv)I saw that the Gbrowse_serv could not seem to display any of the data.

4.       Dumping the sql database from the vbox onto the server mysql seemed to get it to work.

5.       Recently, I have noticed that loading the new data on gbrowse_vbox seems unsuccessful. The apache error logs don’t show anythings specific, but I do get Segmentation faults and “Use of uninitialized value in concatenation or string. (I do not know in what).

6.       I am just not able to see any of the Overview/Region/Detail panels on my screen. When I search for a tem, I sometimes get search results on the screen and sometimes just the Blue header that displays “The following 308 regions match your request “  and then nothing below it in the tracks panel.

7.       I am able to see the whole page except for the tracks. I can rule out the possibility of bad data because It did load and I was able to visualize that same data once. I am just not able to load it up again and visualize it.  

 

 

Please help….

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

 


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FW: Gbrowse2 tracks not visible..possible bug?

Jayaraman, Pushkala

In addition… I get a “Use of uninitialized value in concatenation or string(.) … it points to a line 708 on Render.pm

I have copied the section where it points to using “===========” symbol

 

 

 

 

sub render_body {

  my $self     = shift;

 

  warn "render_body()" if DEBUG;

 

  my $region   = $self->region;

  my $features = $region->features;

  my $settings = $self->state;

  my $source   = $self->data_source;

 

  my $title    = $self->generate_title($features);

 

  my $output;

  $output .= $self->render_html_start($title);

  $output .= $self->render_user_header;

  $output .= $self->render_busy_signal;

  $output .= $self->render_actionmenu;

  $output .= $self->render_top($title,$features);

 

  my $main_page   .= $self->render_navbar($region->seg);

 

 

====It shows error inside this section=======

  if ($region->feature_count > 1) {

      $main_page .= $self->render_multiple_choices($features,$self->state->{name});

      $main_page .= $self->render_toggle_track_table;

  }

 

  elsif (my $seg = $region->seg) {

      $main_page .= $self->render_panels($seg,{overview   => $source->show_section('overview'),

                                               regionview => $source->show_section('region'),

                                               detailview => $source->show_section('detail')});

      $main_page .= $self->render_toggle_track_table;

      $main_page .= $self->render_galaxy_form($seg);

  }

  else {

      $main_page .= $self->render_toggle_track_table;

  }

 

  my $upload_share  = $self->render_upload_share_section;

  my $global_config = $self->render_global_config;

 

 

 

 

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

 

From: Jayaraman, Pushkala [mailto:[hidden email]]
Sent: Monday, June 21, 2010 7:11 AM
To: [hidden email]
Subject: [Gmod-gbrowse] Gbrowse2 tracks not visible..possible bug?

 

Hello,

I seem to be having problems with Gbrowse showing tracks on screen. This is slightly complicated:

1.       I have set up a fully functional gbrowse2 v2.03 on my Virtual Box with saved snapshots.

2.       I upgraded to Gbrowse 2.08 from SVN stable branch last month and set up that on my virtual Box. That seemed to be working too.

3.       I then had Gbrowse2 installed on our development server. This is where problems began,

When I tried to load the exact data that I had displaying successfully on my Virtual Box(lets call it Gbrowse_vbox), onto the gbrowse on the server (lets call it Gbrowse_serv)I saw that the Gbrowse_serv could not seem to display any of the data.

4.       Dumping the sql database from the vbox onto the server mysql seemed to get it to work.

5.       Recently, I have noticed that loading the new data on gbrowse_vbox seems unsuccessful. The apache error logs don’t show anythings specific, but I do get Segmentation faults and “Use of uninitialized value in concatenation or string. (I do not know in what).

6.       I am just not able to see any of the Overview/Region/Detail panels on my screen. When I search for a tem, I sometimes get search results on the screen and sometimes just the Blue header that displays “The following 308 regions match your request “  and then nothing below it in the tracks panel.

7.       I am able to see the whole page except for the tracks. I can rule out the possibility of bad data because It did load and I was able to visualize that same data once. I am just not able to load it up again and visualize it.  

 

 

Please help….

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

 


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ATT7714721.txt (234 bytes) Download Attachment
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Re: Gbrowse2 tracks not visible..possible bug?

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

I'm afraid I'll need more information. Is the in-memory Yeast database working on the development server? If it is, it probably rules out a software problem. What database backend are you using, and how do you load it? What operating system are you using?

When you are unable to upload the "new" data on the Virtual Box, what do you mean by "new"?

Lincoln

On Mon, Jun 21, 2010 at 8:11 AM, Jayaraman, Pushkala <[hidden email]> wrote:

Hello,

I seem to be having problems with Gbrowse showing tracks on screen. This is slightly complicated:

1.       I have set up a fully functional gbrowse2 v2.03 on my Virtual Box with saved snapshots.

2.       I upgraded to Gbrowse 2.08 from SVN stable branch last month and set up that on my virtual Box. That seemed to be working too.

3.       I then had Gbrowse2 installed on our development server. This is where problems began,

When I tried to load the exact data that I had displaying successfully on my Virtual Box(lets call it Gbrowse_vbox), onto the gbrowse on the server (lets call it Gbrowse_serv)I saw that the Gbrowse_serv could not seem to display any of the data.

4.       Dumping the sql database from the vbox onto the server mysql seemed to get it to work.

5.       Recently, I have noticed that loading the new data on gbrowse_vbox seems unsuccessful. The apache error logs don’t show anythings specific, but I do get Segmentation faults and “Use of uninitialized value in concatenation or string. (I do not know in what).

6.       I am just not able to see any of the Overview/Region/Detail panels on my screen. When I search for a tem, I sometimes get search results on the screen and sometimes just the Blue header that displays “The following 308 regions match your request “  and then nothing below it in the tracks panel.

7.       I am able to see the whole page except for the tracks. I can rule out the possibility of bad data because It did load and I was able to visualize that same data once. I am just not able to load it up again and visualize it.  

 

 

Please help….

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

 


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--
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]>

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Re: Gbrowse2 tracks not visible..possible bug?

Jayaraman, Pushkala
RE: [Gmod-gbrowse] Gbrowse2 tracks not visible..possible bug?

Hello Lincoln,

Yes,

The yeast, in-memory database is loading well. Also, the data that I had loaded into the mysql database about a month ago (before I updated gbrowse through svn) is also seems to be rendering tracks on my VirtualBox as well as the server(I create a dump of the dabatase that I used on the VBox and uploaded that same database on the server and it works well)..



I am using a mysql database backend. This is how I load the data

 bp_seqfeature_load.pl -a DBI::mysql -d "DBI:mysql:database=DBNAME;host=HOSTNAME" -c -f filename.gff3



I do not use -c each time. But I seem to have to use it the first time after I newly create a DB. Else it complains about not finding the tables. So it gives out errors like 'cannot load data into .locationlist table or view does not exist'.

But when I use the -c feature, it seems to load it in pretty well. After that, I do not have to use the -c feature when I am adding data into the database.


As you can see in the above two attached pictures, both are feb by very similar conf files except for their name. I simply made a copy of the conf file and renamed one. the data source though, is different. i.e they are being fed from two different mysql databases.

when the database has all the tracks then it seems to generate pictures, but when i only load one feature eg. qtl, then it doesnt show anything..
This is what my conf file looks like:

[GENERAL]

database     = general



autocomplete = 1

search options = default +autocomplete +wildcard       



# turn on remote rendering-- see [TRACK DEFAULTS] for the hosts

# and ports the rendering slaves run on.

renderfarm    = 1



# just the basic track dumper plugin was in before..now added new plugins

plugins = TrackDumper Aligner BatchDumper Submitter OligoFinder FilterTest AttributeHiliter



#balloon tips acknowledge:

balloon tips = 1



# list of tracks to turn on by default

default features = miRNA_Track



# size of the region

max segment     = 1000000000

default segment = 50000



# examples to show in the introduction

examples = Odz3



# feature to show on startup

initial landmark = Chr16



#to generalise searches. the search results will include both gene and protein keywords and will not require specific Gene:xxx or protein:xxx it will search xxx through gene and protein in order of them appearing in the line just below.

automatic classes = RGD Gene



#init codes work like functions built into the code:

init_code         = sub bring_bubble{

                     ------some code--------

                     --------more code------

}

########################

# databases being used #

########################

[general:database]

db_adaptor    = Bio::DB::SeqFeature::Store

db_args       = -adaptor DBI::mysql

              -dsn     DBI:mysql:database=DBNAME;host=HOSTNAME.hmgc.mcw.edu

              -user    USERNAME

              -pass    PASSWORD

########################

# Default glyph settings

########################

[TRACK DEFAULTS]

database      = general

glyph         = generic

height        = 10

bgcolor       = lightgrey

fgcolor       = black

font2color    = blue

label density = 25

bump density  = 100



# where to link to when user clicks in detailed view

link          = AUTO



#################################

# Individual Track glyph settings

#################################



[miRNA_Track]

category      = GENOMIC FEATURES

feature       = miRNA:miRBase

glyph         = dot

fgcolor       = blue

bgcolor       = lightblue

linewidth    = 2

height       = 6

label        = sub{

                     my $feature=shift;

                     my ($miRna)=$feature->display_name;

                     return $miRna;      

              }

key           = miRNAs

link          = sub {

                     my $feature=shift;

                     my ($miRnaID)=$feature->load_id;

                     return "http://microrna.sanger.ac.uk/cgi-bin/sequences/mirna_entry.pl?id=$miRnaID";

              }

balloon hover = sub {bring_bubble(shift)}

balloon sticky = 1

citation      = This track shows rat microRNAs (miRNAs) derived from the <a href="http://microrna.sanger.ac.uk/"> Sanger Institute\'s miRBase</a>. miRBase is the repository for microRNA data, incorporating the database and gene naming roles previously provided by the miRNA Registry. Hovering over a feature provides annotation including miRBase ID and source. Clicking on a feature or selecting the miRBase ID links to the miRBase miRNA Report pages.



[miRNA_Track:overview]

feature       = miRNA:miRBase

glyph         = dot

fgcolor       = blue

bgcolor       = lightblue

linewidth    = 2

height       = 6

label        = sub{

                     my $feature=shift;

                     my ($miRna)=$feature->display_name;

                     return $miRna;      

              }

key           = miRNAs Overview

link          = sub {

                     my $feature=shift;

                     my ($miRnaID)=$feature->load_id;

                     return "http://microrna.sanger.ac.uk/cgi-bin/sequences/mirna_entry.pl?id=$miRnaID";

              }

citation      = This track shows rat microRNAs (miRNAs) derived from the <a href="http://microrna.sanger.ac.uk/"> Sanger Institute\'s miRBase</a>. miRBase is the repository for microRNA data, incorporating the database and gene naming roles previously provided by the miRNA Registry. Hovering over a feature provides annotation including miRBase ID and source. Clicking on a feature or selecting the miRBase ID links to the miRBase miRNA Report pages.



[QTLS]

glyph        = saw_teeth

category      = GENOMIC FEATURES

feature       = QTL:RGD

height       = 5

linewidth     = 3

bgcolor       = maroon

fgcolor       = orange

label        = sub{

                     my $feature=shift;

                     my ($qtlid)=$feature->load_id;

                     my @qtlarr=split(/:/, $qtlid);

                     return "QTL:$qtlarr[1]";

              }

description   = sub{

                     my $feature=shift;

                     my ($desc)=$feature->attributes('Dbxref');

                     my @desc_arr=split(/:/, $desc);

                     return "RGDID:".$desc_arr[1];

                    

              }

link         = sub {

                     my $feature=shift;

                     my ($link)=$feature->attributes('Dbxref');

                     if ($link=~/RGD:(\d+)/) {

                            my $rgdid=$1;

                            return "http://rgd.mcw.edu/objectSearch/qtlReport.jsp?rgd_id=$rgdid";

                     }

              }

balloon hover  = sub {bring_bubble(shift)}      

balloon sticky = 1

key           = RGD QTLs

citation      = This track shows <a href="http://www.rgd.mcw.edu/qtls/"> RGD Rat Quantitative Trait Loci (QTL)</a>. In some cases the boundaries of the QTL have been estimated as explained in <a href="ftp://rgd.mcw.edu/pub/data_release/QTLS_README"> QTLs Readme file</a>. Hovering over a feature provides additional annotation including the name, symbol, LOD (where available), p-value (where available), mapping method, and RGD ID, which links to the RGD QTL report page. Clicking on a feature also links to its RGD report page.



[PGA]

category      = PGA

feature       = PGA:ENU_BN PGA:ENU_FHH PGA:SB_F344

glyph         = diamond

bgcolor       = purple

fgcolor       = pink

key           = PGA

balloon hover  = sub {bring_bubble(shift)}

balloon sticky = 1

select        = source 'SB_F344' 'ENU_FHH' 'ENU_BN'

label         = sub {

                  my $feature=shift;

                  my ($pga_label)= $feature->display_name;

                  return $pga_label

                }

description   = sub {

                  my $feature=shift;

                  my ($pga_desc)= $feature->attributes("Id");

                  return $pga_desc;

                }

link           = sub {

                  my $feature=shift;

                  my ($pga_id)=$feature->attributes("Id");

                  $pga_id=~s/RGD://;

                  return "http://rgd.mcw.edu/tools/strains/strains_view.cgi?id=$pga_id";

                  }

citation      = This track includes the genomic locations of the <a href="http://pga.mcw.edu/"> PhysGen PGA</a> mutant strains developed using ENU mutagenesis or the Sleeping Beauty transposon strategy. Hovering over a feature provides additional annotation including the Gene Name, RGD Strain ID, Strain and Source (ENU_FHH, ENU_BN, SB_F344). Clicking on a feature or selecting the RGD Strain ID links to the strain report pages at RGD.



[CNV]

category     = ANNOTATED VARIANTS

feature       = CNV:Hubrecht_Institute

glyph        = span

fgcolor       = sub {bring_cnv_color(shift)}

bgcolor             = black

font2color    = pink1

linewidth     = 3

height        = 5

label       = sub{

                     my $cnv_feat = shift;

                     my ($cnvID)=$cnv_feat->attributes('Dbxref');

                     return "$cnvID";



              }

description   = sub{

                     my $cnv_feat = shift;

                     my ($type)=$cnv_feat->attributes('type');

                     return "TYPE:$type";



              }

balloon hover = sub {bring_bubble(shift)}

balloon sticky= 1

key           =CNVs

link   = sub{

                     my $cnv_feat = shift;

                     my ($cnvID)=$cnv_feat->attributes('Dbxref');

                     $cnvID =~s/cnv_//i;

                     return "http://h094.niob.knaw.nl/RatCNVs/cgi-bin/cnv.pl?id=$cnvID";



              }

citation      = <a href="http://h094.niob.knaw.nl/RatCNVs/"> Copy Number Variants (CNVs)</a> identified in commonly used laboratory rat strains through combination of computational approaches and experimental analysis as published in Guryev et al.; Distribution and functional impact of DNA copy number variation in the rat. Nature Genetics 40, 538 - 545 (2008). Hovering over a feature provides additional annotation including the CNV ID, Strain, Method, Type, and Source. Clicking on a feature or selecting the CNV ID links to the Hubrecht Institute\'s CNV pages.<br />CNVs are colored based on type as following:<br /><table border="1"><tr><th>Type</th><th>Color</th></tr><tr><td>Collapse</td><td>Purple</td></tr><tr><td>Overprediction</td><td>Yellow</td></tr><tr><td>Loss</td><td>Blue</td></tr><tr><td>Loss+Collapse</td><td>Dark blue</td></tr><tr><td>Loss+Overprediction</td><td>Light blue</td></tr><tr><td>Gain</td><td>Red</td></tr><tr><td>Gain+Collapse</td><td>Dark red</td></tr><tr><td>Gain+Overprediction</td><td>Light red</td></tr></table>





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: Lincoln Stein [[hidden email]]
Sent: Monday, June 21, 2010 10:38 AM
To: Jayaraman, Pushkala
Cc: [hidden email]
Subject: Re: [Gmod-gbrowse] Gbrowse2 tracks not visible..possible bug?



Hi Pushkala,



I'm afraid I'll need more information. Is the in-memory Yeast database working on the development server? If it is, it probably rules out a software problem. What database backend are you using, and how do you load it? What operating system are you using?



When you are unable to upload the "new" data on the Virtual Box, what do you mean by "new"?



Lincoln



On Mon, Jun 21, 2010 at 8:11 AM, Jayaraman, Pushkala <[hidden email]> wrote:

Hello,

I seem to be having problems with Gbrowse showing tracks on screen. This is slightly complicated:

1.       I have set up a fully functional gbrowse2 v2.03 on my Virtual Box with saved snapshots.

2.       I upgraded to Gbrowse 2.08 from SVN stable branch last month and set up that on my virtual Box. That seemed to be working too.

3.       I then had Gbrowse2 installed on our development server. This is where problems began,

When I tried to load the exact data that I had displaying successfully on my Virtual Box(lets call it Gbrowse_vbox), onto the gbrowse on the server (lets call it Gbrowse_serv)I saw that the Gbrowse_serv could not seem to display any of the data.

4.       Dumping the sql database from the vbox onto the server mysql seemed to get it to work.

5.       Recently, I have noticed that loading the new data on gbrowse_vbox seems unsuccessful. The apache error logs don't show anythings specific, but I do get Segmentation faults and "Use of uninitialized value in concatenation or string. (I do not know in what).

6.       I am just not able to see any of the Overview/Region/Detail panels on my screen. When I search for a tem, I sometimes get search results on the screen and sometimes just the Blue header that displays "The following 308 regions match your request "  and then nothing below it in the tracks panel.

7.       I am able to see the whole page except for the tracks. I can rule out the possibility of bad data because It did load and I was able to visualize that same data once. I am just not able to load it up again and visualize it. 





Please help..

Pushkala Jayaraman

Programmer/Analyst

Rat Genome Database

Human and Molecular Genetics Center

Medical College of Wisconsin

Email: [hidden email] <[hidden email]>

Work: 414-955-2229

www.rgd.mcw.edu <http://www.rgd.mcw.edu>




------------------------------------------------------------------------------
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GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
lucky parental unit.  See the prize list and enter to win:
http://p.sf.net/sfu/thinkgeek-promo
_______________________________________________
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[hidden email]
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--
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]>





------------------------------------------------------------------------------
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GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
lucky parental unit.  See the prize list and enter to win:
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_______________________________________________
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qtl tracks (10K) Download Attachment
tracks wont render.png (427K) Download Attachment
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FW: Gbrowse2 tracks not visible..possible bug?

Jayaraman, Pushkala
FW: [Gmod-gbrowse] Gbrowse2 tracks not visible..possible bug?

herewith attached.
Had forgotten to attach the .png for the qtl image file.

Pushkala Jayaraman
Programmer Analyst II
Rat Genome Database
Medical College of Wisconsin, Wauwatosa, WI



-----Original Message-----
From: Jayaraman, Pushkala
Sent: Mon 6/21/2010 11:19 AM
To: Lincoln Stein
Cc: [hidden email]
Subject: RE: [Gmod-gbrowse] Gbrowse2 tracks not visible..possible bug?

Hello Lincoln,

Yes,

The yeast, in-memory database is loading well. Also, the data that I had loaded into the mysql database about a month ago (before I updated gbrowse through svn) is also seems to be rendering tracks on my VirtualBox as well as the server(I create a dump of the dabatase that I used on the VBox and uploaded that same database on the server and it works well)..



I am using a mysql database backend. This is how I load the data

 bp_seqfeature_load.pl -a DBI::mysql -d "DBI:mysql:database=DBNAME;host=HOSTNAME" -c -f filename.gff3



I do not use -c each time. But I seem to have to use it the first time after I newly create a DB. Else it complains about not finding the tables. So it gives out errors like 'cannot load data into .locationlist table or view does not exist'.

But when I use the -c feature, it seems to load it in pretty well. After that, I do not have to use the -c feature when I am adding data into the database.


As you can see in the above two attached pictures, both are feb by very similar conf files except for their name. I simply made a copy of the conf file and renamed one. the data source though, is different. i.e they are being fed from two different mysql databases.

when the database has all the tracks then it seems to generate pictures, but when i only load one feature eg. qtl, then it doesnt show anything..
This is what my conf file looks like:

[GENERAL]

database     = general



autocomplete = 1

search options = default +autocomplete +wildcard       



# turn on remote rendering-- see [TRACK DEFAULTS] for the hosts

# and ports the rendering slaves run on.

renderfarm    = 1



# just the basic track dumper plugin was in before..now added new plugins

plugins = TrackDumper Aligner BatchDumper Submitter OligoFinder FilterTest AttributeHiliter



#balloon tips acknowledge:

balloon tips = 1



# list of tracks to turn on by default

default features = miRNA_Track



# size of the region

max segment     = 1000000000

default segment = 50000



# examples to show in the introduction

examples = Odz3



# feature to show on startup

initial landmark = Chr16



#to generalise searches. the search results will include both gene and protein keywords and will not require specific Gene:xxx or protein:xxx it will search xxx through gene and protein in order of them appearing in the line just below.

automatic classes = RGD Gene



#init codes work like functions built into the code:

init_code         = sub bring_bubble{

                     ------some code--------

                     --------more code------

}

########################

# databases being used #

########################

[general:database]

db_adaptor    = Bio::DB::SeqFeature::Store

db_args       = -adaptor DBI::mysql

              -dsn     DBI:mysql:database=DBNAME;host=HOSTNAME.hmgc.mcw.edu

              -user    USERNAME

              -pass    PASSWORD

########################

# Default glyph settings

########################

[TRACK DEFAULTS]

database      = general

glyph         = generic

height        = 10

bgcolor       = lightgrey

fgcolor       = black

font2color    = blue

label density = 25

bump density  = 100



# where to link to when user clicks in detailed view

link          = AUTO



#################################

# Individual Track glyph settings

#################################



[miRNA_Track]

category      = GENOMIC FEATURES

feature       = miRNA:miRBase

glyph         = dot

fgcolor       = blue

bgcolor       = lightblue

linewidth    = 2

height       = 6

label        = sub{

                     my $feature=shift;

                     my ($miRna)=$feature->display_name;

                     return $miRna;      

              }

key           = miRNAs

link          = sub {

                     my $feature=shift;

                     my ($miRnaID)=$feature->load_id;

                     return "http://microrna.sanger.ac.uk/cgi-bin/sequences/mirna_entry.pl?id=$miRnaID";

              }

balloon hover = sub {bring_bubble(shift)}

balloon sticky = 1

citation      = This track shows rat microRNAs (miRNAs) derived from the <a href="http://microrna.sanger.ac.uk/"> Sanger Institute\'s miRBase</a>. miRBase is the repository for microRNA data, incorporating the database and gene naming roles previously provided by the miRNA Registry. Hovering over a feature provides annotation including miRBase ID and source. Clicking on a feature or selecting the miRBase ID links to the miRBase miRNA Report pages.



[miRNA_Track:overview]

feature       = miRNA:miRBase

glyph         = dot

fgcolor       = blue

bgcolor       = lightblue

linewidth    = 2

height       = 6

label        = sub{

                     my $feature=shift;

                     my ($miRna)=$feature->display_name;

                     return $miRna;      

              }

key           = miRNAs Overview

link          = sub {

                     my $feature=shift;

                     my ($miRnaID)=$feature->load_id;

                     return "http://microrna.sanger.ac.uk/cgi-bin/sequences/mirna_entry.pl?id=$miRnaID";

              }

citation      = This track shows rat microRNAs (miRNAs) derived from the <a href="http://microrna.sanger.ac.uk/"> Sanger Institute\'s miRBase</a>. miRBase is the repository for microRNA data, incorporating the database and gene naming roles previously provided by the miRNA Registry. Hovering over a feature provides annotation including miRBase ID and source. Clicking on a feature or selecting the miRBase ID links to the miRBase miRNA Report pages.



[QTLS]

glyph        = saw_teeth

category      = GENOMIC FEATURES

feature       = QTL:RGD

height       = 5

linewidth     = 3

bgcolor       = maroon

fgcolor       = orange

label        = sub{

                     my $feature=shift;

                     my ($qtlid)=$feature->load_id;

                     my @qtlarr=split(/:/, $qtlid);

                     return "QTL:$qtlarr[1]";

              }

description   = sub{

                     my $feature=shift;

                     my ($desc)=$feature->attributes('Dbxref');

                     my @desc_arr=split(/:/, $desc);

                     return "RGDID:".$desc_arr[1];

                    

              }

link         = sub {

                     my $feature=shift;

                     my ($link)=$feature->attributes('Dbxref');

                     if ($link=~/RGD:(\d+)/) {

                            my $rgdid=$1;

                            return "http://rgd.mcw.edu/objectSearch/qtlReport.jsp?rgd_id=$rgdid";

                     }

              }

balloon hover  = sub {bring_bubble(shift)}      

balloon sticky = 1

key           = RGD QTLs

citation      = This track shows <a href="http://www.rgd.mcw.edu/qtls/"> RGD Rat Quantitative Trait Loci (QTL)</a>. In some cases the boundaries of the QTL have been estimated as explained in <a href="ftp://rgd.mcw.edu/pub/data_release/QTLS_README"> QTLs Readme file</a>. Hovering over a feature provides additional annotation including the name, symbol, LOD (where available), p-value (where available), mapping method, and RGD ID, which links to the RGD QTL report page. Clicking on a feature also links to its RGD report page.



[PGA]

category      = PGA

feature       = PGA:ENU_BN PGA:ENU_FHH PGA:SB_F344

glyph         = diamond

bgcolor       = purple

fgcolor       = pink

key           = PGA

balloon hover  = sub {bring_bubble(shift)}

balloon sticky = 1

select        = source 'SB_F344' 'ENU_FHH' 'ENU_BN'

label         = sub {

                  my $feature=shift;

                  my ($pga_label)= $feature->display_name;

                  return $pga_label

                }

description   = sub {

                  my $feature=shift;

                  my ($pga_desc)= $feature->attributes("Id");

                  return $pga_desc;

                }

link           = sub {

                  my $feature=shift;

                  my ($pga_id)=$feature->attributes("Id");

                  $pga_id=~s/RGD://;

                  return "http://rgd.mcw.edu/tools/strains/strains_view.cgi?id=$pga_id";

                  }

citation      = This track includes the genomic locations of the <a href="http://pga.mcw.edu/"> PhysGen PGA</a> mutant strains developed using ENU mutagenesis or the Sleeping Beauty transposon strategy. Hovering over a feature provides additional annotation including the Gene Name, RGD Strain ID, Strain and Source (ENU_FHH, ENU_BN, SB_F344). Clicking on a feature or selecting the RGD Strain ID links to the strain report pages at RGD.



[CNV]

category     = ANNOTATED VARIANTS

feature       = CNV:Hubrecht_Institute

glyph        = span

fgcolor       = sub {bring_cnv_color(shift)}

bgcolor             = black

font2color    = pink1

linewidth     = 3

height        = 5

label       = sub{

                     my $cnv_feat = shift;

                     my ($cnvID)=$cnv_feat->attributes('Dbxref');

                     return "$cnvID";



              }

description   = sub{

                     my $cnv_feat = shift;

                     my ($type)=$cnv_feat->attributes('type');

                     return "TYPE:$type";



              }

balloon hover = sub {bring_bubble(shift)}

balloon sticky= 1

key           =CNVs

link   = sub{

                     my $cnv_feat = shift;

                     my ($cnvID)=$cnv_feat->attributes('Dbxref');

                     $cnvID =~s/cnv_//i;

                     return "http://h094.niob.knaw.nl/RatCNVs/cgi-bin/cnv.pl?id=$cnvID";



              }

citation      = <a href="http://h094.niob.knaw.nl/RatCNVs/"> Copy Number Variants (CNVs)</a> identified in commonly used laboratory rat strains through combination of computational approaches and experimental analysis as published in Guryev et al.; Distribution and functional impact of DNA copy number variation in the rat. Nature Genetics 40, 538 - 545 (2008). Hovering over a feature provides additional annotation including the CNV ID, Strain, Method, Type, and Source. Clicking on a feature or selecting the CNV ID links to the Hubrecht Institute\'s CNV pages.<br />CNVs are colored based on type as following:<br /><table border="1"><tr><th>Type</th><th>Color</th></tr><tr><td>Collapse</td><td>Purple</td></tr><tr><td>Overprediction</td><td>Yellow</td></tr><tr><td>Loss</td><td>Blue</td></tr><tr><td>Loss+Collapse</td><td>Dark blue</td></tr><tr><td>Loss+Overprediction</td><td>Light blue</td></tr><tr><td>Gain</td><td>Red</td></tr><tr><td>Gain+Collapse</td><td>Dark red</td></tr><tr><td>Gain+Overprediction</td><td>Light red</td></tr></table>





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: Lincoln Stein [[hidden email]]
Sent: Monday, June 21, 2010 10:38 AM
To: Jayaraman, Pushkala
Cc: [hidden email]
Subject: Re: [Gmod-gbrowse] Gbrowse2 tracks not visible..possible bug?



Hi Pushkala,



I'm afraid I'll need more information. Is the in-memory Yeast database working on the development server? If it is, it probably rules out a software problem. What database backend are you using, and how do you load it? What operating system are you using?



When you are unable to upload the "new" data on the Virtual Box, what do you mean by "new"?



Lincoln



On Mon, Jun 21, 2010 at 8:11 AM, Jayaraman, Pushkala <[hidden email]> wrote:

Hello,

I seem to be having problems with Gbrowse showing tracks on screen. This is slightly complicated:

1.       I have set up a fully functional gbrowse2 v2.03 on my Virtual Box with saved snapshots.

2.       I upgraded to Gbrowse 2.08 from SVN stable branch last month and set up that on my virtual Box. That seemed to be working too.

3.       I then had Gbrowse2 installed on our development server. This is where problems began,

When I tried to load the exact data that I had displaying successfully on my Virtual Box(lets call it Gbrowse_vbox), onto the gbrowse on the server (lets call it Gbrowse_serv)I saw that the Gbrowse_serv could not seem to display any of the data.

4.       Dumping the sql database from the vbox onto the server mysql seemed to get it to work.

5.       Recently, I have noticed that loading the new data on gbrowse_vbox seems unsuccessful. The apache error logs don't show anythings specific, but I do get Segmentation faults and "Use of uninitialized value in concatenation or string. (I do not know in what).

6.       I am just not able to see any of the Overview/Region/Detail panels on my screen. When I search for a tem, I sometimes get search results on the screen and sometimes just the Blue header that displays "The following 308 regions match your request "  and then nothing below it in the tracks panel.

7.       I am able to see the whole page except for the tracks. I can rule out the possibility of bad data because It did load and I was able to visualize that same data once. I am just not able to load it up again and visualize it. 





Please help..

Pushkala Jayaraman

Programmer/Analyst

Rat Genome Database

Human and Molecular Genetics Center

Medical College of Wisconsin

Email: [hidden email] <[hidden email]>

Work: 414-955-2229

www.rgd.mcw.edu <http://www.rgd.mcw.edu>




------------------------------------------------------------------------------
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_______________________________________________
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--
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]>








------------------------------------------------------------------------------
ThinkGeek and WIRED's GeekDad team up for the Ultimate
GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
lucky parental unit.  See the prize list and enter to win:
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_______________________________________________
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tracks wont render.png (427K) Download Attachment
qtl.png (10K) Download Attachment
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Re: Gbrowse2 tracks not visible..possible bug?

Lincoln Stein
In reply to this post by Jayaraman, Pushkala
It sounds to me as though you are loading the data correctly. But is there any chance that you used -c inadvertently on one of the subsequent loads and inadvertently removed the chromosomes? The way to check is:

 mysql> select * from name where name like 'chr%'

Lincoln

On Mon, Jun 21, 2010 at 12:19 PM, Jayaraman, Pushkala <[hidden email]> wrote:

Hello Lincoln,

Yes,

The yeast, in-memory database is loading well. Also, the data that I had loaded into the mysql database about a month ago (before I updated gbrowse through svn) is also seems to be rendering tracks on my VirtualBox as well as the server(I create a dump of the dabatase that I used on the VBox and uploaded that same database on the server and it works well)..



I am using a mysql database backend. This is how I load the data

 bp_seqfeature_load.pl -a DBI::mysql -d "DBI:mysql:database=DBNAME;host=HOSTNAME" -c -f filename.gff3



I do not use -c each time. But I seem to have to use it the first time after I newly create a DB. Else it complains about not finding the tables. So it gives out errors like 'cannot load data into .locationlist table or view does not exist'.

But when I use the -c feature, it seems to load it in pretty well. After that, I do not have to use the -c feature when I am adding data into the database.


As you can see in the above two attached pictures, both are feb by very similar conf files except for their name. I simply made a copy of the conf file and renamed one. the data source though, is different. i.e they are being fed from two different mysql databases.

when the database has all the tracks then it seems to generate pictures, but when i only load one feature eg. qtl, then it doesnt show anything..
This is what my conf file looks like:

[GENERAL]

database     = general



autocomplete = 1

search options = default +autocomplete +wildcard       



# turn on remote rendering-- see [TRACK DEFAULTS] for the hosts

# and ports the rendering slaves run on.

renderfarm    = 1



# just the basic track dumper plugin was in before..now added new plugins

plugins = TrackDumper Aligner BatchDumper Submitter OligoFinder FilterTest AttributeHiliter



#balloon tips acknowledge:

balloon tips = 1



# list of tracks to turn on by default

default features = miRNA_Track



# size of the region

max segment     = 1000000000

default segment = 50000



# examples to show in the introduction

examples = Odz3



# feature to show on startup

initial landmark = Chr16



#to generalise searches. the search results will include both gene and protein keywords and will not require specific Gene:xxx or protein:xxx it will search xxx through gene and protein in order of them appearing in the line just below.

automatic classes = RGD Gene



#init codes work like functions built into the code:

init_code         = sub bring_bubble{

                     ------some code--------

                     --------more code------

}

########################

# databases being used #

########################

[general:database]

db_adaptor    = Bio::DB::SeqFeature::Store

db_args       = -adaptor DBI::mysql

              -dsn     DBI:mysql:database=DBNAME;host=HOSTNAME.hmgc.mcw.edu

              -user    USERNAME

              -pass    PASSWORD

########################

# Default glyph settings

########################

[TRACK DEFAULTS]

database      = general

glyph         = generic

height        = 10

bgcolor       = lightgrey

fgcolor       = black

font2color    = blue

label density = 25

bump density  = 100



# where to link to when user clicks in detailed view

link          = AUTO



#################################

# Individual Track glyph settings

#################################



[miRNA_Track]

category      = GENOMIC FEATURES

feature       = miRNA:miRBase

glyph         = dot

fgcolor       = blue

bgcolor       = lightblue

linewidth    = 2

height       = 6

label        = sub{

                     my $feature=shift;

                     my ($miRna)=$feature->display_name;

                     return $miRna;      

              }

key           = miRNAs

link          = sub {

                     my $feature=shift;

                     my ($miRnaID)=$feature->load_id;

                     return "http://microrna.sanger.ac.uk/cgi-bin/sequences/mirna_entry.pl?id=$miRnaID";

              }

balloon hover = sub {bring_bubble(shift)}

balloon sticky = 1

citation      = This track shows rat microRNAs (miRNAs) derived from the <a href="http://microrna.sanger.ac.uk/"> Sanger Institute\'s miRBase</a>. miRBase is the repository for microRNA data, incorporating the database and gene naming roles previously provided by the miRNA Registry. Hovering over a feature provides annotation including miRBase ID and source. Clicking on a feature or selecting the miRBase ID links to the miRBase miRNA Report pages.



[miRNA_Track:overview]

feature       = miRNA:miRBase

glyph         = dot

fgcolor       = blue

bgcolor       = lightblue

linewidth    = 2

height       = 6

label        = sub{

                     my $feature=shift;

                     my ($miRna)=$feature->display_name;

                     return $miRna;      

              }

key           = miRNAs Overview

link          = sub {

                     my $feature=shift;

                     my ($miRnaID)=$feature->load_id;

                     return "http://microrna.sanger.ac.uk/cgi-bin/sequences/mirna_entry.pl?id=$miRnaID";

              }

citation      = This track shows rat microRNAs (miRNAs) derived from the <a href="http://microrna.sanger.ac.uk/"> Sanger Institute\'s miRBase</a>. miRBase is the repository for microRNA data, incorporating the database and gene naming roles previously provided by the miRNA Registry. Hovering over a feature provides annotation including miRBase ID and source. Clicking on a feature or selecting the miRBase ID links to the miRBase miRNA Report pages.



[QTLS]

glyph        = saw_teeth

category      = GENOMIC FEATURES

feature       = QTL:RGD

height       = 5

linewidth     = 3

bgcolor       = maroon

fgcolor       = orange

label        = sub{

                     my $feature=shift;

                     my ($qtlid)=$feature->load_id;

                     my @qtlarr=split(/:/, $qtlid);

                     return "QTL:$qtlarr[1]";

              }

description   = sub{

                     my $feature=shift;

                     my ($desc)=$feature->attributes('Dbxref');

                     my @desc_arr=split(/:/, $desc);

                     return "RGDID:".$desc_arr[1];

                    

              }

link         = sub {

                     my $feature=shift;

                     my ($link)=$feature->attributes('Dbxref');

                     if ($link=~/RGD:(\d+)/) {

                            my $rgdid=$1;

                            return "http://rgd.mcw.edu/objectSearch/qtlReport.jsp?rgd_id=$rgdid";

                     }

              }

balloon hover  = sub {bring_bubble(shift)}      

balloon sticky = 1

key           = RGD QTLs

citation      = This track shows <a href="http://www.rgd.mcw.edu/qtls/"> RGD Rat Quantitative Trait Loci (QTL)</a>. In some cases the boundaries of the QTL have been estimated as explained in <a href="ftp://rgd.mcw.edu/pub/data_release/QTLS_README"> QTLs Readme file</a>. Hovering over a feature provides additional annotation including the name, symbol, LOD (where available), p-value (where available), mapping method, and RGD ID, which links to the RGD QTL report page. Clicking on a feature also links to its RGD report page.



[PGA]

category      = PGA

feature       = PGA:ENU_BN PGA:ENU_FHH PGA:SB_F344

glyph         = diamond

bgcolor       = purple

fgcolor       = pink

key           = PGA

balloon hover  = sub {bring_bubble(shift)}

balloon sticky = 1

select        = source 'SB_F344' 'ENU_FHH' 'ENU_BN'

label         = sub {

                  my $feature=shift;

                  my ($pga_label)= $feature->display_name;

                  return $pga_label

                }

description   = sub {

                  my $feature=shift;

                  my ($pga_desc)= $feature->attributes("Id");

                  return $pga_desc;

                }

link           = sub {

                  my $feature=shift;

                  my ($pga_id)=$feature->attributes("Id");

                  $pga_id=~s/RGD://;

                  return "http://rgd.mcw.edu/tools/strains/strains_view.cgi?id=$pga_id";

                  }

citation      = This track includes the genomic locations of the <a href="http://pga.mcw.edu/"> PhysGen PGA</a> mutant strains developed using ENU mutagenesis or the Sleeping Beauty transposon strategy. Hovering over a feature provides additional annotation including the Gene Name, RGD Strain ID, Strain and Source (ENU_FHH, ENU_BN, SB_F344). Clicking on a feature or selecting the RGD Strain ID links to the strain report pages at RGD.



[CNV]

category     = ANNOTATED VARIANTS

feature       = CNV:Hubrecht_Institute

glyph        = span

fgcolor       = sub {bring_cnv_color(shift)}

bgcolor             = black

font2color    = pink1

linewidth     = 3

height        = 5

label       = sub{

                     my $cnv_feat = shift;

                     my ($cnvID)=$cnv_feat->attributes('Dbxref');

                     return "$cnvID";



              }

description   = sub{

                     my $cnv_feat = shift;

                     my ($type)=$cnv_feat->attributes('type');

                     return "TYPE:$type";



              }

balloon hover = sub {bring_bubble(shift)}

balloon sticky= 1

key           =CNVs

link   = sub{

                     my $cnv_feat = shift;

                     my ($cnvID)=$cnv_feat->attributes('Dbxref');

                     $cnvID =~s/cnv_//i;

                     return "http://h094.niob.knaw.nl/RatCNVs/cgi-bin/cnv.pl?id=$cnvID";



              }

citation      = <a href="http://h094.niob.knaw.nl/RatCNVs/"> Copy Number Variants (CNVs)</a> identified in commonly used laboratory rat strains through combination of computational approaches and experimental analysis as published in Guryev et al.; Distribution and functional impact of DNA copy number variation in the rat. Nature Genetics 40, 538 - 545 (2008). Hovering over a feature provides additional annotation including the CNV ID, Strain, Method, Type, and Source. Clicking on a feature or selecting the CNV ID links to the Hubrecht Institute\'s CNV pages.<br />CNVs are colored based on type as following:<br /><table border="1"><tr><th>Type</th><th>Color</th></tr><tr><td>Collapse</td><td>Purple</td></tr><tr><td>Overprediction</td><td>Yellow</td></tr><tr><td>Loss</td><td>Blue</td></tr><tr><td>Loss+Collapse</td><td>Dark blue</td></tr><tr><td>Loss+Overprediction</td><td>Light blue</td></tr><tr><td>Gain</td><td>Red</td></tr><tr><td>Gain+Collapse</td><td>Dark red</td></tr><tr><td>Gain+Overprediction</td><td>Light red</td></tr></table>







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: Lincoln Stein [[hidden email]]
Sent: Monday, June 21, 2010 10:38 AM
To: Jayaraman, Pushkala
Cc: [hidden email]
Subject: Re: [Gmod-gbrowse] Gbrowse2 tracks not visible..possible bug?




Hi Pushkala,



I'm afraid I'll need more information. Is the in-memory Yeast database working on the development server? If it is, it probably rules out a software problem. What database backend are you using, and how do you load it? What operating system are you using?



When you are unable to upload the "new" data on the Virtual Box, what do you mean by "new"?



Lincoln



On Mon, Jun 21, 2010 at 8:11 AM, Jayaraman, Pushkala <[hidden email]> wrote:

Hello,

I seem to be having problems with Gbrowse showing tracks on screen. This is slightly complicated:

1.       I have set up a fully functional gbrowse2 v2.03 on my Virtual Box with saved snapshots.

2.       I upgraded to Gbrowse 2.08 from SVN stable branch last month and set up that on my virtual Box. That seemed to be working too.

3.       I then had Gbrowse2 installed on our development server. This is where problems began,

When I tried to load the exact data that I had displaying successfully on my Virtual Box(lets call it Gbrowse_vbox), onto the gbrowse on the server (lets call it Gbrowse_serv)I saw that the Gbrowse_serv could not seem to display any of the data.

4.       Dumping the sql database from the vbox onto the server mysql seemed to get it to work.

5.       Recently, I have noticed that loading the new data on gbrowse_vbox seems unsuccessful. The apache error logs don't show anythings specific, but I do get Segmentation faults and "Use of uninitialized value in concatenation or string. (I do not know in what).

6.       I am just not able to see any of the Overview/Region/Detail panels on my screen. When I search for a tem, I sometimes get search results on the screen and sometimes just the Blue header that displays "The following 308 regions match your request "  and then nothing below it in the tracks panel.

7.       I am able to see the whole page except for the tracks. I can rule out the possibility of bad data because It did load and I was able to visualize that same data once. I am just not able to load it up again and visualize it. 





Please help..

Pushkala Jayaraman

Programmer/Analyst

Rat Genome Database

Human and Molecular Genetics Center

Medical College of Wisconsin

Email: [hidden email] <[hidden email]>

Work: 414-955-2229

www.rgd.mcw.edu <http://www.rgd.mcw.edu>





------------------------------------------------------------------------------
ThinkGeek and WIRED's GeekDad team up for the Ultimate
GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
lucky parental unit.  See the prize list and enter to win:
http://p.sf.net/sfu/thinkgeek-promo
_______________________________________________
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]>







--
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]>

------------------------------------------------------------------------------
ThinkGeek and WIRED's GeekDad team up for the Ultimate
GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
lucky parental unit.  See the prize list and enter to win:
http://p.sf.net/sfu/thinkgeek-promo
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
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|

Re: Gbrowse2 tracks not visible..possible bug?

Jayaraman, Pushkala

Hello Lincoln,

This is what I get:

 

mysql> select * from name where name like 'chr%';

+-------+--------+--------------+

| id    | name   | display_name |

+-------+--------+--------------+

| 29168 | Chrm3  |            1 |

| 29169 | Chrm3  |            1 |

| 29172 | Chrm3  |            1 |

|  2076 | Chrna2 |            1 |

|  2078 | Chrna2 |            1 |

|  2080 | Chrna2 |            1 |

|  2082 | Chrna2 |            1 |

|  2084 | Chrna2 |            1 |

|  2086 | Chrna2 |            1 |

|  2088 | Chrna2 |            1 |

|  2089 | Chrna2 |            1 |

+-------+--------+--------------+

11 rows in set (0.00 sec)

 

Why am I not getting any of the chromosome names?

 

 

When I do “head nameof_gff3_file.gff3” I get:

 

Chr15   GenBank chromosome      24425085        28088033        .       +       .       ID=NW_047453;Alias=15;Dbxref=taxon:10116;Note=Rattus norvegicus chromosome 15 genomic cont

ig%2C reference assembly (based on RGSC v3.4).,GENOME ANNOTATION REFSEQ: Features on this sequence have been produced for build 4 version 1 of the NCBI's genome annotation [see d

ocumentation]. The DNA sequence is version 3.4 'November 2004 Update' of the Rat genome assembly,produced by the Baylor College of Medicine Human Genome Sequencing Center (BCM- H

GSC) as part of the Rat Genome Sequencing Consortium (RGSC). This supersedes all prior versions of the Rat assembly (2.0,2.1,3.0,3.1 3.2 and 3.3) (see http://www.hgsc.bcm.tmc.edu

/projects/rat/). ;chromosome=15;comment1=GENOME ANNOTATION REFSEQ: Features on this sequence have been produced for build 4 version 1 of the NCBI's genome annotation [see documen

tation]. The DNA sequence is version 3.4 'November 2004 Update' of the Rat genome assembly%2C produced by the Baylor College of Medicine Human Genome Sequencing Center (BCM- HGSC

) as part of the Rat Genome Sequencing Consortium (RGSC). This supersedes all prior versions of the Rat assembly (2.0%2C 2.1%2C 3.0%2C 3.1 3.2 and 3.3) (see http://www.hgsc.bcm.tmc.edu/projects/rat/). ;date=03-JUL-2006;mol_type=genomic DNA;organism=Rattus norvegicus;strain=BN/SsNHsdMCW;

Chr15   GenBank pseudogene      24427872        24428719        .       -       .       ID=LOC498499;Dbxref=GeneID:498499;Note=Derived by automated computational analysis using gene prediction method: GNOMON. Supporting evidence includes similarity to: 98 ESTs%2C 6 Proteins;gene=LOC498499;pseudo=_no_value;

 

 

Which clearly shows the chromosome feature right on top.

 

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: Lincoln Stein [mailto:[hidden email]]
Sent: Monday, June 21, 2010 11:33 AM
To: Jayaraman, Pushkala
Cc: [hidden email]
Subject: Re: [Gmod-gbrowse] Gbrowse2 tracks not visible..possible bug?

 

It sounds to me as though you are loading the data correctly. But is there any chance that you used -c inadvertently on one of the subsequent loads and inadvertently removed the chromosomes? The way to check is:

 

 mysql> select * from name where name like 'chr%'

 

Lincoln

On Mon, Jun 21, 2010 at 12:19 PM, Jayaraman, Pushkala <[hidden email]> wrote:

Hello Lincoln,

Yes,

The yeast, in-memory database is loading well. Also, the data that I had loaded into the mysql database about a month ago (before I updated gbrowse through svn) is also seems to be rendering tracks on my VirtualBox as well as the server(I create a dump of the dabatase that I used on the VBox and uploaded that same database on the server and it works well)..



I am using a mysql database backend. This is how I load the data

 bp_seqfeature_load.pl -a DBI::mysql -d "DBI:mysql:database=DBNAME;host=HOSTNAME" -c -f filename.gff3



I do not use -c each time. But I seem to have to use it the first time after I newly create a DB. Else it complains about not finding the tables. So it gives out errors like 'cannot load data into .locationlist table or view does not exist'.

But when I use the -c feature, it seems to load it in pretty well. After that, I do not have to use the -c feature when I am adding data into the database.


As you can see in the above two attached pictures, both are feb by very similar conf files except for their name. I simply made a copy of the conf file and renamed one. the data source though, is different. i.e they are being fed from two different mysql databases.

when the database has all the tracks then it seems to generate pictures, but when i only load one feature eg. qtl, then it doesnt show anything..
This is what my conf file looks like:

[GENERAL]

database     = general



autocomplete = 1

search options = default +autocomplete +wildcard       



# turn on remote rendering-- see [TRACK DEFAULTS] for the hosts

# and ports the rendering slaves run on.

renderfarm    = 1



# just the basic track dumper plugin was in before..now added new plugins

plugins = TrackDumper Aligner BatchDumper Submitter OligoFinder FilterTest AttributeHiliter



#balloon tips acknowledge:

balloon tips = 1



# list of tracks to turn on by default

default features = miRNA_Track



# size of the region

max segment     = 1000000000

default segment = 50000



# examples to show in the introduction

examples = Odz3



# feature to show on startup

initial landmark = Chr16



#to generalise searches. the search results will include both gene and protein keywords and will not require specific Gene:xxx or protein:xxx it will search xxx through gene and protein in order of them appearing in the line just below.

automatic classes = RGD Gene



#init codes work like functions built into the code:

init_code         = sub bring_bubble{

                     ------some code--------

                     --------more code------

}

########################

# databases being used #

########################

[general:database]

db_adaptor    = Bio::DB::SeqFeature::Store

db_args       = -adaptor DBI::mysql

              -dsn     DBI:mysql:database=DBNAME;host=HOSTNAME.hmgc.mcw.edu

              -user    USERNAME

              -pass    PASSWORD

########################

# Default glyph settings

########################

[TRACK DEFAULTS]

database      = general

glyph         = generic

height        = 10

bgcolor       = lightgrey

fgcolor       = black

font2color    = blue

label density = 25

bump density  = 100



# where to link to when user clicks in detailed view

link          = AUTO



#################################

# Individual Track glyph settings

#################################



[miRNA_Track]

category      = GENOMIC FEATURES

feature       = miRNA:miRBase

glyph         = dot

fgcolor       = blue

bgcolor       = lightblue

linewidth    = 2

height       = 6

label        = sub{

                     my $feature=shift;

                     my ($miRna)=$feature->display_name;

                     return $miRna;      

              }

key           = miRNAs

link          = sub {

                     my $feature=shift;

                     my ($miRnaID)=$feature->load_id;

                     return "http://microrna.sanger.ac.uk/cgi-bin/sequences/mirna_entry.pl?id=$miRnaID";

              }

balloon hover = sub {bring_bubble(shift)}

balloon sticky = 1

citation      = This track shows rat microRNAs (miRNAs) derived from the <a href="http://microrna.sanger.ac.uk/"> Sanger Institute\'s miRBase</a>. miRBase is the repository for microRNA data, incorporating the database and gene naming roles previously provided by the miRNA Registry. Hovering over a feature provides annotation including miRBase ID and source. Clicking on a feature or selecting the miRBase ID links to the miRBase miRNA Report pages.



[miRNA_Track:overview]

feature       = miRNA:miRBase

glyph         = dot

fgcolor       = blue

bgcolor       = lightblue

linewidth    = 2

height       = 6

label        = sub{

                     my $feature=shift;

                     my ($miRna)=$feature->display_name;

                     return $miRna;      

              }

key           = miRNAs Overview

link          = sub {

                     my $feature=shift;

                     my ($miRnaID)=$feature->load_id;

                     return "http://microrna.sanger.ac.uk/cgi-bin/sequences/mirna_entry.pl?id=$miRnaID";

              }

citation      = This track shows rat microRNAs (miRNAs) derived from the <a href="http://microrna.sanger.ac.uk/"> Sanger Institute\'s miRBase</a>. miRBase is the repository for microRNA data, incorporating the database and gene naming roles previously provided by the miRNA Registry. Hovering over a feature provides annotation including miRBase ID and source. Clicking on a feature or selecting the miRBase ID links to the miRBase miRNA Report pages.



[QTLS]

glyph        = saw_teeth

category      = GENOMIC FEATURES

feature       = QTL:RGD

height       = 5

linewidth     = 3

bgcolor       = maroon

fgcolor       = orange

label        = sub{

                     my $feature=shift;

                     my ($qtlid)=$feature->load_id;

                     my @qtlarr=split(/:/, $qtlid);

                     return "QTL:$qtlarr[1]";

              }

description   = sub{

                     my $feature=shift;

                     my ($desc)=$feature->attributes('Dbxref');

                     my @desc_arr=split(/:/, $desc);

                     return "RGDID:".$desc_arr[1];

                    

              }

link         = sub {

                     my $feature=shift;

                     my ($link)=$feature->attributes('Dbxref');

                     if ($link=~/RGD:(\d+)/) {

                            my $rgdid=$1;

                            return "http://rgd.mcw.edu/objectSearch/qtlReport.jsp?rgd_id=$rgdid";

                     }

              }

balloon hover  = sub {bring_bubble(shift)}      

balloon sticky = 1

key           = RGD QTLs

citation      = This track shows <a href="http://www.rgd.mcw.edu/qtls/"> RGD Rat Quantitative Trait Loci (QTL)</a>. In some cases the boundaries of the QTL have been estimated as explained in <a href="ftp://rgd.mcw.edu/pub/data_release/QTLS_README"> QTLs Readme file</a>. Hovering over a feature provides additional annotation including the name, symbol, LOD (where available), p-value (where available), mapping method, and RGD ID, which links to the RGD QTL report page. Clicking on a feature also links to its RGD report page.



[PGA]

category      = PGA

feature       = PGA:ENU_BN PGA:ENU_FHH PGA:SB_F344

glyph         = diamond

bgcolor       = purple

fgcolor       = pink

key           = PGA

balloon hover  = sub {bring_bubble(shift)}

balloon sticky = 1

select        = source 'SB_F344' 'ENU_FHH' 'ENU_BN'

label         = sub {

                  my $feature=shift;

                  my ($pga_label)= $feature->display_name;

                  return $pga_label

                }

description   = sub {

                  my $feature=shift;

                  my ($pga_desc)= $feature->attributes("Id");

                  return $pga_desc;

                }

link           = sub {

                  my $feature=shift;

                  my ($pga_id)=$feature->attributes("Id");

                  $pga_id=~s/RGD://;

                  return "http://rgd.mcw.edu/tools/strains/strains_view.cgi?id=$pga_id";

                  }

citation      = This track includes the genomic locations of the <a href="http://pga.mcw.edu/"> PhysGen PGA</a> mutant strains developed using ENU mutagenesis or the Sleeping Beauty transposon strategy. Hovering over a feature provides additional annotation including the Gene Name, RGD Strain ID, Strain and Source (ENU_FHH, ENU_BN, SB_F344). Clicking on a feature or selecting the RGD Strain ID links to the strain report pages at RGD.



[CNV]

category     = ANNOTATED VARIANTS

feature       = CNV:Hubrecht_Institute

glyph        = span

fgcolor       = sub {bring_cnv_color(shift)}

bgcolor             = black

font2color    = pink1

linewidth     = 3

height        = 5

label       = sub{

                     my $cnv_feat = shift;

                     my ($cnvID)=$cnv_feat->attributes('Dbxref');

                     return "$cnvID";



              }

description   = sub{

                     my $cnv_feat = shift;

                     my ($type)=$cnv_feat->attributes('type');

                     return "TYPE:$type";



              }

balloon hover = sub {bring_bubble(shift)}

balloon sticky= 1

key           =CNVs

link   = sub{

                     my $cnv_feat = shift;

                     my ($cnvID)=$cnv_feat->attributes('Dbxref');

                     $cnvID =~s/cnv_//i;

                     return "http://h094.niob.knaw.nl/RatCNVs/cgi-bin/cnv.pl?id=$cnvID";



              }

citation      = <a href="http://h094.niob.knaw.nl/RatCNVs/"> Copy Number Variants (CNVs)</a> identified in commonly used laboratory rat strains through combination of computational approaches and experimental analysis as published in Guryev et al.; Distribution and functional impact of DNA copy number variation in the rat. Nature Genetics 40, 538 - 545 (2008). Hovering over a feature provides additional annotation including the CNV ID, Strain, Method, Type, and Source. Clicking on a feature or selecting the CNV ID links to the Hubrecht Institute\'s CNV pages.<br />CNVs are colored based on type as following:<br /><table border="1"><tr><th>Type</th><th>Color</th></tr><tr><td>Collapse</td><td>Purple</td></tr><tr><td>Overprediction</td><td>Yellow</td></tr><tr><td>Loss</td><td>Blue</td></tr><tr><td>Loss+Collapse</td><td>Dark blue</td></tr><tr><td>Loss+Overprediction</td><td>Light blue</td></tr><tr><td>Gain</td><td>Red</td></tr><tr><td>Gain+Collapse</td><td>Dark red</td></tr><tr><td>Gain+Overprediction</td><td>Light red</td></tr></table>







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: Lincoln Stein [[hidden email]]

Sent: Monday, June 21, 2010 10:38 AM
To: Jayaraman, Pushkala
Cc: [hidden email]
Subject: Re: [Gmod-gbrowse] Gbrowse2 tracks not visible..possible bug?





Hi Pushkala,



I'm afraid I'll need more information. Is the in-memory Yeast database working on the development server? If it is, it probably rules out a software problem. What database backend are you using, and how do you load it? What operating system are you using?



When you are unable to upload the "new" data on the Virtual Box, what do you mean by "new"?



Lincoln



On Mon, Jun 21, 2010 at 8:11 AM, Jayaraman, Pushkala <[hidden email]> wrote:

Hello,

I seem to be having problems with Gbrowse showing tracks on screen. This is slightly complicated:

1.       I have set up a fully functional gbrowse2 v2.03 on my Virtual Box with saved snapshots.

2.       I upgraded to Gbrowse 2.08 from SVN stable branch last month and set up that on my virtual Box. That seemed to be working too.

3.       I then had Gbrowse2 installed on our development server. This is where problems began,

When I tried to load the exact data that I had displaying successfully on my Virtual Box(lets call it Gbrowse_vbox), onto the gbrowse on the server (lets call it Gbrowse_serv)I saw that the Gbrowse_serv could not seem to display any of the data.

4.       Dumping the sql database from the vbox onto the server mysql seemed to get it to work.

5.       Recently, I have noticed that loading the new data on gbrowse_vbox seems unsuccessful. The apache error logs don't show anythings specific, but I do get Segmentation faults and "Use of uninitialized value in concatenation or string. (I do not know in what).

6.       I am just not able to see any of the Overview/Region/Detail panels on my screen. When I search for a tem, I sometimes get search results on the screen and sometimes just the Blue header that displays "The following 308 regions match your request "  and then nothing below it in the tracks panel.

7.       I am able to see the whole page except for the tracks. I can rule out the possibility of bad data because It did load and I was able to visualize that same data once. I am just not able to load it up again and visualize it. 





Please help..

Pushkala Jayaraman

Programmer/Analyst

Rat Genome Database

Human and Molecular Genetics Center

Medical College of Wisconsin

Email: [hidden email] <[hidden email]>

Work: 414-955-2229

www.rgd.mcw.edu <http://www.rgd.mcw.edu>






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101 College St., Suite 800
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416 673-8514
Assistant: Renata Musa <[hidden email]>






--
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]>


------------------------------------------------------------------------------
ThinkGeek and WIRED's GeekDad team up for the Ultimate
GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
lucky parental unit.  See the prize list and enter to win:
http://p.sf.net/sfu/thinkgeek-promo
_______________________________________________
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https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
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Re: Gbrowse2 tracks not visible..possible bug?

Scott Cain
Pushkala,

You need "Name=Chr15" in column nine of that first line; that is what
identifies it as being Chr15.

Scott


On Mon, Jun 21, 2010 at 12:42 PM, Jayaraman, Pushkala
<[hidden email]> wrote:

> Hello Lincoln,
>
> This is what I get:
>
>
>
> mysql> select * from name where name like 'chr%';
>
> +-------+--------+--------------+
>
> | id    | name   | display_name |
>
> +-------+--------+--------------+
>
> | 29168 | Chrm3  |            1 |
>
> | 29169 | Chrm3  |            1 |
>
> | 29172 | Chrm3  |            1 |
>
> |  2076 | Chrna2 |            1 |
>
> |  2078 | Chrna2 |            1 |
>
> |  2080 | Chrna2 |            1 |
>
> |  2082 | Chrna2 |            1 |
>
> |  2084 | Chrna2 |            1 |
>
> |  2086 | Chrna2 |            1 |
>
> |  2088 | Chrna2 |            1 |
>
> |  2089 | Chrna2 |            1 |
>
> +-------+--------+--------------+
>
> 11 rows in set (0.00 sec)
>
>
>
> Why am I not getting any of the chromosome names?
>
>
>
>
>
> When I do “head nameof_gff3_file.gff3” I get:
>
>
>
> Chr15   GenBank chromosome      24425085        28088033        .       +
>    .       ID=NW_047453;Alias=15;Dbxref=taxon:10116;Note=Rattus norvegicus
> chromosome 15 genomic cont
>
> ig%2C reference assembly (based on RGSC v3.4).,GENOME ANNOTATION REFSEQ:
> Features on this sequence have been produced for build 4 version 1 of the
> NCBI's genome annotation [see d
>
> ocumentation]. The DNA sequence is version 3.4 'November 2004 Update' of the
> Rat genome assembly,produced by the Baylor College of Medicine Human Genome
> Sequencing Center (BCM- H
>
> GSC) as part of the Rat Genome Sequencing Consortium (RGSC). This supersedes
> all prior versions of the Rat assembly (2.0,2.1,3.0,3.1 3.2 and 3.3) (see
> http://www.hgsc.bcm.tmc.edu
>
> /projects/rat/). ;chromosome=15;comment1=GENOME ANNOTATION REFSEQ: Features
> on this sequence have been produced for build 4 version 1 of the NCBI's
> genome annotation [see documen
>
> tation]. The DNA sequence is version 3.4 'November 2004 Update' of the Rat
> genome assembly%2C produced by the Baylor College of Medicine Human Genome
> Sequencing Center (BCM- HGSC
>
> ) as part of the Rat Genome Sequencing Consortium (RGSC). This supersedes
> all prior versions of the Rat assembly (2.0%2C 2.1%2C 3.0%2C 3.1 3.2 and
> 3.3) (see http://www.hgsc.bcm.tmc.edu/projects/rat/).
> ;date=03-JUL-2006;mol_type=genomic DNA;organism=Rattus
> norvegicus;strain=BN/SsNHsdMCW;
>
> Chr15   GenBank pseudogene      24427872        24428719        .
> -       .       ID=LOC498499;Dbxref=GeneID:498499;Note=Derived by automated
> computational analysis using gene prediction method: GNOMON. Supporting
> evidence includes similarity to: 98 ESTs%2C 6
> Proteins;gene=LOC498499;pseudo=_no_value;
>
>
>
>
>
> Which clearly shows the chromosome feature right on top.
>
>
>
> 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: Lincoln Stein [mailto:[hidden email]]
> Sent: Monday, June 21, 2010 11:33 AM
> To: Jayaraman, Pushkala
> Cc: [hidden email]
> Subject: Re: [Gmod-gbrowse] Gbrowse2 tracks not visible..possible bug?
>
>
>
> It sounds to me as though you are loading the data correctly. But is there
> any chance that you used -c inadvertently on one of the subsequent loads and
> inadvertently removed the chromosomes? The way to check is:
>
>
>
>  mysql> select * from name where name like 'chr%'
>
>
>
> Lincoln
>
> On Mon, Jun 21, 2010 at 12:19 PM, Jayaraman, Pushkala <[hidden email]>
> wrote:
>
> Hello Lincoln,
>
> Yes,
>
> The yeast, in-memory database is loading well. Also, the data that I had
> loaded into the mysql database about a month ago (before I updated gbrowse
> through svn) is also seems to be rendering tracks on my VirtualBox as well
> as the server(I create a dump of the dabatase that I used on the VBox and
> uploaded that same database on the server and it works well)..
>
>
>
> I am using a mysql database backend. This is how I load the data
>
>  bp_seqfeature_load.pl -a DBI::mysql -d
> "DBI:mysql:database=DBNAME;host=HOSTNAME" -c -f filename.gff3
>
>
>
> I do not use -c each time. But I seem to have to use it the first time after
> I newly create a DB. Else it complains about not finding the tables. So it
> gives out errors like 'cannot load data into .locationlist table or view
> does not exist'.
>
> But when I use the -c feature, it seems to load it in pretty well. After
> that, I do not have to use the -c feature when I am adding data into the
> database.
>
>
> As you can see in the above two attached pictures, both are feb by very
> similar conf files except for their name. I simply made a copy of the conf
> file and renamed one. the data source though, is different. i.e they are
> being fed from two different mysql databases.
>
> when the database has all the tracks then it seems to generate pictures, but
> when i only load one feature eg. qtl, then it doesnt show anything..
> This is what my conf file looks like:
>
> [GENERAL]
>
> database     = general
>
>
>
> autocomplete = 1
>
> search options = default +autocomplete +wildcard
>
>
>
> # turn on remote rendering-- see [TRACK DEFAULTS] for the hosts
>
> # and ports the rendering slaves run on.
>
> renderfarm    = 1
>
>
>
> # just the basic track dumper plugin was in before..now added new plugins
>
> plugins = TrackDumper Aligner BatchDumper Submitter OligoFinder FilterTest
> AttributeHiliter
>
>
>
> #balloon tips acknowledge:
>
> balloon tips = 1
>
>
>
> # list of tracks to turn on by default
>
> default features = miRNA_Track
>
>
>
> # size of the region
>
> max segment     = 1000000000
>
> default segment = 50000
>
>
>
> # examples to show in the introduction
>
> examples = Odz3
>
>
>
> # feature to show on startup
>
> initial landmark = Chr16
>
>
>
> #to generalise searches. the search results will include both gene and
> protein keywords and will not require specific Gene:xxx or protein:xxx it
> will search xxx through gene and protein in order of them appearing in the
> line just below.
>
> automatic classes = RGD Gene
>
>
>
> #init codes work like functions built into the code:
>
> init_code         = sub bring_bubble{
>
>                      ------some code--------
>
>                      --------more code------
>
> }
>
> ########################
>
> # databases being used #
>
> ########################
>
> [general:database]
>
> db_adaptor    = Bio::DB::SeqFeature::Store
>
> db_args       = -adaptor DBI::mysql
>
>               -dsn     DBI:mysql:database=DBNAME;host=HOSTNAME.hmgc.mcw.edu
>
>               -user    USERNAME
>
>               -pass    PASSWORD
>
> ########################
>
> # Default glyph settings
>
> ########################
>
> [TRACK DEFAULTS]
>
> database      = general
>
> glyph         = generic
>
> height        = 10
>
> bgcolor       = lightgrey
>
> fgcolor       = black
>
> font2color    = blue
>
> label density = 25
>
> bump density  = 100
>
>
>
> # where to link to when user clicks in detailed view
>
> link          = AUTO
>
>
>
> #################################
>
> # Individual Track glyph settings
>
> #################################
>
>
>
> [miRNA_Track]
>
> category      = GENOMIC FEATURES
>
> feature       = miRNA:miRBase
>
> glyph         = dot
>
> fgcolor       = blue
>
> bgcolor       = lightblue
>
> linewidth    = 2
>
> height       = 6
>
> label        = sub{
>
>                      my $feature=shift;
>
>                      my ($miRna)=$feature->display_name;
>
>                      return $miRna;
>
>               }
>
> key           = miRNAs
>
> link          = sub {
>
>                      my $feature=shift;
>
>                      my ($miRnaID)=$feature->load_id;
>
>                      return
> "http://microrna.sanger.ac.uk/cgi-bin/sequences/mirna_entry.pl?id=$miRnaID";
>
>               }
>
> balloon hover = sub {bring_bubble(shift)}
>
> balloon sticky = 1
>
> citation      = This track shows rat microRNAs (miRNAs) derived from the <a
> href="http://microrna.sanger.ac.uk/"> Sanger Institute\'s miRBase</a>.
> miRBase is the repository for microRNA data, incorporating the database and
> gene naming roles previously provided by the miRNA Registry. Hovering over a
> feature provides annotation including miRBase ID and source. Clicking on a
> feature or selecting the miRBase ID links to the miRBase miRNA Report pages.
>
>
>
> [miRNA_Track:overview]
>
> feature       = miRNA:miRBase
>
> glyph         = dot
>
> fgcolor       = blue
>
> bgcolor       = lightblue
>
> linewidth    = 2
>
> height       = 6
>
> label        = sub{
>
>                      my $feature=shift;
>
>                      my ($miRna)=$feature->display_name;
>
>                      return $miRna;
>
>               }
>
> key           = miRNAs Overview
>
> link          = sub {
>
>                      my $feature=shift;
>
>                      my ($miRnaID)=$feature->load_id;
>
>                      return
> "http://microrna.sanger.ac.uk/cgi-bin/sequences/mirna_entry.pl?id=$miRnaID";
>
>               }
>
> citation      = This track shows rat microRNAs (miRNAs) derived from the <a
> href="http://microrna.sanger.ac.uk/"> Sanger Institute\'s miRBase</a>.
> miRBase is the repository for microRNA data, incorporating the database and
> gene naming roles previously provided by the miRNA Registry. Hovering over a
> feature provides annotation including miRBase ID and source. Clicking on a
> feature or selecting the miRBase ID links to the miRBase miRNA Report pages.
>
>
>
> [QTLS]
>
> glyph        = saw_teeth
>
> category      = GENOMIC FEATURES
>
> feature       = QTL:RGD
>
> height       = 5
>
> linewidth     = 3
>
> bgcolor       = maroon
>
> fgcolor       = orange
>
> label        = sub{
>
>                      my $feature=shift;
>
>                      my ($qtlid)=$feature->load_id;
>
>                      my @qtlarr=split(/:/, $qtlid);
>
>                      return "QTL:$qtlarr[1]";
>
>               }
>
> description   = sub{
>
>                      my $feature=shift;
>
>                      my ($desc)=$feature->attributes('Dbxref');
>
>                      my @desc_arr=split(/:/, $desc);
>
>                      return "RGDID:".$desc_arr[1];
>
>
>
>               }
>
> link         = sub {
>
>                      my $feature=shift;
>
>                      my ($link)=$feature->attributes('Dbxref');
>
>                      if ($link=~/RGD:(\d+)/) {
>
>                             my $rgdid=$1;
>
>                             return
> "http://rgd.mcw.edu/objectSearch/qtlReport.jsp?rgd_id=$rgdid";
>
>                      }
>
>               }
>
> balloon hover  = sub {bring_bubble(shift)}
>
> balloon sticky = 1
>
> key           = RGD QTLs
>
> citation      = This track shows <a href="http://www.rgd.mcw.edu/qtls/"> RGD
> Rat Quantitative Trait Loci (QTL)</a>. In some cases the boundaries of the
> QTL have been estimated as explained in <a
> href="ftp://rgd.mcw.edu/pub/data_release/QTLS_README"> QTLs Readme file</a>.
> Hovering over a feature provides additional annotation including the name,
> symbol, LOD (where available), p-value (where available), mapping method,
> and RGD ID, which links to the RGD QTL report page. Clicking on a feature
> also links to its RGD report page.
>
>
>
> [PGA]
>
> category      = PGA
>
> feature       = PGA:ENU_BN PGA:ENU_FHH PGA:SB_F344
>
> glyph         = diamond
>
> bgcolor       = purple
>
> fgcolor       = pink
>
> key           = PGA
>
> balloon hover  = sub {bring_bubble(shift)}
>
> balloon sticky = 1
>
> select        = source 'SB_F344' 'ENU_FHH' 'ENU_BN'
>
> label         = sub {
>
>                   my $feature=shift;
>
>                   my ($pga_label)= $feature->display_name;
>
>                   return $pga_label
>
>                 }
>
> description   = sub {
>
>                   my $feature=shift;
>
>                   my ($pga_desc)= $feature->attributes("Id");
>
>                   return $pga_desc;
>
>                 }
>
> link           = sub {
>
>                   my $feature=shift;
>
>                   my ($pga_id)=$feature->attributes("Id");
>
>                   $pga_id=~s/RGD://;
>
>                   return
> "http://rgd.mcw.edu/tools/strains/strains_view.cgi?id=$pga_id";
>
>                   }
>
> citation      = This track includes the genomic locations of the <a
> href="http://pga.mcw.edu/"> PhysGen PGA</a> mutant strains developed using
> ENU mutagenesis or the Sleeping Beauty transposon strategy. Hovering over a
> feature provides additional annotation including the Gene Name, RGD Strain
> ID, Strain and Source (ENU_FHH, ENU_BN, SB_F344). Clicking on a feature or
> selecting the RGD Strain ID links to the strain report pages at RGD.
>
>
>
> [CNV]
>
> category     = ANNOTATED VARIANTS
>
> feature       = CNV:Hubrecht_Institute
>
> glyph        = span
>
> fgcolor       = sub {bring_cnv_color(shift)}
>
> bgcolor             = black
>
> font2color    = pink1
>
> linewidth     = 3
>
> height        = 5
>
> label       = sub{
>
>                      my $cnv_feat = shift;
>
>                      my ($cnvID)=$cnv_feat->attributes('Dbxref');
>
>                      return "$cnvID";
>
>
>
>               }
>
> description   = sub{
>
>                      my $cnv_feat = shift;
>
>                      my ($type)=$cnv_feat->attributes('type');
>
>                      return "TYPE:$type";
>
>
>
>               }
>
> balloon hover = sub {bring_bubble(shift)}
>
> balloon sticky= 1
>
> key           =CNVs
>
> link   = sub{
>
>                      my $cnv_feat = shift;
>
>                      my ($cnvID)=$cnv_feat->attributes('Dbxref');
>
>                      $cnvID =~s/cnv_//i;
>
>                      return
> "http://h094.niob.knaw.nl/RatCNVs/cgi-bin/cnv.pl?id=$cnvID";
>
>
>
>               }
>
> citation      = <a href="http://h094.niob.knaw.nl/RatCNVs/"> Copy Number
> Variants (CNVs)</a> identified in commonly used laboratory rat strains
> through combination of computational approaches and experimental analysis as
> published in Guryev et al.; Distribution and functional impact of DNA copy
> number variation in the rat. Nature Genetics 40, 538 - 545 (2008). Hovering
> over a feature provides additional annotation including the CNV ID, Strain,
> Method, Type, and Source. Clicking on a feature or selecting the CNV ID
> links to the Hubrecht Institute\'s CNV pages.<br />CNVs are colored based on
> type as following:<br /><table
> border="1"><tr><th>Type</th><th>Color</th></tr><tr><td>Collapse</td><td>Purple</td></tr><tr><td>Overprediction</td><td>Yellow</td></tr><tr><td>Loss</td><td>Blue</td></tr><tr><td>Loss+Collapse</td><td>Dark
> blue</td></tr><tr><td>Loss+Overprediction</td><td>Light
> blue</td></tr><tr><td>Gain</td><td>Red</td></tr><tr><td>Gain+Collapse</td><td>Dark
> red</td></tr><tr><td>Gain+Overprediction</td><td>Light red</td></tr></table>
>
>
>
>
>
> 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: Lincoln Stein [mailto:[hidden email]]
>
> Sent: Monday, June 21, 2010 10:38 AM
> To: Jayaraman, Pushkala
> Cc: [hidden email]
> Subject: Re: [Gmod-gbrowse] Gbrowse2 tracks not visible..possible bug?
>
>
>
> Hi Pushkala,
>
>
>
> I'm afraid I'll need more information. Is the in-memory Yeast database
> working on the development server? If it is, it probably rules out a
> software problem. What database backend are you using, and how do you load
> it? What operating system are you using?
>
>
>
> When you are unable to upload the "new" data on the Virtual Box, what do you
> mean by "new"?
>
>
>
> Lincoln
>
>
>
> On Mon, Jun 21, 2010 at 8:11 AM, Jayaraman, Pushkala <[hidden email]>
> wrote:
>
> Hello,
>
> I seem to be having problems with Gbrowse showing tracks on screen. This is
> slightly complicated:
>
> 1.       I have set up a fully functional gbrowse2 v2.03 on my Virtual Box
> with saved snapshots.
>
> 2.       I upgraded to Gbrowse 2.08 from SVN stable branch last month and
> set up that on my virtual Box. That seemed to be working too.
>
> 3.       I then had Gbrowse2 installed on our development server. This is
> where problems began,
>
> When I tried to load the exact data that I had displaying successfully on my
> Virtual Box(lets call it Gbrowse_vbox), onto the gbrowse on the server (lets
> call it Gbrowse_serv)I saw that the Gbrowse_serv could not seem to display
> any of the data.
>
> 4.       Dumping the sql database from the vbox onto the server mysql seemed
> to get it to work.
>
> 5.       Recently, I have noticed that loading the new data on gbrowse_vbox
> seems unsuccessful. The apache error logs don't show anythings specific, but
> I do get Segmentation faults and "Use of uninitialized value in
> concatenation or string. (I do not know in what).
>
> 6.       I am just not able to see any of the Overview/Region/Detail panels
> on my screen. When I search for a tem, I sometimes get search results on the
> screen and sometimes just the Blue header that displays "The following 308
> regions match your request "  and then nothing below it in the tracks panel.
>
> 7.       I am able to see the whole page except for the tracks. I can rule
> out the possibility of bad data because It did load and I was able to
> visualize that same data once. I am just not able to load it up again and
> visualize it.
>
>
>
>
>
> Please help..
>
> Pushkala Jayaraman
>
> Programmer/Analyst
>
> Rat Genome Database
>
> Human and Molecular Genetics Center
>
> Medical College of Wisconsin
>
> Email: [hidden email] <mailto:[hidden email]>
>
> Work: 414-955-2229
>
> www.rgd.mcw.edu <http://www.rgd.mcw.edu>
>
>
>
>
> ------------------------------------------------------------------------------
> ThinkGeek and WIRED's GeekDad team up for the Ultimate
> GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
> lucky parental unit.  See the prize list and enter to win:
> http://p.sf.net/sfu/thinkgeek-promo
> _______________________________________________
> 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]>
>
>
>
>
>
>
> --
> 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]>
>
> ------------------------------------------------------------------------------
> ThinkGeek and WIRED's GeekDad team up for the Ultimate
> GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
> lucky parental unit.  See the prize list and enter to win:
> http://p.sf.net/sfu/thinkgeek-promo
> _______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>
>



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

------------------------------------------------------------------------------
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GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
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Re: Gbrowse2 tracks not visible..possible bug?

Jayaraman, Pushkala
In reply to this post by Jayaraman, Pushkala

I went ahead and checked the working copies (which fed data into the working data sources) with the same sql query and I get lists of the chromosome and I get back values:

 

mysql> select * from name where name like 'chr%' limit 5;

+--------+---------------------------+--------------+

| id     | name                      | display_name |

+--------+---------------------------+--------------+

|   2220 | chr1                      |            1 |

| 406088 | chr1                      |            1 |

|   1961 | chr10                     |            1 |

| 404537 | chr10                     |            1 |

|   2862 | chr10:127915135-127915215 |            1 |

+--------+---------------------------+--------------+

5 rows in set (0.00 sec)

 

 

But when I did this to the most recent database which fed data into the “erroneous data sources” I get back empty set or gene names similar to Chrm3  but no ‘chromosome’

 

Is this the 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: Jayaraman, Pushkala [mailto:[hidden email]]
Sent: Monday, June 21, 2010 11:42 AM
To: Lincoln Stein
Cc: [hidden email]
Subject: Re: [Gmod-gbrowse] Gbrowse2 tracks not visible..possible bug?

 

Hello Lincoln,

This is what I get:

 

mysql> select * from name where name like 'chr%';

+-------+--------+--------------+

| id    | name   | display_name |

+-------+--------+--------------+

| 29168 | Chrm3  |            1 |

| 29169 | Chrm3  |            1 |

| 29172 | Chrm3  |            1 |

|  2076 | Chrna2 |            1 |

|  2078 | Chrna2 |            1 |

|  2080 | Chrna2 |            1 |

|  2082 | Chrna2 |            1 |

|  2084 | Chrna2 |            1 |

|  2086 | Chrna2 |            1 |

|  2088 | Chrna2 |            1 |

|  2089 | Chrna2 |            1 |

+-------+--------+--------------+

11 rows in set (0.00 sec)

 

Why am I not getting any of the chromosome names?

 

 

When I do “head nameof_gff3_file.gff3” I get:

 

Chr15   GenBank chromosome      24425085        28088033        .       +       .       ID=NW_047453;Alias=15;Dbxref=taxon:10116;Note=Rattus norvegicus chromosome 15 genomic cont

ig%2C reference assembly (based on RGSC v3.4).,GENOME ANNOTATION REFSEQ: Features on this sequence have been produced for build 4 version 1 of the NCBI's genome annotation [see d

ocumentation]. The DNA sequence is version 3.4 'November 2004 Update' of the Rat genome assembly,produced by the Baylor College of Medicine Human Genome Sequencing Center (BCM- H

GSC) as part of the Rat Genome Sequencing Consortium (RGSC). This supersedes all prior versions of the Rat assembly (2.0,2.1,3.0,3.1 3.2 and 3.3) (see http://www.hgsc.bcm.tmc.edu

/projects/rat/). ;chromosome=15;comment1=GENOME ANNOTATION REFSEQ: Features on this sequence have been produced for build 4 version 1 of the NCBI's genome annotation [see documen

tation]. The DNA sequence is version 3.4 'November 2004 Update' of the Rat genome assembly%2C produced by the Baylor College of Medicine Human Genome Sequencing Center (BCM- HGSC

) as part of the Rat Genome Sequencing Consortium (RGSC). This supersedes all prior versions of the Rat assembly (2.0%2C 2.1%2C 3.0%2C 3.1 3.2 and 3.3) (see http://www.hgsc.bcm.tmc.edu/projects/rat/). ;date=03-JUL-2006;mol_type=genomic DNA;organism=Rattus norvegicus;strain=BN/SsNHsdMCW;

Chr15   GenBank pseudogene      24427872        24428719        .       -       .       ID=LOC498499;Dbxref=GeneID:498499;Note=Derived by automated computational analysis using gene prediction method: GNOMON. Supporting evidence includes similarity to: 98 ESTs%2C 6 Proteins;gene=LOC498499;pseudo=_no_value;

 

 

Which clearly shows the chromosome feature right on top.

 

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: Lincoln Stein [mailto:[hidden email]]
Sent: Monday, June 21, 2010 11:33 AM
To: Jayaraman, Pushkala
Cc: [hidden email]
Subject: Re: [Gmod-gbrowse] Gbrowse2 tracks not visible..possible bug?

 

It sounds to me as though you are loading the data correctly. But is there any chance that you used -c inadvertently on one of the subsequent loads and inadvertently removed the chromosomes? The way to check is:

 

 mysql> select * from name where name like 'chr%'

 

Lincoln

On Mon, Jun 21, 2010 at 12:19 PM, Jayaraman, Pushkala <[hidden email]> wrote:

Hello Lincoln,

Yes,

The yeast, in-memory database is loading well. Also, the data that I had loaded into the mysql database about a month ago (before I updated gbrowse through svn) is also seems to be rendering tracks on my VirtualBox as well as the server(I create a dump of the dabatase that I used on the VBox and uploaded that same database on the server and it works well)..



I am using a mysql database backend. This is how I load the data

 bp_seqfeature_load.pl -a DBI::mysql -d "DBI:mysql:database=DBNAME;host=HOSTNAME" -c -f filename.gff3



I do not use -c each time. But I seem to have to use it the first time after I newly create a DB. Else it complains about not finding the tables. So it gives out errors like 'cannot load data into .locationlist table or view does not exist'.

But when I use the -c feature, it seems to load it in pretty well. After that, I do not have to use the -c feature when I am adding data into the database.


As you can see in the above two attached pictures, both are feb by very similar conf files except for their name. I simply made a copy of the conf file and renamed one. the data source though, is different. i.e they are being fed from two different mysql databases.

when the database has all the tracks then it seems to generate pictures, but when i only load one feature eg. qtl, then it doesnt show anything..
This is what my conf file looks like:

[GENERAL]

database     = general



autocomplete = 1

search options = default +autocomplete +wildcard       



# turn on remote rendering-- see [TRACK DEFAULTS] for the hosts

# and ports the rendering slaves run on.

renderfarm    = 1



# just the basic track dumper plugin was in before..now added new plugins

plugins = TrackDumper Aligner BatchDumper Submitter OligoFinder FilterTest AttributeHiliter



#balloon tips acknowledge:

balloon tips = 1



# list of tracks to turn on by default

default features = miRNA_Track



# size of the region

max segment     = 1000000000

default segment = 50000



# examples to show in the introduction

examples = Odz3



# feature to show on startup

initial landmark = Chr16



#to generalise searches. the search results will include both gene and protein keywords and will not require specific Gene:xxx or protein:xxx it will search xxx through gene and protein in order of them appearing in the line just below.

automatic classes = RGD Gene



#init codes work like functions built into the code:

init_code         = sub bring_bubble{

                     ------some code--------

                     --------more code------

}

########################

# databases being used #

########################

[general:database]

db_adaptor    = Bio::DB::SeqFeature::Store

db_args       = -adaptor DBI::mysql

              -dsn     DBI:mysql:database=DBNAME;host=HOSTNAME.hmgc.mcw.edu

              -user    USERNAME

              -pass    PASSWORD

########################

# Default glyph settings

########################

[TRACK DEFAULTS]

database      = general

glyph         = generic

height        = 10

bgcolor       = lightgrey

fgcolor       = black

font2color    = blue

label density = 25

bump density  = 100



# where to link to when user clicks in detailed view

link          = AUTO



#################################

# Individual Track glyph settings

#################################



[miRNA_Track]

category      = GENOMIC FEATURES

feature       = miRNA:miRBase

glyph         = dot

fgcolor       = blue

bgcolor       = lightblue

linewidth    = 2

height       = 6

label        = sub{

                     my $feature=shift;

                     my ($miRna)=$feature->display_name;

                     return $miRna;      

              }

key           = miRNAs

link          = sub {

                     my $feature=shift;

                     my ($miRnaID)=$feature->load_id;

                     return "http://microrna.sanger.ac.uk/cgi-bin/sequences/mirna_entry.pl?id=$miRnaID";

              }

balloon hover = sub {bring_bubble(shift)}

balloon sticky = 1

citation      = This track shows rat microRNAs (miRNAs) derived from the <a href="http://microrna.sanger.ac.uk/"> Sanger Institute\'s miRBase</a>. miRBase is the repository for microRNA data, incorporating the database and gene naming roles previously provided by the miRNA Registry. Hovering over a feature provides annotation including miRBase ID and source. Clicking on a feature or selecting the miRBase ID links to the miRBase miRNA Report pages.



[miRNA_Track:overview]

feature       = miRNA:miRBase

glyph         = dot

fgcolor       = blue

bgcolor       = lightblue

linewidth    = 2

height       = 6

label        = sub{

                     my $feature=shift;

                     my ($miRna)=$feature->display_name;

                     return $miRna;      

              }

key           = miRNAs Overview

link          = sub {

                     my $feature=shift;

                     my ($miRnaID)=$feature->load_id;

                     return "http://microrna.sanger.ac.uk/cgi-bin/sequences/mirna_entry.pl?id=$miRnaID";

              }

citation      = This track shows rat microRNAs (miRNAs) derived from the <a href="http://microrna.sanger.ac.uk/"> Sanger Institute\'s miRBase</a>. miRBase is the repository for microRNA data, incorporating the database and gene naming roles previously provided by the miRNA Registry. Hovering over a feature provides annotation including miRBase ID and source. Clicking on a feature or selecting the miRBase ID links to the miRBase miRNA Report pages.



[QTLS]

glyph        = saw_teeth

category      = GENOMIC FEATURES

feature       = QTL:RGD

height       = 5

linewidth     = 3

bgcolor       = maroon

fgcolor       = orange

label        = sub{

                     my $feature=shift;

                     my ($qtlid)=$feature->load_id;

                     my @qtlarr=split(/:/, $qtlid);

                     return "QTL:$qtlarr[1]";

              }

description   = sub{

                     my $feature=shift;

                     my ($desc)=$feature->attributes('Dbxref');

                     my @desc_arr=split(/:/, $desc);

                     return "RGDID:".$desc_arr[1];

                    

              }

link         = sub {

                     my $feature=shift;

                     my ($link)=$feature->attributes('Dbxref');

                     if ($link=~/RGD:(\d+)/) {

                            my $rgdid=$1;

                            return "http://rgd.mcw.edu/objectSearch/qtlReport.jsp?rgd_id=$rgdid";

                     }

              }

balloon hover  = sub {bring_bubble(shift)}      

balloon sticky = 1

key           = RGD QTLs

citation      = This track shows <a href="http://www.rgd.mcw.edu/qtls/"> RGD Rat Quantitative Trait Loci (QTL)</a>. In some cases the boundaries of the QTL have been estimated as explained in <a href="ftp://rgd.mcw.edu/pub/data_release/QTLS_README"> QTLs Readme file</a>. Hovering over a feature provides additional annotation including the name, symbol, LOD (where available), p-value (where available), mapping method, and RGD ID, which links to the RGD QTL report page. Clicking on a feature also links to its RGD report page.



[PGA]

category      = PGA

feature       = PGA:ENU_BN PGA:ENU_FHH PGA:SB_F344

glyph         = diamond

bgcolor       = purple

fgcolor       = pink

key           = PGA

balloon hover  = sub {bring_bubble(shift)}

balloon sticky = 1

select        = source 'SB_F344' 'ENU_FHH' 'ENU_BN'

label         = sub {

                  my $feature=shift;

                  my ($pga_label)= $feature->display_name;

                  return $pga_label

                }

description   = sub {

                  my $feature=shift;

                  my ($pga_desc)= $feature->attributes("Id");

                  return $pga_desc;

                }

link           = sub {

                  my $feature=shift;

                  my ($pga_id)=$feature->attributes("Id");

                  $pga_id=~s/RGD://;

                  return "http://rgd.mcw.edu/tools/strains/strains_view.cgi?id=$pga_id";

                  }

citation      = This track includes the genomic locations of the <a href="http://pga.mcw.edu/"> PhysGen PGA</a> mutant strains developed using ENU mutagenesis or the Sleeping Beauty transposon strategy. Hovering over a feature provides additional annotation including the Gene Name, RGD Strain ID, Strain and Source (ENU_FHH, ENU_BN, SB_F344). Clicking on a feature or selecting the RGD Strain ID links to the strain report pages at RGD.



[CNV]

category     = ANNOTATED VARIANTS

feature       = CNV:Hubrecht_Institute

glyph        = span

fgcolor       = sub {bring_cnv_color(shift)}

bgcolor             = black

font2color    = pink1

linewidth     = 3

height        = 5

label       = sub{

                     my $cnv_feat = shift;

                     my ($cnvID)=$cnv_feat->attributes('Dbxref');

                     return "$cnvID";



              }

description   = sub{

                     my $cnv_feat = shift;

                     my ($type)=$cnv_feat->attributes('type');

                     return "TYPE:$type";



              }

balloon hover = sub {bring_bubble(shift)}

balloon sticky= 1

key           =CNVs

link   = sub{

                     my $cnv_feat = shift;

                     my ($cnvID)=$cnv_feat->attributes('Dbxref');

                     $cnvID =~s/cnv_//i;

                     return "http://h094.niob.knaw.nl/RatCNVs/cgi-bin/cnv.pl?id=$cnvID";



              }

citation      = <a href="http://h094.niob.knaw.nl/RatCNVs/"> Copy Number Variants (CNVs)</a> identified in commonly used laboratory rat strains through combination of computational approaches and experimental analysis as published in Guryev et al.; Distribution and functional impact of DNA copy number variation in the rat. Nature Genetics 40, 538 - 545 (2008). Hovering over a feature provides additional annotation including the CNV ID, Strain, Method, Type, and Source. Clicking on a feature or selecting the CNV ID links to the Hubrecht Institute\'s CNV pages.<br />CNVs are colored based on type as following:<br /><table border="1"><tr><th>Type</th><th>Color</th></tr><tr><td>Collapse</td><td>Purple</td></tr><tr><td>Overprediction</td><td>Yellow</td></tr><tr><td>Loss</td><td>Blue</td></tr><tr><td>Loss+Collapse</td><td>Dark blue</td></tr><tr><td>Loss+Overprediction</td><td>Light blue</td></tr><tr><td>Gain</td><td>Red</td></tr><tr><td>Gain+Collapse</td><td>Dark red</td></tr><tr><td>Gain+Overprediction</td><td>Light red</td></tr></table>







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: Lincoln Stein [[hidden email]]

Sent: Monday, June 21, 2010 10:38 AM
To: Jayaraman, Pushkala
Cc: [hidden email]
Subject: Re: [Gmod-gbrowse] Gbrowse2 tracks not visible..possible bug?





Hi Pushkala,



I'm afraid I'll need more information. Is the in-memory Yeast database working on the development server? If it is, it probably rules out a software problem. What database backend are you using, and how do you load it? What operating system are you using?



When you are unable to upload the "new" data on the Virtual Box, what do you mean by "new"?



Lincoln



On Mon, Jun 21, 2010 at 8:11 AM, Jayaraman, Pushkala <[hidden email]> wrote:

Hello,

I seem to be having problems with Gbrowse showing tracks on screen. This is slightly complicated:

1.       I have set up a fully functional gbrowse2 v2.03 on my Virtual Box with saved snapshots.

2.       I upgraded to Gbrowse 2.08 from SVN stable branch last month and set up that on my virtual Box. That seemed to be working too.

3.       I then had Gbrowse2 installed on our development server. This is where problems began,

When I tried to load the exact data that I had displaying successfully on my Virtual Box(lets call it Gbrowse_vbox), onto the gbrowse on the server (lets call it Gbrowse_serv)I saw that the Gbrowse_serv could not seem to display any of the data.

4.       Dumping the sql database from the vbox onto the server mysql seemed to get it to work.

5.       Recently, I have noticed that loading the new data on gbrowse_vbox seems unsuccessful. The apache error logs don't show anythings specific, but I do get Segmentation faults and "Use of uninitialized value in concatenation or string. (I do not know in what).

6.       I am just not able to see any of the Overview/Region/Detail panels on my screen. When I search for a tem, I sometimes get search results on the screen and sometimes just the Blue header that displays "The following 308 regions match your request "  and then nothing below it in the tracks panel.

7.       I am able to see the whole page except for the tracks. I can rule out the possibility of bad data because It did load and I was able to visualize that same data once. I am just not able to load it up again and visualize it. 





Please help..

Pushkala Jayaraman

Programmer/Analyst

Rat Genome Database

Human and Molecular Genetics Center

Medical College of Wisconsin

Email: [hidden email] <[hidden email]>

Work: 414-955-2229

www.rgd.mcw.edu <http://www.rgd.mcw.edu>






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Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <[hidden email]>





--
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]>


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Re: Gbrowse2 tracks not visible..possible bug?

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

The first column is used for the reference sequence coordinate, and is not always the same as the name of the chromosome. Each chromosome line should have a tag of the form "Name=Chr3" in the last column of the GFF3. Please try appending:

;Name=Chr3

to the end of each GFF3 line. Please be sure to change the chromosome name appropriately, and don't forget to separate the Name tag from the other tags using the semicolon character.

Lincoln

On Mon, Jun 21, 2010 at 12:42 PM, Jayaraman, Pushkala <[hidden email]> wrote:

Hello Lincoln,

This is what I get:

 

mysql> select * from name where name like 'chr%';

+-------+--------+--------------+

| id    | name   | display_name |

+-------+--------+--------------+

| 29168 | Chrm3  |            1 |

| 29169 | Chrm3  |            1 |

| 29172 | Chrm3  |            1 |

|  2076 | Chrna2 |            1 |

|  2078 | Chrna2 |            1 |

|  2080 | Chrna2 |            1 |

|  2082 | Chrna2 |            1 |

|  2084 | Chrna2 |            1 |

|  2086 | Chrna2 |            1 |

|  2088 | Chrna2 |            1 |

|  2089 | Chrna2 |            1 |

+-------+--------+--------------+

11 rows in set (0.00 sec)

 

Why am I not getting any of the chromosome names?

 

 

When I do “head nameof_gff3_file.gff3” I get:

 

Chr15   GenBank chromosome      24425085        28088033        .       +       .       ID=NW_047453;Alias=15;Dbxref=taxon:10116;Note=Rattus norvegicus chromosome 15 genomic cont

ig%2C reference assembly (based on RGSC v3.4).,GENOME ANNOTATION REFSEQ: Features on this sequence have been produced for build 4 version 1 of the NCBI's genome annotation [see d

ocumentation]. The DNA sequence is version 3.4 'November 2004 Update' of the Rat genome assembly,produced by the Baylor College of Medicine Human Genome Sequencing Center (BCM- H

GSC) as part of the Rat Genome Sequencing Consortium (RGSC). This supersedes all prior versions of the Rat assembly (2.0,2.1,3.0,3.1 3.2 and 3.3) (see http://www.hgsc.bcm.tmc.edu

/projects/rat/). ;chromosome=15;comment1=GENOME ANNOTATION REFSEQ: Features on this sequence have been produced for build 4 version 1 of the NCBI's genome annotation [see documen

tation]. The DNA sequence is version 3.4 'November 2004 Update' of the Rat genome assembly%2C produced by the Baylor College of Medicine Human Genome Sequencing Center (BCM- HGSC

) as part of the Rat Genome Sequencing Consortium (RGSC). This supersedes all prior versions of the Rat assembly (2.0%2C 2.1%2C 3.0%2C 3.1 3.2 and 3.3) (see http://www.hgsc.bcm.tmc.edu/projects/rat/). ;date=03-JUL-2006;mol_type=genomic DNA;organism=Rattus norvegicus;strain=BN/SsNHsdMCW;

Chr15   GenBank pseudogene      24427872        24428719        .       -       .       ID=LOC498499;Dbxref=GeneID:498499;Note=Derived by automated computational analysis using gene prediction method: GNOMON. Supporting evidence includes similarity to: 98 ESTs%2C 6 Proteins;gene=LOC498499;pseudo=_no_value;

 

 

Which clearly shows the chromosome feature right on top.

 

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: Lincoln Stein [mailto:[hidden email]]
Sent: Monday, June 21, 2010 11:33 AM


To: Jayaraman, Pushkala
Cc: [hidden email]
Subject: Re: [Gmod-gbrowse] Gbrowse2 tracks not visible..possible bug?

 

It sounds to me as though you are loading the data correctly. But is there any chance that you used -c inadvertently on one of the subsequent loads and inadvertently removed the chromosomes? The way to check is:

 

 mysql> select * from name where name like 'chr%'

 

Lincoln

On Mon, Jun 21, 2010 at 12:19 PM, Jayaraman, Pushkala <[hidden email]> wrote:

Hello Lincoln,

Yes,

The yeast, in-memory database is loading well. Also, the data that I had loaded into the mysql database about a month ago (before I updated gbrowse through svn) is also seems to be rendering tracks on my VirtualBox as well as the server(I create a dump of the dabatase that I used on the VBox and uploaded that same database on the server and it works well)..



I am using a mysql database backend. This is how I load the data

 bp_seqfeature_load.pl -a DBI::mysql -d "DBI:mysql:database=DBNAME;host=HOSTNAME" -c -f filename.gff3



I do not use -c each time. But I seem to have to use it the first time after I newly create a DB. Else it complains about not finding the tables. So it gives out errors like 'cannot load data into .locationlist table or view does not exist'.

But when I use the -c feature, it seems to load it in pretty well. After that, I do not have to use the -c feature when I am adding data into the database.


As you can see in the above two attached pictures, both are feb by very similar conf files except for their name. I simply made a copy of the conf file and renamed one. the data source though, is different. i.e they are being fed from two different mysql databases.

when the database has all the tracks then it seems to generate pictures, but when i only load one feature eg. qtl, then it doesnt show anything..
This is what my conf file looks like:

[GENERAL]

database     = general



autocomplete = 1

search options = default +autocomplete +wildcard       



# turn on remote rendering-- see [TRACK DEFAULTS] for the hosts

# and ports the rendering slaves run on.

renderfarm    = 1



# just the basic track dumper plugin was in before..now added new plugins

plugins = TrackDumper Aligner BatchDumper Submitter OligoFinder FilterTest AttributeHiliter



#balloon tips acknowledge:

balloon tips = 1



# list of tracks to turn on by default

default features = miRNA_Track



# size of the region

max segment     = 1000000000

default segment = 50000



# examples to show in the introduction

examples = Odz3



# feature to show on startup

initial landmark = Chr16



#to generalise searches. the search results will include both gene and protein keywords and will not require specific Gene:xxx or protein:xxx it will search xxx through gene and protein in order of them appearing in the line just below.

automatic classes = RGD Gene



#init codes work like functions built into the code:

init_code         = sub bring_bubble{

                     ------some code--------

                     --------more code------

}

########################

# databases being used #

########################

[general:database]

db_adaptor    = Bio::DB::SeqFeature::Store

db_args       = -adaptor DBI::mysql

              -dsn     DBI:mysql:database=DBNAME;host=HOSTNAME.hmgc.mcw.edu

              -user    USERNAME

              -pass    PASSWORD

########################

# Default glyph settings

########################

[TRACK DEFAULTS]

database      = general

glyph         = generic

height        = 10

bgcolor       = lightgrey

fgcolor       = black

font2color    = blue

label density = 25

bump density  = 100



# where to link to when user clicks in detailed view

link          = AUTO



#################################

# Individual Track glyph settings

#################################



[miRNA_Track]

category      = GENOMIC FEATURES

feature       = miRNA:miRBase

glyph         = dot

fgcolor       = blue

bgcolor       = lightblue

linewidth    = 2

height       = 6

label        = sub{

                     my $feature=shift;

                     my ($miRna)=$feature->display_name;

                     return $miRna;      

              }

key           = miRNAs

link          = sub {

                     my $feature=shift;

                     my ($miRnaID)=$feature->load_id;

                     return "http://microrna.sanger.ac.uk/cgi-bin/sequences/mirna_entry.pl?id=$miRnaID";

              }

balloon hover = sub {bring_bubble(shift)}

balloon sticky = 1

citation      = This track shows rat microRNAs (miRNAs) derived from the <a href="http://microrna.sanger.ac.uk/"> Sanger Institute\'s miRBase</a>. miRBase is the repository for microRNA data, incorporating the database and gene naming roles previously provided by the miRNA Registry. Hovering over a feature provides annotation including miRBase ID and source. Clicking on a feature or selecting the miRBase ID links to the miRBase miRNA Report pages.



[miRNA_Track:overview]

feature       = miRNA:miRBase

glyph         = dot

fgcolor       = blue

bgcolor       = lightblue

linewidth    = 2

height       = 6

label        = sub{

                     my $feature=shift;

                     my ($miRna)=$feature->display_name;

                     return $miRna;      

              }

key           = miRNAs Overview

link          = sub {

                     my $feature=shift;

                     my ($miRnaID)=$feature->load_id;

                     return "http://microrna.sanger.ac.uk/cgi-bin/sequences/mirna_entry.pl?id=$miRnaID";

              }

citation      = This track shows rat microRNAs (miRNAs) derived from the <a href="http://microrna.sanger.ac.uk/"> Sanger Institute\'s miRBase</a>. miRBase is the repository for microRNA data, incorporating the database and gene naming roles previously provided by the miRNA Registry. Hovering over a feature provides annotation including miRBase ID and source. Clicking on a feature or selecting the miRBase ID links to the miRBase miRNA Report pages.



[QTLS]

glyph        = saw_teeth

category      = GENOMIC FEATURES

feature       = QTL:RGD

height       = 5

linewidth     = 3

bgcolor       = maroon

fgcolor       = orange

label        = sub{

                     my $feature=shift;

                     my ($qtlid)=$feature->load_id;

                     my @qtlarr=split(/:/, $qtlid);

                     return "QTL:$qtlarr[1]";

              }

description   = sub{

                     my $feature=shift;

                     my ($desc)=$feature->attributes('Dbxref');

                     my @desc_arr=split(/:/, $desc);

                     return "RGDID:".$desc_arr[1];

                    

              }

link         = sub {

                     my $feature=shift;

                     my ($link)=$feature->attributes('Dbxref');

                     if ($link=~/RGD:(\d+)/) {

                            my $rgdid=$1;

                            return "http://rgd.mcw.edu/objectSearch/qtlReport.jsp?rgd_id=$rgdid";

                     }

              }

balloon hover  = sub {bring_bubble(shift)}      

balloon sticky = 1

key           = RGD QTLs

citation      = This track shows <a href="http://www.rgd.mcw.edu/qtls/"> RGD Rat Quantitative Trait Loci (QTL)</a>. In some cases the boundaries of the QTL have been estimated as explained in <a href="ftp://rgd.mcw.edu/pub/data_release/QTLS_README"> QTLs Readme file</a>. Hovering over a feature provides additional annotation including the name, symbol, LOD (where available), p-value (where available), mapping method, and RGD ID, which links to the RGD QTL report page. Clicking on a feature also links to its RGD report page.



[PGA]

category      = PGA

feature       = PGA:ENU_BN PGA:ENU_FHH PGA:SB_F344

glyph         = diamond

bgcolor       = purple

fgcolor       = pink

key           = PGA

balloon hover  = sub {bring_bubble(shift)}

balloon sticky = 1

select        = source 'SB_F344' 'ENU_FHH' 'ENU_BN'

label         = sub {

                  my $feature=shift;

                  my ($pga_label)= $feature->display_name;

                  return $pga_label

                }

description   = sub {

                  my $feature=shift;

                  my ($pga_desc)= $feature->attributes("Id");

                  return $pga_desc;

                }

link           = sub {

                  my $feature=shift;

                  my ($pga_id)=$feature->attributes("Id");

                  $pga_id=~s/RGD://;

                  return "http://rgd.mcw.edu/tools/strains/strains_view.cgi?id=$pga_id";

                  }

citation      = This track includes the genomic locations of the <a href="http://pga.mcw.edu/"> PhysGen PGA</a> mutant strains developed using ENU mutagenesis or the Sleeping Beauty transposon strategy. Hovering over a feature provides additional annotation including the Gene Name, RGD Strain ID, Strain and Source (ENU_FHH, ENU_BN, SB_F344). Clicking on a feature or selecting the RGD Strain ID links to the strain report pages at RGD.



[CNV]

category     = ANNOTATED VARIANTS

feature       = CNV:Hubrecht_Institute

glyph        = span

fgcolor       = sub {bring_cnv_color(shift)}

bgcolor             = black

font2color    = pink1

linewidth     = 3

height        = 5

label       = sub{

                     my $cnv_feat = shift;

                     my ($cnvID)=$cnv_feat->attributes('Dbxref');

                     return "$cnvID";



              }

description   = sub{

                     my $cnv_feat = shift;

                     my ($type)=$cnv_feat->attributes('type');

                     return "TYPE:$type";



              }

balloon hover = sub {bring_bubble(shift)}

balloon sticky= 1

key           =CNVs

link   = sub{

                     my $cnv_feat = shift;

                     my ($cnvID)=$cnv_feat->attributes('Dbxref');

                     $cnvID =~s/cnv_//i;

                     return "http://h094.niob.knaw.nl/RatCNVs/cgi-bin/cnv.pl?id=$cnvID";



              }

citation      = <a href="http://h094.niob.knaw.nl/RatCNVs/"> Copy Number Variants (CNVs)</a> identified in commonly used laboratory rat strains through combination of computational approaches and experimental analysis as published in Guryev et al.; Distribution and functional impact of DNA copy number variation in the rat. Nature Genetics 40, 538 - 545 (2008). Hovering over a feature provides additional annotation including the CNV ID, Strain, Method, Type, and Source. Clicking on a feature or selecting the CNV ID links to the Hubrecht Institute\'s CNV pages.<br />CNVs are colored based on type as following:<br /><table border="1"><tr><th>Type</th><th>Color</th></tr><tr><td>Collapse</td><td>Purple</td></tr><tr><td>Overprediction</td><td>Yellow</td></tr><tr><td>Loss</td><td>Blue</td></tr><tr><td>Loss+Collapse</td><td>Dark blue</td></tr><tr><td>Loss+Overprediction</td><td>Light blue</td></tr><tr><td>Gain</td><td>Red</td></tr><tr><td>Gain+Collapse</td><td>Dark red</td></tr><tr><td>Gain+Overprediction</td><td>Light red</td></tr></table>







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: Lincoln Stein [[hidden email]]

Sent: Monday, June 21, 2010 10:38 AM
To: Jayaraman, Pushkala
Cc: [hidden email]
Subject: Re: [Gmod-gbrowse] Gbrowse2 tracks not visible..possible bug?





Hi Pushkala,



I'm afraid I'll need more information. Is the in-memory Yeast database working on the development server? If it is, it probably rules out a software problem. What database backend are you using, and how do you load it? What operating system are you using?



When you are unable to upload the "new" data on the Virtual Box, what do you mean by "new"?



Lincoln



On Mon, Jun 21, 2010 at 8:11 AM, Jayaraman, Pushkala <[hidden email]> wrote:

Hello,

I seem to be having problems with Gbrowse showing tracks on screen. This is slightly complicated:

1.       I have set up a fully functional gbrowse2 v2.03 on my Virtual Box with saved snapshots.

2.       I upgraded to Gbrowse 2.08 from SVN stable branch last month and set up that on my virtual Box. That seemed to be working too.

3.       I then had Gbrowse2 installed on our development server. This is where problems began,

When I tried to load the exact data that I had displaying successfully on my Virtual Box(lets call it Gbrowse_vbox), onto the gbrowse on the server (lets call it Gbrowse_serv)I saw that the Gbrowse_serv could not seem to display any of the data.

4.       Dumping the sql database from the vbox onto the server mysql seemed to get it to work.

5.       Recently, I have noticed that loading the new data on gbrowse_vbox seems unsuccessful. The apache error logs don't show anythings specific, but I do get Segmentation faults and "Use of uninitialized value in concatenation or string. (I do not know in what).

6.       I am just not able to see any of the Overview/Region/Detail panels on my screen. When I search for a tem, I sometimes get search results on the screen and sometimes just the Blue header that displays "The following 308 regions match your request "  and then nothing below it in the tracks panel.

7.       I am able to see the whole page except for the tracks. I can rule out the possibility of bad data because It did load and I was able to visualize that same data once. I am just not able to load it up again and visualize it. 





Please help..

Pushkala Jayaraman

Programmer/Analyst

Rat Genome Database

Human and Molecular Genetics Center

Medical College of Wisconsin

Email: [hidden email] <[hidden email]>

Work: 414-955-2229

www.rgd.mcw.edu <http://www.rgd.mcw.edu>






------------------------------------------------------------------------------
ThinkGeek and WIRED's GeekDad team up for the Ultimate
GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
lucky parental unit.  See the prize list and enter to win:
http://p.sf.net/sfu/thinkgeek-promo
_______________________________________________
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[hidden email]
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--
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]>






--
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]>




--
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]>

------------------------------------------------------------------------------
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GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
lucky parental unit.  See the prize list and enter to win:
http://p.sf.net/sfu/thinkgeek-promo
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Re: Gbrowse2 tracks not visible..possible bug?

Lincoln Stein
In reply to this post by Jayaraman, Pushkala
This is exactly the problem.

Lincoln

On Mon, Jun 21, 2010 at 12:52 PM, Jayaraman, Pushkala <[hidden email]> wrote:

I went ahead and checked the working copies (which fed data into the working data sources) with the same sql query and I get lists of the chromosome and I get back values:

 

mysql> select * from name where name like 'chr%' limit 5;

+--------+---------------------------+--------------+

| id     | name                      | display_name |

+--------+---------------------------+--------------+

|   2220 | chr1                      |            1 |

| 406088 | chr1                      |            1 |

|   1961 | chr10                     |            1 |

| 404537 | chr10                     |            1 |

|   2862 | chr10:127915135-127915215 |            1 |

+--------+---------------------------+--------------+

5 rows in set (0.00 sec)

 

 

But when I did this to the most recent database which fed data into the “erroneous data sources” I get back empty set or gene names similar to Chrm3  but no ‘chromosome’

 

Is this the 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: Jayaraman, Pushkala [mailto:[hidden email]]
Sent: Monday, June 21, 2010 11:42 AM
To: Lincoln Stein


Cc: [hidden email]
Subject: Re: [Gmod-gbrowse] Gbrowse2 tracks not visible..possible bug?

 

Hello Lincoln,

This is what I get:

 

mysql> select * from name where name like 'chr%';

+-------+--------+--------------+

| id    | name   | display_name |

+-------+--------+--------------+

| 29168 | Chrm3  |            1 |

| 29169 | Chrm3  |            1 |

| 29172 | Chrm3  |            1 |

|  2076 | Chrna2 |            1 |

|  2078 | Chrna2 |            1 |

|  2080 | Chrna2 |            1 |

|  2082 | Chrna2 |            1 |

|  2084 | Chrna2 |            1 |

|  2086 | Chrna2 |            1 |

|  2088 | Chrna2 |            1 |

|  2089 | Chrna2 |            1 |

+-------+--------+--------------+

11 rows in set (0.00 sec)

 

Why am I not getting any of the chromosome names?

 

 

When I do “head nameof_gff3_file.gff3” I get:

 

Chr15   GenBank chromosome      24425085        28088033        .       +       .       ID=NW_047453;Alias=15;Dbxref=taxon:10116;Note=Rattus norvegicus chromosome 15 genomic cont

ig%2C reference assembly (based on RGSC v3.4).,GENOME ANNOTATION REFSEQ: Features on this sequence have been produced for build 4 version 1 of the NCBI's genome annotation [see d

ocumentation]. The DNA sequence is version 3.4 'November 2004 Update' of the Rat genome assembly,produced by the Baylor College of Medicine Human Genome Sequencing Center (BCM- H

GSC) as part of the Rat Genome Sequencing Consortium (RGSC). This supersedes all prior versions of the Rat assembly (2.0,2.1,3.0,3.1 3.2 and 3.3) (see http://www.hgsc.bcm.tmc.edu

/projects/rat/). ;chromosome=15;comment1=GENOME ANNOTATION REFSEQ: Features on this sequence have been produced for build 4 version 1 of the NCBI's genome annotation [see documen

tation]. The DNA sequence is version 3.4 'November 2004 Update' of the Rat genome assembly%2C produced by the Baylor College of Medicine Human Genome Sequencing Center (BCM- HGSC

) as part of the Rat Genome Sequencing Consortium (RGSC). This supersedes all prior versions of the Rat assembly (2.0%2C 2.1%2C 3.0%2C 3.1 3.2 and 3.3) (see http://www.hgsc.bcm.tmc.edu/projects/rat/). ;date=03-JUL-2006;mol_type=genomic DNA;organism=Rattus norvegicus;strain=BN/SsNHsdMCW;

Chr15   GenBank pseudogene      24427872        24428719        .       -       .       ID=LOC498499;Dbxref=GeneID:498499;Note=Derived by automated computational analysis using gene prediction method: GNOMON. Supporting evidence includes similarity to: 98 ESTs%2C 6 Proteins;gene=LOC498499;pseudo=_no_value;

 

 

Which clearly shows the chromosome feature right on top.

 

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: Lincoln Stein [mailto:[hidden email]]
Sent: Monday, June 21, 2010 11:33 AM
To: Jayaraman, Pushkala
Cc: [hidden email]
Subject: Re: [Gmod-gbrowse] Gbrowse2 tracks not visible..possible bug?

 

It sounds to me as though you are loading the data correctly. But is there any chance that you used -c inadvertently on one of the subsequent loads and inadvertently removed the chromosomes? The way to check is:

 

 mysql> select * from name where name like 'chr%'

 

Lincoln

On Mon, Jun 21, 2010 at 12:19 PM, Jayaraman, Pushkala <[hidden email]> wrote:

Hello Lincoln,

Yes,

The yeast, in-memory database is loading well. Also, the data that I had loaded into the mysql database about a month ago (before I updated gbrowse through svn) is also seems to be rendering tracks on my VirtualBox as well as the server(I create a dump of the dabatase that I used on the VBox and uploaded that same database on the server and it works well)..



I am using a mysql database backend. This is how I load the data

 bp_seqfeature_load.pl -a DBI::mysql -d "DBI:mysql:database=DBNAME;host=HOSTNAME" -c -f filename.gff3



I do not use -c each time. But I seem to have to use it the first time after I newly create a DB. Else it complains about not finding the tables. So it gives out errors like 'cannot load data into .locationlist table or view does not exist'.

But when I use the -c feature, it seems to load it in pretty well. After that, I do not have to use the -c feature when I am adding data into the database.


As you can see in the above two attached pictures, both are feb by very similar conf files except for their name. I simply made a copy of the conf file and renamed one. the data source though, is different. i.e they are being fed from two different mysql databases.

when the database has all the tracks then it seems to generate pictures, but when i only load one feature eg. qtl, then it doesnt show anything..
This is what my conf file looks like:

[GENERAL]

database     = general



autocomplete = 1

search options = default +autocomplete +wildcard       



# turn on remote rendering-- see [TRACK DEFAULTS] for the hosts

# and ports the rendering slaves run on.

renderfarm    = 1



# just the basic track dumper plugin was in before..now added new plugins

plugins = TrackDumper Aligner BatchDumper Submitter OligoFinder FilterTest AttributeHiliter



#balloon tips acknowledge:

balloon tips = 1



# list of tracks to turn on by default

default features = miRNA_Track



# size of the region

max segment     = 1000000000

default segment = 50000



# examples to show in the introduction

examples = Odz3



# feature to show on startup

initial landmark = Chr16



#to generalise searches. the search results will include both gene and protein keywords and will not require specific Gene:xxx or protein:xxx it will search xxx through gene and protein in order of them appearing in the line just below.

automatic classes = RGD Gene



#init codes work like functions built into the code:

init_code         = sub bring_bubble{

                     ------some code--------

                     --------more code------

}

########################

# databases being used #

########################

[general:database]

db_adaptor    = Bio::DB::SeqFeature::Store

db_args       = -adaptor DBI::mysql

              -dsn     DBI:mysql:database=DBNAME;host=HOSTNAME.hmgc.mcw.edu

              -user    USERNAME

              -pass    PASSWORD

########################

# Default glyph settings

########################

[TRACK DEFAULTS]

database      = general

glyph         = generic

height        = 10

bgcolor       = lightgrey

fgcolor       = black

font2color    = blue

label density = 25

bump density  = 100



# where to link to when user clicks in detailed view

link          = AUTO



#################################

# Individual Track glyph settings

#################################



[miRNA_Track]

category      = GENOMIC FEATURES

feature       = miRNA:miRBase

glyph         = dot

fgcolor       = blue

bgcolor       = lightblue

linewidth    = 2

height       = 6

label        = sub{

                     my $feature=shift;

                     my ($miRna)=$feature->display_name;

                     return $miRna;      

              }

key           = miRNAs

link          = sub {

                     my $feature=shift;

                     my ($miRnaID)=$feature->load_id;

                     return "http://microrna.sanger.ac.uk/cgi-bin/sequences/mirna_entry.pl?id=$miRnaID";

              }

balloon hover = sub {bring_bubble(shift)}

balloon sticky = 1

citation      = This track shows rat microRNAs (miRNAs) derived from the <a href="http://microrna.sanger.ac.uk/"> Sanger Institute\'s miRBase</a>. miRBase is the repository for microRNA data, incorporating the database and gene naming roles previously provided by the miRNA Registry. Hovering over a feature provides annotation including miRBase ID and source. Clicking on a feature or selecting the miRBase ID links to the miRBase miRNA Report pages.



[miRNA_Track:overview]

feature       = miRNA:miRBase

glyph         = dot

fgcolor       = blue

bgcolor       = lightblue

linewidth    = 2

height       = 6

label        = sub{

                     my $feature=shift;

                     my ($miRna)=$feature->display_name;

                     return $miRna;      

              }

key           = miRNAs Overview

link          = sub {

                     my $feature=shift;

                     my ($miRnaID)=$feature->load_id;

                     return "http://microrna.sanger.ac.uk/cgi-bin/sequences/mirna_entry.pl?id=$miRnaID";

              }

citation      = This track shows rat microRNAs (miRNAs) derived from the <a href="http://microrna.sanger.ac.uk/"> Sanger Institute\'s miRBase</a>. miRBase is the repository for microRNA data, incorporating the database and gene naming roles previously provided by the miRNA Registry. Hovering over a feature provides annotation including miRBase ID and source. Clicking on a feature or selecting the miRBase ID links to the miRBase miRNA Report pages.



[QTLS]

glyph        = saw_teeth

category      = GENOMIC FEATURES

feature       = QTL:RGD

height       = 5

linewidth     = 3

bgcolor       = maroon

fgcolor       = orange

label        = sub{

                     my $feature=shift;

                     my ($qtlid)=$feature->load_id;

                     my @qtlarr=split(/:/, $qtlid);

                     return "QTL:$qtlarr[1]";

              }

description   = sub{

                     my $feature=shift;

                     my ($desc)=$feature->attributes('Dbxref');

                     my @desc_arr=split(/:/, $desc);

                     return "RGDID:".$desc_arr[1];

                    

              }

link         = sub {

                     my $feature=shift;

                     my ($link)=$feature->attributes('Dbxref');

                     if ($link=~/RGD:(\d+)/) {

                            my $rgdid=$1;

                            return "http://rgd.mcw.edu/objectSearch/qtlReport.jsp?rgd_id=$rgdid";

                     }

              }

balloon hover  = sub {bring_bubble(shift)}      

balloon sticky = 1

key           = RGD QTLs

citation      = This track shows <a href="http://www.rgd.mcw.edu/qtls/"> RGD Rat Quantitative Trait Loci (QTL)</a>. In some cases the boundaries of the QTL have been estimated as explained in <a href="ftp://rgd.mcw.edu/pub/data_release/QTLS_README"> QTLs Readme file</a>. Hovering over a feature provides additional annotation including the name, symbol, LOD (where available), p-value (where available), mapping method, and RGD ID, which links to the RGD QTL report page. Clicking on a feature also links to its RGD report page.



[PGA]

category      = PGA

feature       = PGA:ENU_BN PGA:ENU_FHH PGA:SB_F344

glyph         = diamond

bgcolor       = purple

fgcolor       = pink

key           = PGA

balloon hover  = sub {bring_bubble(shift)}

balloon sticky = 1

select        = source 'SB_F344' 'ENU_FHH' 'ENU_BN'

label         = sub {

                  my $feature=shift;

                  my ($pga_label)= $feature->display_name;

                  return $pga_label

                }

description   = sub {

                  my $feature=shift;

                  my ($pga_desc)= $feature->attributes("Id");

                  return $pga_desc;

                }

link           = sub {

                  my $feature=shift;

                  my ($pga_id)=$feature->attributes("Id");

                  $pga_id=~s/RGD://;

                  return "http://rgd.mcw.edu/tools/strains/strains_view.cgi?id=$pga_id";

                  }

citation      = This track includes the genomic locations of the <a href="http://pga.mcw.edu/"> PhysGen PGA</a> mutant strains developed using ENU mutagenesis or the Sleeping Beauty transposon strategy. Hovering over a feature provides additional annotation including the Gene Name, RGD Strain ID, Strain and Source (ENU_FHH, ENU_BN, SB_F344). Clicking on a feature or selecting the RGD Strain ID links to the strain report pages at RGD.



[CNV]

category     = ANNOTATED VARIANTS

feature       = CNV:Hubrecht_Institute

glyph        = span

fgcolor       = sub {bring_cnv_color(shift)}

bgcolor             = black

font2color    = pink1

linewidth     = 3

height        = 5

label       = sub{

                     my $cnv_feat = shift;

                     my ($cnvID)=$cnv_feat->attributes('Dbxref');

                     return "$cnvID";



              }

description   = sub{

                     my $cnv_feat = shift;

                     my ($type)=$cnv_feat->attributes('type');

                     return "TYPE:$type";



              }

balloon hover = sub {bring_bubble(shift)}

balloon sticky= 1

key           =CNVs

link   = sub{

                     my $cnv_feat = shift;

                     my ($cnvID)=$cnv_feat->attributes('Dbxref');

                     $cnvID =~s/cnv_//i;

                     return "http://h094.niob.knaw.nl/RatCNVs/cgi-bin/cnv.pl?id=$cnvID";



              }

citation      = <a href="http://h094.niob.knaw.nl/RatCNVs/"> Copy Number Variants (CNVs)</a> identified in commonly used laboratory rat strains through combination of computational approaches and experimental analysis as published in Guryev et al.; Distribution and functional impact of DNA copy number variation in the rat. Nature Genetics 40, 538 - 545 (2008). Hovering over a feature provides additional annotation including the CNV ID, Strain, Method, Type, and Source. Clicking on a feature or selecting the CNV ID links to the Hubrecht Institute\'s CNV pages.<br />CNVs are colored based on type as following:<br /><table border="1"><tr><th>Type</th><th>Color</th></tr><tr><td>Collapse</td><td>Purple</td></tr><tr><td>Overprediction</td><td>Yellow</td></tr><tr><td>Loss</td><td>Blue</td></tr><tr><td>Loss+Collapse</td><td>Dark blue</td></tr><tr><td>Loss+Overprediction</td><td>Light blue</td></tr><tr><td>Gain</td><td>Red</td></tr><tr><td>Gain+Collapse</td><td>Dark red</td></tr><tr><td>Gain+Overprediction</td><td>Light red</td></tr></table>







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: Lincoln Stein [[hidden email]]

Sent: Monday, June 21, 2010 10:38 AM
To: Jayaraman, Pushkala
Cc: [hidden email]
Subject: Re: [Gmod-gbrowse] Gbrowse2 tracks not visible..possible bug?





Hi Pushkala,



I'm afraid I'll need more information. Is the in-memory Yeast database working on the development server? If it is, it probably rules out a software problem. What database backend are you using, and how do you load it? What operating system are you using?



When you are unable to upload the "new" data on the Virtual Box, what do you mean by "new"?



Lincoln



On Mon, Jun 21, 2010 at 8:11 AM, Jayaraman, Pushkala <[hidden email]> wrote:

Hello,

I seem to be having problems with Gbrowse showing tracks on screen. This is slightly complicated:

1.       I have set up a fully functional gbrowse2 v2.03 on my Virtual Box with saved snapshots.

2.       I upgraded to Gbrowse 2.08 from SVN stable branch last month and set up that on my virtual Box. That seemed to be working too.

3.       I then had Gbrowse2 installed on our development server. This is where problems began,

When I tried to load the exact data that I had displaying successfully on my Virtual Box(lets call it Gbrowse_vbox), onto the gbrowse on the server (lets call it Gbrowse_serv)I saw that the Gbrowse_serv could not seem to display any of the data.

4.       Dumping the sql database from the vbox onto the server mysql seemed to get it to work.

5.       Recently, I have noticed that loading the new data on gbrowse_vbox seems unsuccessful. The apache error logs don't show anythings specific, but I do get Segmentation faults and "Use of uninitialized value in concatenation or string. (I do not know in what).

6.       I am just not able to see any of the Overview/Region/Detail panels on my screen. When I search for a tem, I sometimes get search results on the screen and sometimes just the Blue header that displays "The following 308 regions match your request "  and then nothing below it in the tracks panel.

7.       I am able to see the whole page except for the tracks. I can rule out the possibility of bad data because It did load and I was able to visualize that same data once. I am just not able to load it up again and visualize it. 





Please help..

Pushkala Jayaraman

Programmer/Analyst

Rat Genome Database

Human and Molecular Genetics Center

Medical College of Wisconsin

Email: [hidden email] <[hidden email]>

Work: 414-955-2229

www.rgd.mcw.edu <http://www.rgd.mcw.edu>






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





--
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]>




--
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]>

------------------------------------------------------------------------------
ThinkGeek and WIRED's GeekDad team up for the Ultimate
GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
lucky parental unit.  See the prize list and enter to win:
http://p.sf.net/sfu/thinkgeek-promo
_______________________________________________
Gmod-gbrowse mailing list
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Re: Gbrowse2 tracks not visible..possible bug?

Jayaraman, Pushkala
In reply to this post by Lincoln Stein

But I have a question regarding the exact same thing:

 

So If I were to upload just the QTL feature or just the PGA feature. Which is not a part of the “gene” or its children, but an independent feature altogether,

Even then, do I need to have the ‘chromosome’ (and all its attributes) as the first line of the qtl gff3 file?(which goes to say, any gff3 file that I create for QTLs, PGAs, miRNAs, SNPs must have a ‘chromosome’ line added for each of the chromosomes that contain the mentioned features?)

 

If not,

Then why doesn’t gbrowse show me that track? There is just the QTLs data without the chromosome line..(I used to be able to see those tracks initially...on Gbrowse2.03. I do not know how.. )

 

What must I do in that case?

 

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: Lincoln Stein [mailto:[hidden email]]
Sent: Monday, June 21, 2010 11:52 AM
To: Jayaraman, Pushkala
Cc: [hidden email]
Subject: Re: [Gmod-gbrowse] Gbrowse2 tracks not visible..possible bug?

 

Hi Pushkala,

 

The first column is used for the reference sequence coordinate, and is not always the same as the name of the chromosome. Each chromosome line should have a tag of the form "Name=Chr3" in the last column of the GFF3. Please try appending:

 

;Name=Chr3

 

to the end of each GFF3 line. Please be sure to change the chromosome name appropriately, and don't forget to separate the Name tag from the other tags using the semicolon character.

 

Lincoln

 

On Mon, Jun 21, 2010 at 12:42 PM, Jayaraman, Pushkala <[hidden email]> wrote:

Hello Lincoln,

This is what I get:

 

mysql> select * from name where name like 'chr%';

+-------+--------+--------------+

| id    | name   | display_name |

+-------+--------+--------------+

| 29168 | Chrm3  |            1 |

| 29169 | Chrm3  |            1 |

| 29172 | Chrm3  |            1 |

|  2076 | Chrna2 |            1 |

|  2078 | Chrna2 |            1 |

|  2080 | Chrna2 |            1 |

|  2082 | Chrna2 |            1 |

|  2084 | Chrna2 |            1 |

|  2086 | Chrna2 |            1 |

|  2088 | Chrna2 |            1 |

|  2089 | Chrna2 |            1 |

+-------+--------+--------------+

11 rows in set (0.00 sec)

 

Why am I not getting any of the chromosome names?

 

 

When I do “head nameof_gff3_file.gff3” I get:

 

Chr15   GenBank chromosome      24425085        28088033        .       +       .       ID=NW_047453;Alias=15;Dbxref=taxon:10116;Note=Rattus norvegicus chromosome 15 genomic cont

ig%2C reference assembly (based on RGSC v3.4).,GENOME ANNOTATION REFSEQ: Features on this sequence have been produced for build 4 version 1 of the NCBI's genome annotation [see d

ocumentation]. The DNA sequence is version 3.4 'November 2004 Update' of the Rat genome assembly,produced by the Baylor College of Medicine Human Genome Sequencing Center (BCM- H

GSC) as part of the Rat Genome Sequencing Consortium (RGSC). This supersedes all prior versions of the Rat assembly (2.0,2.1,3.0,3.1 3.2 and 3.3) (see http://www.hgsc.bcm.tmc.edu

/projects/rat/). ;chromosome=15;comment1=GENOME ANNOTATION REFSEQ: Features on this sequence have been produced for build 4 version 1 of the NCBI's genome annotation [see documen

tation]. The DNA sequence is version 3.4 'November 2004 Update' of the Rat genome assembly%2C produced by the Baylor College of Medicine Human Genome Sequencing Center (BCM- HGSC

) as part of the Rat Genome Sequencing Consortium (RGSC). This supersedes all prior versions of the Rat assembly (2.0%2C 2.1%2C 3.0%2C 3.1 3.2 and 3.3) (see http://www.hgsc.bcm.tmc.edu/projects/rat/). ;date=03-JUL-2006;mol_type=genomic DNA;organism=Rattus norvegicus;strain=BN/SsNHsdMCW;

Chr15   GenBank pseudogene      24427872        24428719        .       -       .       ID=LOC498499;Dbxref=GeneID:498499;Note=Derived by automated computational analysis using gene prediction method: GNOMON. Supporting evidence includes similarity to: 98 ESTs%2C 6 Proteins;gene=LOC498499;pseudo=_no_value;

 

 

Which clearly shows the chromosome feature right on top.

 

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: Lincoln Stein [mailto:[hidden email]]
Sent: Monday, June 21, 2010 11:33 AM


To: Jayaraman, Pushkala
Cc: [hidden email]
Subject: Re: [Gmod-gbrowse] Gbrowse2 tracks not visible..possible bug?

 

It sounds to me as though you are loading the data correctly. But is there any chance that you used -c inadvertently on one of the subsequent loads and inadvertently removed the chromosomes? The way to check is:

 

 mysql> select * from name where name like 'chr%'

 

Lincoln

On Mon, Jun 21, 2010 at 12:19 PM, Jayaraman, Pushkala <[hidden email]> wrote:

Hello Lincoln,

Yes,

The yeast, in-memory database is loading well. Also, the data that I had loaded into the mysql database about a month ago (before I updated gbrowse through svn) is also seems to be rendering tracks on my VirtualBox as well as the server(I create a dump of the dabatase that I used on the VBox and uploaded that same database on the server and it works well)..



I am using a mysql database backend. This is how I load the data

 bp_seqfeature_load.pl -a DBI::mysql -d "DBI:mysql:database=DBNAME;host=HOSTNAME" -c -f filename.gff3



I do not use -c each time. But I seem to have to use it the first time after I newly create a DB. Else it complains about not finding the tables. So it gives out errors like 'cannot load data into .locationlist table or view does not exist'.

But when I use the -c feature, it seems to load it in pretty well. After that, I do not have to use the -c feature when I am adding data into the database.


As you can see in the above two attached pictures, both are feb by very similar conf files except for their name. I simply made a copy of the conf file and renamed one. the data source though, is different. i.e they are being fed from two different mysql databases.

when the database has all the tracks then it seems to generate pictures, but when i only load one feature eg. qtl, then it doesnt show anything..
This is what my conf file looks like:

[GENERAL]

database     = general



autocomplete = 1

search options = default +autocomplete +wildcard       



# turn on remote rendering-- see [TRACK DEFAULTS] for the hosts

# and ports the rendering slaves run on.

renderfarm    = 1



# just the basic track dumper plugin was in before..now added new plugins

plugins = TrackDumper Aligner BatchDumper Submitter OligoFinder FilterTest AttributeHiliter



#balloon tips acknowledge:

balloon tips = 1



# list of tracks to turn on by default

default features = miRNA_Track



# size of the region

max segment     = 1000000000

default segment = 50000



# examples to show in the introduction

examples = Odz3



# feature to show on startup

initial landmark = Chr16



#to generalise searches. the search results will include both gene and protein keywords and will not require specific Gene:xxx or protein:xxx it will search xxx through gene and protein in order of them appearing in the line just below.

automatic classes = RGD Gene



#init codes work like functions built into the code:

init_code         = sub bring_bubble{

                     ------some code--------

                     --------more code------

}

########################

# databases being used #

########################

[general:database]

db_adaptor    = Bio::DB::SeqFeature::Store

db_args       = -adaptor DBI::mysql

              -dsn     DBI:mysql:database=DBNAME;host=HOSTNAME.hmgc.mcw.edu

              -user    USERNAME

              -pass    PASSWORD

########################

# Default glyph settings

########################

[TRACK DEFAULTS]

database      = general

glyph         = generic

height        = 10

bgcolor       = lightgrey

fgcolor       = black

font2color    = blue

label density = 25

bump density  = 100



# where to link to when user clicks in detailed view

link          = AUTO



#################################

# Individual Track glyph settings

#################################



[miRNA_Track]

category      = GENOMIC FEATURES

feature       = miRNA:miRBase

glyph         = dot

fgcolor       = blue

bgcolor       = lightblue

linewidth    = 2

height       = 6

label        = sub{

                     my $feature=shift;

                     my ($miRna)=$feature->display_name;

                     return $miRna;      

              }

key           = miRNAs

link          = sub {

                     my $feature=shift;

                     my ($miRnaID)=$feature->load_id;

                     return "http://microrna.sanger.ac.uk/cgi-bin/sequences/mirna_entry.pl?id=$miRnaID";

              }

balloon hover = sub {bring_bubble(shift)}

balloon sticky = 1

citation      = This track shows rat microRNAs (miRNAs) derived from the <a href="http://microrna.sanger.ac.uk/"> Sanger Institute\'s miRBase</a>. miRBase is the repository for microRNA data, incorporating the database and gene naming roles previously provided by the miRNA Registry. Hovering over a feature provides annotation including miRBase ID and source. Clicking on a feature or selecting the miRBase ID links to the miRBase miRNA Report pages.



[miRNA_Track:overview]

feature       = miRNA:miRBase

glyph         = dot

fgcolor       = blue

bgcolor       = lightblue

linewidth    = 2

height       = 6

label        = sub{

                     my $feature=shift;

                     my ($miRna)=$feature->display_name;

                     return $miRna;      

              }

key           = miRNAs Overview

link          = sub {

                     my $feature=shift;

                     my ($miRnaID)=$feature->load_id;

                     return "http://microrna.sanger.ac.uk/cgi-bin/sequences/mirna_entry.pl?id=$miRnaID";

              }

citation      = This track shows rat microRNAs (miRNAs) derived from the <a href="http://microrna.sanger.ac.uk/"> Sanger Institute\'s miRBase</a>. miRBase is the repository for microRNA data, incorporating the database and gene naming roles previously provided by the miRNA Registry. Hovering over a feature provides annotation including miRBase ID and source. Clicking on a feature or selecting the miRBase ID links to the miRBase miRNA Report pages.



[QTLS]

glyph        = saw_teeth

category      = GENOMIC FEATURES

feature       = QTL:RGD

height       = 5

linewidth     = 3

bgcolor       = maroon

fgcolor       = orange

label        = sub{

                     my $feature=shift;

                     my ($qtlid)=$feature->load_id;

                     my @qtlarr=split(/:/, $qtlid);

                     return "QTL:$qtlarr[1]";

              }

description   = sub{

                     my $feature=shift;

                     my ($desc)=$feature->attributes('Dbxref');

                     my @desc_arr=split(/:/, $desc);

                     return "RGDID:".$desc_arr[1];

                    

              }

link         = sub {

                     my $feature=shift;

                     my ($link)=$feature->attributes('Dbxref');

                     if ($link=~/RGD:(\d+)/) {

                            my $rgdid=$1;

                            return "http://rgd.mcw.edu/objectSearch/qtlReport.jsp?rgd_id=$rgdid";

                     }

              }

balloon hover  = sub {bring_bubble(shift)}      

balloon sticky = 1

key           = RGD QTLs

citation      = This track shows <a href="http://www.rgd.mcw.edu/qtls/"> RGD Rat Quantitative Trait Loci (QTL)</a>. In some cases the boundaries of the QTL have been estimated as explained in <a href="ftp://rgd.mcw.edu/pub/data_release/QTLS_README"> QTLs Readme file</a>. Hovering over a feature provides additional annotation including the name, symbol, LOD (where available), p-value (where available), mapping method, and RGD ID, which links to the RGD QTL report page. Clicking on a feature also links to its RGD report page.



[PGA]

category      = PGA

feature       = PGA:ENU_BN PGA:ENU_FHH PGA:SB_F344

glyph         = diamond

bgcolor       = purple

fgcolor       = pink

key           = PGA

balloon hover  = sub {bring_bubble(shift)}

balloon sticky = 1

select        = source 'SB_F344' 'ENU_FHH' 'ENU_BN'

label         = sub {

                  my $feature=shift;

                  my ($pga_label)= $feature->display_name;

                  return $pga_label

                }

description   = sub {

                  my $feature=shift;

                  my ($pga_desc)= $feature->attributes("Id");

                  return $pga_desc;

                }

link           = sub {

                  my $feature=shift;

                  my ($pga_id)=$feature->attributes("Id");

                  $pga_id=~s/RGD://;

                  return "http://rgd.mcw.edu/tools/strains/strains_view.cgi?id=$pga_id";

                  }

citation      = This track includes the genomic locations of the <a href="http://pga.mcw.edu/"> PhysGen PGA</a> mutant strains developed using ENU mutagenesis or the Sleeping Beauty transposon strategy. Hovering over a feature provides additional annotation including the Gene Name, RGD Strain ID, Strain and Source (ENU_FHH, ENU_BN, SB_F344). Clicking on a feature or selecting the RGD Strain ID links to the strain report pages at RGD.



[CNV]

category     = ANNOTATED VARIANTS

feature       = CNV:Hubrecht_Institute

glyph        = span

fgcolor       = sub {bring_cnv_color(shift)}

bgcolor             = black

font2color    = pink1

linewidth     = 3

height        = 5

label       = sub{

                     my $cnv_feat = shift;

                     my ($cnvID)=$cnv_feat->attributes('Dbxref');

                     return "$cnvID";



              }

description   = sub{

                     my $cnv_feat = shift;

                     my ($type)=$cnv_feat->attributes('type');

                     return "TYPE:$type";



              }

balloon hover = sub {bring_bubble(shift)}

balloon sticky= 1

key           =CNVs

link   = sub{

                     my $cnv_feat = shift;

                     my ($cnvID)=$cnv_feat->attributes('Dbxref');

                     $cnvID =~s/cnv_//i;

                     return "http://h094.niob.knaw.nl/RatCNVs/cgi-bin/cnv.pl?id=$cnvID";



              }

citation      = <a href="http://h094.niob.knaw.nl/RatCNVs/"> Copy Number Variants (CNVs)</a> identified in commonly used laboratory rat strains through combination of computational approaches and experimental analysis as published in Guryev et al.; Distribution and functional impact of DNA copy number variation in the rat. Nature Genetics 40, 538 - 545 (2008). Hovering over a feature provides additional annotation including the CNV ID, Strain, Method, Type, and Source. Clicking on a feature or selecting the CNV ID links to the Hubrecht Institute\'s CNV pages.<br />CNVs are colored based on type as following:<br /><table border="1"><tr><th>Type</th><th>Color</th></tr><tr><td>Collapse</td><td>Purple</td></tr><tr><td>Overprediction</td><td>Yellow</td></tr><tr><td>Loss</td><td>Blue</td></tr><tr><td>Loss+Collapse</td><td>Dark blue</td></tr><tr><td>Loss+Overprediction</td><td>Light blue</td></tr><tr><td>Gain</td><td>Red</td></tr><tr><td>Gain+Collapse</td><td>Dark red</td></tr><tr><td>Gain+Overprediction</td><td>Light red</td></tr></table>







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: Lincoln Stein [[hidden email]]

Sent: Monday, June 21, 2010 10:38 AM
To: Jayaraman, Pushkala
Cc: [hidden email]
Subject: Re: [Gmod-gbrowse] Gbrowse2 tracks not visible..possible bug?





Hi Pushkala,



I'm afraid I'll need more information. Is the in-memory Yeast database working on the development server? If it is, it probably rules out a software problem. What database backend are you using, and how do you load it? What operating system are you using?



When you are unable to upload the "new" data on the Virtual Box, what do you mean by "new"?



Lincoln



On Mon, Jun 21, 2010 at 8:11 AM, Jayaraman, Pushkala <[hidden email]> wrote:

Hello,

I seem to be having problems with Gbrowse showing tracks on screen. This is slightly complicated:

1.       I have set up a fully functional gbrowse2 v2.03 on my Virtual Box with saved snapshots.

2.       I upgraded to Gbrowse 2.08 from SVN stable branch last month and set up that on my virtual Box. That seemed to be working too.

3.       I then had Gbrowse2 installed on our development server. This is where problems began,

When I tried to load the exact data that I had displaying successfully on my Virtual Box(lets call it Gbrowse_vbox), onto the gbrowse on the server (lets call it Gbrowse_serv)I saw that the Gbrowse_serv could not seem to display any of the data.

4.       Dumping the sql database from the vbox onto the server mysql seemed to get it to work.

5.       Recently, I have noticed that loading the new data on gbrowse_vbox seems unsuccessful. The apache error logs don't show anythings specific, but I do get Segmentation faults and "Use of uninitialized value in concatenation or string. (I do not know in what).

6.       I am just not able to see any of the Overview/Region/Detail panels on my screen. When I search for a tem, I sometimes get search results on the screen and sometimes just the Blue header that displays "The following 308 regions match your request "  and then nothing below it in the tracks panel.

7.       I am able to see the whole page except for the tracks. I can rule out the possibility of bad data because It did load and I was able to visualize that same data once. I am just not able to load it up again and visualize it. 





Please help..

Pushkala Jayaraman

Programmer/Analyst

Rat Genome Database

Human and Molecular Genetics Center

Medical College of Wisconsin

Email: [hidden email] <[hidden email]>

Work: 414-955-2229

www.rgd.mcw.edu <http://www.rgd.mcw.edu>






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





--
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]>




--
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]>


------------------------------------------------------------------------------
ThinkGeek and WIRED's GeekDad team up for the Ultimate
GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
lucky parental unit.  See the prize list and enter to win:
http://p.sf.net/sfu/thinkgeek-promo
_______________________________________________
Gmod-gbrowse mailing list
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Re: Gbrowse2 tracks not visible..possible bug?

Lincoln Stein
You need the chromosome lines in only one of the GFF3 files. Ordinarily you would put it into a separate "scaffolds" directory.

[GENERAL]
description   = My database
database      = scaffolds

[scaffolds:database]
db_adaptor    = Bio::DB::SeqFeature::Store
db_args       = -adaptor memory
                -dir    /var/www/gbrowse2/databases/my_scaffolds <-- this is where the chromosome GFF3 file goes
search options = default +autocomplete

[annotations:database]
db_adaptor    = Bio::DB::SeqFeature::Store
db_args       = -adaptor memory
                -dir    /var/www/gbrowse2/databases/annotations <-- this is where everything else goes
search options = default +autocomplete

[TRACK DEFAULTS]
glyph       = generic
database    = annotations <-- this makes the annotations db the default for track definitions
height      = 8
bgcolor     = cyan
fgcolor     = black
label density = 25
bump density  = 100


Lincoln

On Mon, Jun 21, 2010 at 1:02 PM, Jayaraman, Pushkala <[hidden email]> wrote:

But I have a question regarding the exact same thing:

 

So If I were to upload just the QTL feature or just the PGA feature. Which is not a part of the “gene” or its children, but an independent feature altogether,

Even then, do I need to have the ‘chromosome’ (and all its attributes) as the first line of the qtl gff3 file?(which goes to say, any gff3 file that I create for QTLs, PGAs, miRNAs, SNPs must have a ‘chromosome’ line added for each of the chromosomes that contain the mentioned features?)

 

If not,

Then why doesn’t gbrowse show me that track? There is just the QTLs data without the chromosome line..(I used to be able to see those tracks initially...on Gbrowse2.03. I do not know how.. )

 

What must I do in that case?

 

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: Lincoln Stein [mailto:[hidden email]]
Sent: Monday, June 21, 2010 11:52 AM


To: Jayaraman, Pushkala
Cc: [hidden email]
Subject: Re: [Gmod-gbrowse] Gbrowse2 tracks not visible..possible bug?

 

Hi Pushkala,

 

The first column is used for the reference sequence coordinate, and is not always the same as the name of the chromosome. Each chromosome line should have a tag of the form "Name=Chr3" in the last column of the GFF3. Please try appending:

 

;Name=Chr3

 

to the end of each GFF3 line. Please be sure to change the chromosome name appropriately, and don't forget to separate the Name tag from the other tags using the semicolon character.

 

Lincoln

 

On Mon, Jun 21, 2010 at 12:42 PM, Jayaraman, Pushkala <[hidden email]> wrote:

Hello Lincoln,

This is what I get:

 

mysql> select * from name where name like 'chr%';

+-------+--------+--------------+

| id    | name   | display_name |

+-------+--------+--------------+

| 29168 | Chrm3  |            1 |

| 29169 | Chrm3  |            1 |

| 29172 | Chrm3  |            1 |

|  2076 | Chrna2 |            1 |

|  2078 | Chrna2 |            1 |

|  2080 | Chrna2 |            1 |

|  2082 | Chrna2 |            1 |

|  2084 | Chrna2 |            1 |

|  2086 | Chrna2 |            1 |

|  2088 | Chrna2 |            1 |

|  2089 | Chrna2 |            1 |

+-------+--------+--------------+

11 rows in set (0.00 sec)

 

Why am I not getting any of the chromosome names?

 

 

When I do “head nameof_gff3_file.gff3” I get:

 

Chr15   GenBank chromosome      24425085        28088033        .       +       .       ID=NW_047453;Alias=15;Dbxref=taxon:10116;Note=Rattus norvegicus chromosome 15 genomic cont

ig%2C reference assembly (based on RGSC v3.4).,GENOME ANNOTATION REFSEQ: Features on this sequence have been produced for build 4 version 1 of the NCBI's genome annotation [see d

ocumentation]. The DNA sequence is version 3.4 'November 2004 Update' of the Rat genome assembly,produced by the Baylor College of Medicine Human Genome Sequencing Center (BCM- H

GSC) as part of the Rat Genome Sequencing Consortium (RGSC). This supersedes all prior versions of the Rat assembly (2.0,2.1,3.0,3.1 3.2 and 3.3) (see http://www.hgsc.bcm.tmc.edu

/projects/rat/). ;chromosome=15;comment1=GENOME ANNOTATION REFSEQ: Features on this sequence have been produced for build 4 version 1 of the NCBI's genome annotation [see documen

tation]. The DNA sequence is version 3.4 'November 2004 Update' of the Rat genome assembly%2C produced by the Baylor College of Medicine Human Genome Sequencing Center (BCM- HGSC

) as part of the Rat Genome Sequencing Consortium (RGSC). This supersedes all prior versions of the Rat assembly (2.0%2C 2.1%2C 3.0%2C 3.1 3.2 and 3.3) (see http://www.hgsc.bcm.tmc.edu/projects/rat/). ;date=03-JUL-2006;mol_type=genomic DNA;organism=Rattus norvegicus;strain=BN/SsNHsdMCW;

Chr15   GenBank pseudogene      24427872        24428719        .       -       .       ID=LOC498499;Dbxref=GeneID:498499;Note=Derived by automated computational analysis using gene prediction method: GNOMON. Supporting evidence includes similarity to: 98 ESTs%2C 6 Proteins;gene=LOC498499;pseudo=_no_value;

 

 

Which clearly shows the chromosome feature right on top.

 

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: Lincoln Stein [mailto:[hidden email]]
Sent: Monday, June 21, 2010 11:33 AM


To: Jayaraman, Pushkala
Cc: [hidden email]
Subject: Re: [Gmod-gbrowse] Gbrowse2 tracks not visible..possible bug?

 

It sounds to me as though you are loading the data correctly. But is there any chance that you used -c inadvertently on one of the subsequent loads and inadvertently removed the chromosomes? The way to check is:

 

 mysql> select * from name where name like 'chr%'

 

Lincoln

On Mon, Jun 21, 2010 at 12:19 PM, Jayaraman, Pushkala <[hidden email]> wrote:

Hello Lincoln,

Yes,

The yeast, in-memory database is loading well. Also, the data that I had loaded into the mysql database about a month ago (before I updated gbrowse through svn) is also seems to be rendering tracks on my VirtualBox as well as the server(I create a dump of the dabatase that I used on the VBox and uploaded that same database on the server and it works well)..



I am using a mysql database backend. This is how I load the data

 bp_seqfeature_load.pl -a DBI::mysql -d "DBI:mysql:database=DBNAME;host=HOSTNAME" -c -f filename.gff3



I do not use -c each time. But I seem to have to use it the first time after I newly create a DB. Else it complains about not finding the tables. So it gives out errors like 'cannot load data into .locationlist table or view does not exist'.

But when I use the -c feature, it seems to load it in pretty well. After that, I do not have to use the -c feature when I am adding data into the database.


As you can see in the above two attached pictures, both are feb by very similar conf files except for their name. I simply made a copy of the conf file and renamed one. the data source though, is different. i.e they are being fed from two different mysql databases.

when the database has all the tracks then it seems to generate pictures, but when i only load one feature eg. qtl, then it doesnt show anything..
This is what my conf file looks like:

[GENERAL]

database     = general



autocomplete = 1

search options = default +autocomplete +wildcard       



# turn on remote rendering-- see [TRACK DEFAULTS] for the hosts

# and ports the rendering slaves run on.

renderfarm    = 1



# just the basic track dumper plugin was in before..now added new plugins

plugins = TrackDumper Aligner BatchDumper Submitter OligoFinder FilterTest AttributeHiliter



#balloon tips acknowledge:

balloon tips = 1



# list of tracks to turn on by default

default features = miRNA_Track



# size of the region

max segment     = 1000000000

default segment = 50000



# examples to show in the introduction

examples = Odz3



# feature to show on startup

initial landmark = Chr16



#to generalise searches. the search results will include both gene and protein keywords and will not require specific Gene:xxx or protein:xxx it will search xxx through gene and protein in order of them appearing in the line just below.

automatic classes = RGD Gene



#init codes work like functions built into the code:

init_code         = sub bring_bubble{

                     ------some code--------

                     --------more code------

}

########################

# databases being used #

########################

[general:database]

db_adaptor    = Bio::DB::SeqFeature::Store

db_args       = -adaptor DBI::mysql

              -dsn     DBI:mysql:database=DBNAME;host=HOSTNAME.hmgc.mcw.edu

              -user    USERNAME

              -pass    PASSWORD

########################

# Default glyph settings

########################

[TRACK DEFAULTS]

database      = general

glyph         = generic

height        = 10

bgcolor       = lightgrey

fgcolor       = black

font2color    = blue

label density = 25

bump density  = 100



# where to link to when user clicks in detailed view

link          = AUTO



#################################

# Individual Track glyph settings

#################################



[miRNA_Track]

category      = GENOMIC FEATURES

feature       = miRNA:miRBase

glyph         = dot

fgcolor       = blue

bgcolor       = lightblue

linewidth    = 2

height       = 6

label        = sub{

                     my $feature=shift;

                     my ($miRna)=$feature->display_name;

                     return $miRna;      

              }

key           = miRNAs

link          = sub {

                     my $feature=shift;

                     my ($miRnaID)=$feature->load_id;

                     return "http://microrna.sanger.ac.uk/cgi-bin/sequences/mirna_entry.pl?id=$miRnaID";

              }

balloon hover = sub {bring_bubble(shift)}

balloon sticky = 1

citation      = This track shows rat microRNAs (miRNAs) derived from the <a href="http://microrna.sanger.ac.uk/"> Sanger Institute\'s miRBase</a>. miRBase is the repository for microRNA data, incorporating the database and gene naming roles previously provided by the miRNA Registry. Hovering over a feature provides annotation including miRBase ID and source. Clicking on a feature or selecting the miRBase ID links to the miRBase miRNA Report pages.



[miRNA_Track:overview]

feature       = miRNA:miRBase

glyph         = dot

fgcolor       = blue

bgcolor       = lightblue

linewidth    = 2

height       = 6

label        = sub{

                     my $feature=shift;

                     my ($miRna)=$feature->display_name;

                     return $miRna;      

              }

key           = miRNAs Overview

link          = sub {

                     my $feature=shift;

                     my ($miRnaID)=$feature->load_id;

                     return "http://microrna.sanger.ac.uk/cgi-bin/sequences/mirna_entry.pl?id=$miRnaID";

              }

citation      = This track shows rat microRNAs (miRNAs) derived from the <a href="http://microrna.sanger.ac.uk/"> Sanger Institute\'s miRBase</a>. miRBase is the repository for microRNA data, incorporating the database and gene naming roles previously provided by the miRNA Registry. Hovering over a feature provides annotation including miRBase ID and source. Clicking on a feature or selecting the miRBase ID links to the miRBase miRNA Report pages.



[QTLS]

glyph        = saw_teeth

category      = GENOMIC FEATURES

feature       = QTL:RGD

height       = 5

linewidth     = 3

bgcolor       = maroon

fgcolor       = orange

label        = sub{

                     my $feature=shift;

                     my ($qtlid)=$feature->load_id;

                     my @qtlarr=split(/:/, $qtlid);

                     return "QTL:$qtlarr[1]";

              }

description   = sub{

                     my $feature=shift;

                     my ($desc)=$feature->attributes('Dbxref');

                     my @desc_arr=split(/:/, $desc);

                     return "RGDID:".$desc_arr[1];

                    

              }

link         = sub {

                     my $feature=shift;

                     my ($link)=$feature->attributes('Dbxref');

                     if ($link=~/RGD:(\d+)/) {

                            my $rgdid=$1;

                            return "http://rgd.mcw.edu/objectSearch/qtlReport.jsp?rgd_id=$rgdid";

                     }

              }

balloon hover  = sub {bring_bubble(shift)}      

balloon sticky = 1

key           = RGD QTLs

citation      = This track shows <a href="http://www.rgd.mcw.edu/qtls/"> RGD Rat Quantitative Trait Loci (QTL)</a>. In some cases the boundaries of the QTL have been estimated as explained in <a href="ftp://rgd.mcw.edu/pub/data_release/QTLS_README"> QTLs Readme file</a>. Hovering over a feature provides additional annotation including the name, symbol, LOD (where available), p-value (where available), mapping method, and RGD ID, which links to the RGD QTL report page. Clicking on a feature also links to its RGD report page.



[PGA]

category      = PGA

feature       = PGA:ENU_BN PGA:ENU_FHH PGA:SB_F344

glyph         = diamond

bgcolor       = purple

fgcolor       = pink

key           = PGA

balloon hover  = sub {bring_bubble(shift)}

balloon sticky = 1

select        = source 'SB_F344' 'ENU_FHH' 'ENU_BN'

label         = sub {

                  my $feature=shift;

                  my ($pga_label)= $feature->display_name;

                  return $pga_label

                }

description   = sub {

                  my $feature=shift;

                  my ($pga_desc)= $feature->attributes("Id");

                  return $pga_desc;

                }

link           = sub {

                  my $feature=shift;

                  my ($pga_id)=$feature->attributes("Id");

                  $pga_id=~s/RGD://;

                  return "http://rgd.mcw.edu/tools/strains/strains_view.cgi?id=$pga_id";

                  }

citation      = This track includes the genomic locations of the <a href="http://pga.mcw.edu/"> PhysGen PGA</a> mutant strains developed using ENU mutagenesis or the Sleeping Beauty transposon strategy. Hovering over a feature provides additional annotation including the Gene Name, RGD Strain ID, Strain and Source (ENU_FHH, ENU_BN, SB_F344). Clicking on a feature or selecting the RGD Strain ID links to the strain report pages at RGD.



[CNV]

category     = ANNOTATED VARIANTS

feature       = CNV:Hubrecht_Institute

glyph        = span

fgcolor       = sub {bring_cnv_color(shift)}

bgcolor             = black

font2color    = pink1

linewidth     = 3

height        = 5

label       = sub{

                     my $cnv_feat = shift;

                     my ($cnvID)=$cnv_feat->attributes('Dbxref');

                     return "$cnvID";



              }

description   = sub{

                     my $cnv_feat = shift;

                     my ($type)=$cnv_feat->attributes('type');

                     return "TYPE:$type";



              }

balloon hover = sub {bring_bubble(shift)}

balloon sticky= 1

key           =CNVs

link   = sub{

                     my $cnv_feat = shift;

                     my ($cnvID)=$cnv_feat->attributes('Dbxref');

                     $cnvID =~s/cnv_//i;

                     return "http://h094.niob.knaw.nl/RatCNVs/cgi-bin/cnv.pl?id=$cnvID";



              }

citation      = <a href="http://h094.niob.knaw.nl/RatCNVs/"> Copy Number Variants (CNVs)</a> identified in commonly used laboratory rat strains through combination of computational approaches and experimental analysis as published in Guryev et al.; Distribution and functional impact of DNA copy number variation in the rat. Nature Genetics 40, 538 - 545 (2008). Hovering over a feature provides additional annotation including the CNV ID, Strain, Method, Type, and Source. Clicking on a feature or selecting the CNV ID links to the Hubrecht Institute\'s CNV pages.<br />CNVs are colored based on type as following:<br /><table border="1"><tr><th>Type</th><th>Color</th></tr><tr><td>Collapse</td><td>Purple</td></tr><tr><td>Overprediction</td><td>Yellow</td></tr><tr><td>Loss</td><td>Blue</td></tr><tr><td>Loss+Collapse</td><td>Dark blue</td></tr><tr><td>Loss+Overprediction</td><td>Light blue</td></tr><tr><td>Gain</td><td>Red</td></tr><tr><td>Gain+Collapse</td><td>Dark red</td></tr><tr><td>Gain+Overprediction</td><td>Light red</td></tr></table>







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: Lincoln Stein [[hidden email]]

Sent: Monday, June 21, 2010 10:38 AM
To: Jayaraman, Pushkala
Cc: [hidden email]
Subject: Re: [Gmod-gbrowse] Gbrowse2 tracks not visible..possible bug?





Hi Pushkala,



I'm afraid I'll need more information. Is the in-memory Yeast database working on the development server? If it is, it probably rules out a software problem. What database backend are you using, and how do you load it? What operating system are you using?



When you are unable to upload the "new" data on the Virtual Box, what do you mean by "new"?



Lincoln



On Mon, Jun 21, 2010 at 8:11 AM, Jayaraman, Pushkala <[hidden email]> wrote:

Hello,

I seem to be having problems with Gbrowse showing tracks on screen. This is slightly complicated:

1.       I have set up a fully functional gbrowse2 v2.03 on my Virtual Box with saved snapshots.

2.       I upgraded to Gbrowse 2.08 from SVN stable branch last month and set up that on my virtual Box. That seemed to be working too.

3.       I then had Gbrowse2 installed on our development server. This is where problems began,

When I tried to load the exact data that I had displaying successfully on my Virtual Box(lets call it Gbrowse_vbox), onto the gbrowse on the server (lets call it Gbrowse_serv)I saw that the Gbrowse_serv could not seem to display any of the data.

4.       Dumping the sql database from the vbox onto the server mysql seemed to get it to work.

5.       Recently, I have noticed that loading the new data on gbrowse_vbox seems unsuccessful. The apache error logs don't show anythings specific, but I do get Segmentation faults and "Use of uninitialized value in concatenation or string. (I do not know in what).

6.       I am just not able to see any of the Overview/Region/Detail panels on my screen. When I search for a tem, I sometimes get search results on the screen and sometimes just the Blue header that displays "The following 308 regions match your request "  and then nothing below it in the tracks panel.

7.       I am able to see the whole page except for the tracks. I can rule out the possibility of bad data because It did load and I was able to visualize that same data once. I am just not able to load it up again and visualize it. 





Please help..

Pushkala Jayaraman

Programmer/Analyst

Rat Genome Database

Human and Molecular Genetics Center

Medical College of Wisconsin

Email: [hidden email] <[hidden email]>

Work: 414-955-2229

www.rgd.mcw.edu <http://www.rgd.mcw.edu>






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416 673-8514
Assistant: Renata Musa <[hidden email]>





--
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]>




--
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]>




--
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]>

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Re: Gbrowse2 tracks not visible..possible bug?

Jayaraman, Pushkala
In reply to this post by Scott Cain
Thanks Guys,
I'll make the necessary changes..
I will also reconfigure my conf file so as to have my chromosome data in another small database called scaffolds...
Thanks again,
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


-----Original Message-----
From: Scott Cain [mailto:[hidden email]]
Sent: Monday, June 21, 2010 11:47 AM
To: Jayaraman, Pushkala
Cc: Lincoln Stein; [hidden email]
Subject: Re: [Gmod-gbrowse] Gbrowse2 tracks not visible..possible bug?

Pushkala,

You need "Name=Chr15" in column nine of that first line; that is what
identifies it as being Chr15.

Scott


On Mon, Jun 21, 2010 at 12:42 PM, Jayaraman, Pushkala
<[hidden email]> wrote:

> Hello Lincoln,
>
> This is what I get:
>
>
>
> mysql> select * from name where name like 'chr%';
>
> +-------+--------+--------------+
>
> | id    | name   | display_name |
>
> +-------+--------+--------------+
>
> | 29168 | Chrm3  |            1 |
>
> | 29169 | Chrm3  |            1 |
>
> | 29172 | Chrm3  |            1 |
>
> |  2076 | Chrna2 |            1 |
>
> |  2078 | Chrna2 |            1 |
>
> |  2080 | Chrna2 |            1 |
>
> |  2082 | Chrna2 |            1 |
>
> |  2084 | Chrna2 |            1 |
>
> |  2086 | Chrna2 |            1 |
>
> |  2088 | Chrna2 |            1 |
>
> |  2089 | Chrna2 |            1 |
>
> +-------+--------+--------------+
>
> 11 rows in set (0.00 sec)
>
>
>
> Why am I not getting any of the chromosome names?
>
>
>
>
>
> When I do "head nameof_gff3_file.gff3" I get:
>
>
>
> Chr15   GenBank chromosome      24425085        28088033        .       +
>    .       ID=NW_047453;Alias=15;Dbxref=taxon:10116;Note=Rattus norvegicus
> chromosome 15 genomic cont
>
> ig%2C reference assembly (based on RGSC v3.4).,GENOME ANNOTATION REFSEQ:
> Features on this sequence have been produced for build 4 version 1 of the
> NCBI's genome annotation [see d
>
> ocumentation]. The DNA sequence is version 3.4 'November 2004 Update' of the
> Rat genome assembly,produced by the Baylor College of Medicine Human Genome
> Sequencing Center (BCM- H
>
> GSC) as part of the Rat Genome Sequencing Consortium (RGSC). This supersedes
> all prior versions of the Rat assembly (2.0,2.1,3.0,3.1 3.2 and 3.3) (see
> http://www.hgsc.bcm.tmc.edu
>
> /projects/rat/). ;chromosome=15;comment1=GENOME ANNOTATION REFSEQ: Features
> on this sequence have been produced for build 4 version 1 of the NCBI's
> genome annotation [see documen
>
> tation]. The DNA sequence is version 3.4 'November 2004 Update' of the Rat
> genome assembly%2C produced by the Baylor College of Medicine Human Genome
> Sequencing Center (BCM- HGSC
>
> ) as part of the Rat Genome Sequencing Consortium (RGSC). This supersedes
> all prior versions of the Rat assembly (2.0%2C 2.1%2C 3.0%2C 3.1 3.2 and
> 3.3) (see http://www.hgsc.bcm.tmc.edu/projects/rat/).
> ;date=03-JUL-2006;mol_type=genomic DNA;organism=Rattus
> norvegicus;strain=BN/SsNHsdMCW;
>
> Chr15   GenBank pseudogene      24427872        24428719        .
> -       .       ID=LOC498499;Dbxref=GeneID:498499;Note=Derived by automated
> computational analysis using gene prediction method: GNOMON. Supporting
> evidence includes similarity to: 98 ESTs%2C 6
> Proteins;gene=LOC498499;pseudo=_no_value;
>
>
>
>
>
> Which clearly shows the chromosome feature right on top.
>
>
>
> 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: Lincoln Stein [mailto:[hidden email]]
> Sent: Monday, June 21, 2010 11:33 AM
> To: Jayaraman, Pushkala
> Cc: [hidden email]
> Subject: Re: [Gmod-gbrowse] Gbrowse2 tracks not visible..possible bug?
>
>
>
> It sounds to me as though you are loading the data correctly. But is there
> any chance that you used -c inadvertently on one of the subsequent loads and
> inadvertently removed the chromosomes? The way to check is:
>
>
>
>  mysql> select * from name where name like 'chr%'
>
>
>
> Lincoln
>
> On Mon, Jun 21, 2010 at 12:19 PM, Jayaraman, Pushkala <[hidden email]>
> wrote:
>
> Hello Lincoln,
>
> Yes,
>
> The yeast, in-memory database is loading well. Also, the data that I had
> loaded into the mysql database about a month ago (before I updated gbrowse
> through svn) is also seems to be rendering tracks on my VirtualBox as well
> as the server(I create a dump of the dabatase that I used on the VBox and
> uploaded that same database on the server and it works well)..
>
>
>
> I am using a mysql database backend. This is how I load the data
>
>  bp_seqfeature_load.pl -a DBI::mysql -d
> "DBI:mysql:database=DBNAME;host=HOSTNAME" -c -f filename.gff3
>
>
>
> I do not use -c each time. But I seem to have to use it the first time after
> I newly create a DB. Else it complains about not finding the tables. So it
> gives out errors like 'cannot load data into .locationlist table or view
> does not exist'.
>
> But when I use the -c feature, it seems to load it in pretty well. After
> that, I do not have to use the -c feature when I am adding data into the
> database.
>
>
> As you can see in the above two attached pictures, both are feb by very
> similar conf files except for their name. I simply made a copy of the conf
> file and renamed one. the data source though, is different. i.e they are
> being fed from two different mysql databases.
>
> when the database has all the tracks then it seems to generate pictures, but
> when i only load one feature eg. qtl, then it doesnt show anything..
> This is what my conf file looks like:
>
> [GENERAL]
>
> database     = general
>
>
>
> autocomplete = 1
>
> search options = default +autocomplete +wildcard
>
>
>
> # turn on remote rendering-- see [TRACK DEFAULTS] for the hosts
>
> # and ports the rendering slaves run on.
>
> renderfarm    = 1
>
>
>
> # just the basic track dumper plugin was in before..now added new plugins
>
> plugins = TrackDumper Aligner BatchDumper Submitter OligoFinder FilterTest
> AttributeHiliter
>
>
>
> #balloon tips acknowledge:
>
> balloon tips = 1
>
>
>
> # list of tracks to turn on by default
>
> default features = miRNA_Track
>
>
>
> # size of the region
>
> max segment     = 1000000000
>
> default segment = 50000
>
>
>
> # examples to show in the introduction
>
> examples = Odz3
>
>
>
> # feature to show on startup
>
> initial landmark = Chr16
>
>
>
> #to generalise searches. the search results will include both gene and
> protein keywords and will not require specific Gene:xxx or protein:xxx it
> will search xxx through gene and protein in order of them appearing in the
> line just below.
>
> automatic classes = RGD Gene
>
>
>
> #init codes work like functions built into the code:
>
> init_code         = sub bring_bubble{
>
>                      ------some code--------
>
>                      --------more code------
>
> }
>
> ########################
>
> # databases being used #
>
> ########################
>
> [general:database]
>
> db_adaptor    = Bio::DB::SeqFeature::Store
>
> db_args       = -adaptor DBI::mysql
>
>               -dsn     DBI:mysql:database=DBNAME;host=HOSTNAME.hmgc.mcw.edu
>
>               -user    USERNAME
>
>               -pass    PASSWORD
>
> ########################
>
> # Default glyph settings
>
> ########################
>
> [TRACK DEFAULTS]
>
> database      = general
>
> glyph         = generic
>
> height        = 10
>
> bgcolor       = lightgrey
>
> fgcolor       = black
>
> font2color    = blue
>
> label density = 25
>
> bump density  = 100
>
>
>
> # where to link to when user clicks in detailed view
>
> link          = AUTO
>
>
>
> #################################
>
> # Individual Track glyph settings
>
> #################################
>
>
>
> [miRNA_Track]
>
> category      = GENOMIC FEATURES
>
> feature       = miRNA:miRBase
>
> glyph         = dot
>
> fgcolor       = blue
>
> bgcolor       = lightblue
>
> linewidth    = 2
>
> height       = 6
>
> label        = sub{
>
>                      my $feature=shift;
>
>                      my ($miRna)=$feature->display_name;
>
>                      return $miRna;
>
>               }
>
> key           = miRNAs
>
> link          = sub {
>
>                      my $feature=shift;
>
>                      my ($miRnaID)=$feature->load_id;
>
>                      return
> "http://microrna.sanger.ac.uk/cgi-bin/sequences/mirna_entry.pl?id=$miRnaID";
>
>               }
>
> balloon hover = sub {bring_bubble(shift)}
>
> balloon sticky = 1
>
> citation      = This track shows rat microRNAs (miRNAs) derived from the <a
> href="http://microrna.sanger.ac.uk/"> Sanger Institute\'s miRBase</a>.
> miRBase is the repository for microRNA data, incorporating the database and
> gene naming roles previously provided by the miRNA Registry. Hovering over a
> feature provides annotation including miRBase ID and source. Clicking on a
> feature or selecting the miRBase ID links to the miRBase miRNA Report pages.
>
>
>
> [miRNA_Track:overview]
>
> feature       = miRNA:miRBase
>
> glyph         = dot
>
> fgcolor       = blue
>
> bgcolor       = lightblue
>
> linewidth    = 2
>
> height       = 6
>
> label        = sub{
>
>                      my $feature=shift;
>
>                      my ($miRna)=$feature->display_name;
>
>                      return $miRna;
>
>               }
>
> key           = miRNAs Overview
>
> link          = sub {
>
>                      my $feature=shift;
>
>                      my ($miRnaID)=$feature->load_id;
>
>                      return
> "http://microrna.sanger.ac.uk/cgi-bin/sequences/mirna_entry.pl?id=$miRnaID";
>
>               }
>
> citation      = This track shows rat microRNAs (miRNAs) derived from the <a
> href="http://microrna.sanger.ac.uk/"> Sanger Institute\'s miRBase</a>.
> miRBase is the repository for microRNA data, incorporating the database and
> gene naming roles previously provided by the miRNA Registry. Hovering over a
> feature provides annotation including miRBase ID and source. Clicking on a
> feature or selecting the miRBase ID links to the miRBase miRNA Report pages.
>
>
>
> [QTLS]
>
> glyph        = saw_teeth
>
> category      = GENOMIC FEATURES
>
> feature       = QTL:RGD
>
> height       = 5
>
> linewidth     = 3
>
> bgcolor       = maroon
>
> fgcolor       = orange
>
> label        = sub{
>
>                      my $feature=shift;
>
>                      my ($qtlid)=$feature->load_id;
>
>                      my @qtlarr=split(/:/, $qtlid);
>
>                      return "QTL:$qtlarr[1]";
>
>               }
>
> description   = sub{
>
>                      my $feature=shift;
>
>                      my ($desc)=$feature->attributes('Dbxref');
>
>                      my @desc_arr=split(/:/, $desc);
>
>                      return "RGDID:".$desc_arr[1];
>
>
>
>               }
>
> link         = sub {
>
>                      my $feature=shift;
>
>                      my ($link)=$feature->attributes('Dbxref');
>
>                      if ($link=~/RGD:(\d+)/) {
>
>                             my $rgdid=$1;
>
>                             return
> "http://rgd.mcw.edu/objectSearch/qtlReport.jsp?rgd_id=$rgdid";
>
>                      }
>
>               }
>
> balloon hover  = sub {bring_bubble(shift)}
>
> balloon sticky = 1
>
> key           = RGD QTLs
>
> citation      = This track shows <a href="http://www.rgd.mcw.edu/qtls/"> RGD
> Rat Quantitative Trait Loci (QTL)</a>. In some cases the boundaries of the
> QTL have been estimated as explained in <a
> href="ftp://rgd.mcw.edu/pub/data_release/QTLS_README"> QTLs Readme file</a>.
> Hovering over a feature provides additional annotation including the name,
> symbol, LOD (where available), p-value (where available), mapping method,
> and RGD ID, which links to the RGD QTL report page. Clicking on a feature
> also links to its RGD report page.
>
>
>
> [PGA]
>
> category      = PGA
>
> feature       = PGA:ENU_BN PGA:ENU_FHH PGA:SB_F344
>
> glyph         = diamond
>
> bgcolor       = purple
>
> fgcolor       = pink
>
> key           = PGA
>
> balloon hover  = sub {bring_bubble(shift)}
>
> balloon sticky = 1
>
> select        = source 'SB_F344' 'ENU_FHH' 'ENU_BN'
>
> label         = sub {
>
>                   my $feature=shift;
>
>                   my ($pga_label)= $feature->display_name;
>
>                   return $pga_label
>
>                 }
>
> description   = sub {
>
>                   my $feature=shift;
>
>                   my ($pga_desc)= $feature->attributes("Id");
>
>                   return $pga_desc;
>
>                 }
>
> link           = sub {
>
>                   my $feature=shift;
>
>                   my ($pga_id)=$feature->attributes("Id");
>
>                   $pga_id=~s/RGD://;
>
>                   return
> "http://rgd.mcw.edu/tools/strains/strains_view.cgi?id=$pga_id";
>
>                   }
>
> citation      = This track includes the genomic locations of the <a
> href="http://pga.mcw.edu/"> PhysGen PGA</a> mutant strains developed using
> ENU mutagenesis or the Sleeping Beauty transposon strategy. Hovering over a
> feature provides additional annotation including the Gene Name, RGD Strain
> ID, Strain and Source (ENU_FHH, ENU_BN, SB_F344). Clicking on a feature or
> selecting the RGD Strain ID links to the strain report pages at RGD.
>
>
>
> [CNV]
>
> category     = ANNOTATED VARIANTS
>
> feature       = CNV:Hubrecht_Institute
>
> glyph        = span
>
> fgcolor       = sub {bring_cnv_color(shift)}
>
> bgcolor             = black
>
> font2color    = pink1
>
> linewidth     = 3
>
> height        = 5
>
> label       = sub{
>
>                      my $cnv_feat = shift;
>
>                      my ($cnvID)=$cnv_feat->attributes('Dbxref');
>
>                      return "$cnvID";
>
>
>
>               }
>
> description   = sub{
>
>                      my $cnv_feat = shift;
>
>                      my ($type)=$cnv_feat->attributes('type');
>
>                      return "TYPE:$type";
>
>
>
>               }
>
> balloon hover = sub {bring_bubble(shift)}
>
> balloon sticky= 1
>
> key           =CNVs
>
> link   = sub{
>
>                      my $cnv_feat = shift;
>
>                      my ($cnvID)=$cnv_feat->attributes('Dbxref');
>
>                      $cnvID =~s/cnv_//i;
>
>                      return
> "http://h094.niob.knaw.nl/RatCNVs/cgi-bin/cnv.pl?id=$cnvID";
>
>
>
>               }
>
> citation      = <a href="http://h094.niob.knaw.nl/RatCNVs/"> Copy Number
> Variants (CNVs)</a> identified in commonly used laboratory rat strains
> through combination of computational approaches and experimental analysis as
> published in Guryev et al.; Distribution and functional impact of DNA copy
> number variation in the rat. Nature Genetics 40, 538 - 545 (2008). Hovering
> over a feature provides additional annotation including the CNV ID, Strain,
> Method, Type, and Source. Clicking on a feature or selecting the CNV ID
> links to the Hubrecht Institute\'s CNV pages.<br />CNVs are colored based on
> type as following:<br /><table
> border="1"><tr><th>Type</th><th>Color</th></tr><tr><td>Collapse</td><td>Purple</td></tr><tr><td>Overprediction</td><td>Yellow</td></tr><tr><td>Loss</td><td>Blue</td></tr><tr><td>Loss+Collapse</td><td>Dark
> blue</td></tr><tr><td>Loss+Overprediction</td><td>Light
> blue</td></tr><tr><td>Gain</td><td>Red</td></tr><tr><td>Gain+Collapse</td><td>Dark
> red</td></tr><tr><td>Gain+Overprediction</td><td>Light red</td></tr></table>
>
>
>
>
>
> 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: Lincoln Stein [mailto:[hidden email]]
>
> Sent: Monday, June 21, 2010 10:38 AM
> To: Jayaraman, Pushkala
> Cc: [hidden email]
> Subject: Re: [Gmod-gbrowse] Gbrowse2 tracks not visible..possible bug?
>
>
>
> Hi Pushkala,
>
>
>
> I'm afraid I'll need more information. Is the in-memory Yeast database
> working on the development server? If it is, it probably rules out a
> software problem. What database backend are you using, and how do you load
> it? What operating system are you using?
>
>
>
> When you are unable to upload the "new" data on the Virtual Box, what do you
> mean by "new"?
>
>
>
> Lincoln
>
>
>
> On Mon, Jun 21, 2010 at 8:11 AM, Jayaraman, Pushkala <[hidden email]>
> wrote:
>
> Hello,
>
> I seem to be having problems with Gbrowse showing tracks on screen. This is
> slightly complicated:
>
> 1.       I have set up a fully functional gbrowse2 v2.03 on my Virtual Box
> with saved snapshots.
>
> 2.       I upgraded to Gbrowse 2.08 from SVN stable branch last month and
> set up that on my virtual Box. That seemed to be working too.
>
> 3.       I then had Gbrowse2 installed on our development server. This is
> where problems began,
>
> When I tried to load the exact data that I had displaying successfully on my
> Virtual Box(lets call it Gbrowse_vbox), onto the gbrowse on the server (lets
> call it Gbrowse_serv)I saw that the Gbrowse_serv could not seem to display
> any of the data.
>
> 4.       Dumping the sql database from the vbox onto the server mysql seemed
> to get it to work.
>
> 5.       Recently, I have noticed that loading the new data on gbrowse_vbox
> seems unsuccessful. The apache error logs don't show anythings specific, but
> I do get Segmentation faults and "Use of uninitialized value in
> concatenation or string. (I do not know in what).
>
> 6.       I am just not able to see any of the Overview/Region/Detail panels
> on my screen. When I search for a tem, I sometimes get search results on the
> screen and sometimes just the Blue header that displays "The following 308
> regions match your request "  and then nothing below it in the tracks panel.
>
> 7.       I am able to see the whole page except for the tracks. I can rule
> out the possibility of bad data because It did load and I was able to
> visualize that same data once. I am just not able to load it up again and
> visualize it.
>
>
>
>
>
> Please help..
>
> Pushkala Jayaraman
>
> Programmer/Analyst
>
> Rat Genome Database
>
> Human and Molecular Genetics Center
>
> Medical College of Wisconsin
>
> Email: [hidden email] <mailto:[hidden email]>
>
> Work: 414-955-2229
>
> www.rgd.mcw.edu <http://www.rgd.mcw.edu>
>
>
>
>
> ------------------------------------------------------------------------------
> ThinkGeek and WIRED's GeekDad team up for the Ultimate
> GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
> lucky parental unit.  See the prize list and enter to win:
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> [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]>
>
>
>
>
>
>
> --
> 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]>
>
> ------------------------------------------------------------------------------
> ThinkGeek and WIRED's GeekDad team up for the Ultimate
> GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
> lucky parental unit.  See the prize list and enter to win:
> http://p.sf.net/sfu/thinkgeek-promo
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> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>
>



--
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GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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Re: Gbrowse2 tracks not visible..possible bug?

Jayaraman, Pushkala
In reply to this post by Scott Cain
It works now
:)

Thanks all..

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


-----Original Message-----
From: Scott Cain [mailto:[hidden email]]
Sent: Monday, June 21, 2010 11:47 AM
To: Jayaraman, Pushkala
Cc: Lincoln Stein; [hidden email]
Subject: Re: [Gmod-gbrowse] Gbrowse2 tracks not visible..possible bug?

Pushkala,

You need "Name=Chr15" in column nine of that first line; that is what
identifies it as being Chr15.

Scott


On Mon, Jun 21, 2010 at 12:42 PM, Jayaraman, Pushkala
<[hidden email]> wrote:

> Hello Lincoln,
>
> This is what I get:
>
>
>
> mysql> select * from name where name like 'chr%';
>
> +-------+--------+--------------+
>
> | id    | name   | display_name |
>
> +-------+--------+--------------+
>
> | 29168 | Chrm3  |            1 |
>
> | 29169 | Chrm3  |            1 |
>
> | 29172 | Chrm3  |            1 |
>
> |  2076 | Chrna2 |            1 |
>
> |  2078 | Chrna2 |            1 |
>
> |  2080 | Chrna2 |            1 |
>
> |  2082 | Chrna2 |            1 |
>
> |  2084 | Chrna2 |            1 |
>
> |  2086 | Chrna2 |            1 |
>
> |  2088 | Chrna2 |            1 |
>
> |  2089 | Chrna2 |            1 |
>
> +-------+--------+--------------+
>
> 11 rows in set (0.00 sec)
>
>
>
> Why am I not getting any of the chromosome names?
>
>
>
>
>
> When I do "head nameof_gff3_file.gff3" I get:
>
>
>
> Chr15   GenBank chromosome      24425085        28088033        .       +
>    .       ID=NW_047453;Alias=15;Dbxref=taxon:10116;Note=Rattus norvegicus
> chromosome 15 genomic cont
>
> ig%2C reference assembly (based on RGSC v3.4).,GENOME ANNOTATION REFSEQ:
> Features on this sequence have been produced for build 4 version 1 of the
> NCBI's genome annotation [see d
>
> ocumentation]. The DNA sequence is version 3.4 'November 2004 Update' of the
> Rat genome assembly,produced by the Baylor College of Medicine Human Genome
> Sequencing Center (BCM- H
>
> GSC) as part of the Rat Genome Sequencing Consortium (RGSC). This supersedes
> all prior versions of the Rat assembly (2.0,2.1,3.0,3.1 3.2 and 3.3) (see
> http://www.hgsc.bcm.tmc.edu
>
> /projects/rat/). ;chromosome=15;comment1=GENOME ANNOTATION REFSEQ: Features
> on this sequence have been produced for build 4 version 1 of the NCBI's
> genome annotation [see documen
>
> tation]. The DNA sequence is version 3.4 'November 2004 Update' of the Rat
> genome assembly%2C produced by the Baylor College of Medicine Human Genome
> Sequencing Center (BCM- HGSC
>
> ) as part of the Rat Genome Sequencing Consortium (RGSC). This supersedes
> all prior versions of the Rat assembly (2.0%2C 2.1%2C 3.0%2C 3.1 3.2 and
> 3.3) (see http://www.hgsc.bcm.tmc.edu/projects/rat/).
> ;date=03-JUL-2006;mol_type=genomic DNA;organism=Rattus
> norvegicus;strain=BN/SsNHsdMCW;
>
> Chr15   GenBank pseudogene      24427872        24428719        .
> -       .       ID=LOC498499;Dbxref=GeneID:498499;Note=Derived by automated
> computational analysis using gene prediction method: GNOMON. Supporting
> evidence includes similarity to: 98 ESTs%2C 6
> Proteins;gene=LOC498499;pseudo=_no_value;
>
>
>
>
>
> Which clearly shows the chromosome feature right on top.
>
>
>
> 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: Lincoln Stein [mailto:[hidden email]]
> Sent: Monday, June 21, 2010 11:33 AM
> To: Jayaraman, Pushkala
> Cc: [hidden email]
> Subject: Re: [Gmod-gbrowse] Gbrowse2 tracks not visible..possible bug?
>
>
>
> It sounds to me as though you are loading the data correctly. But is there
> any chance that you used -c inadvertently on one of the subsequent loads and
> inadvertently removed the chromosomes? The way to check is:
>
>
>
>  mysql> select * from name where name like 'chr%'
>
>
>
> Lincoln
>
> On Mon, Jun 21, 2010 at 12:19 PM, Jayaraman, Pushkala <[hidden email]>
> wrote:
>
> Hello Lincoln,
>
> Yes,
>
> The yeast, in-memory database is loading well. Also, the data that I had
> loaded into the mysql database about a month ago (before I updated gbrowse
> through svn) is also seems to be rendering tracks on my VirtualBox as well
> as the server(I create a dump of the dabatase that I used on the VBox and
> uploaded that same database on the server and it works well)..
>
>
>
> I am using a mysql database backend. This is how I load the data
>
>  bp_seqfeature_load.pl -a DBI::mysql -d
> "DBI:mysql:database=DBNAME;host=HOSTNAME" -c -f filename.gff3
>
>
>
> I do not use -c each time. But I seem to have to use it the first time after
> I newly create a DB. Else it complains about not finding the tables. So it
> gives out errors like 'cannot load data into .locationlist table or view
> does not exist'.
>
> But when I use the -c feature, it seems to load it in pretty well. After
> that, I do not have to use the -c feature when I am adding data into the
> database.
>
>
> As you can see in the above two attached pictures, both are feb by very
> similar conf files except for their name. I simply made a copy of the conf
> file and renamed one. the data source though, is different. i.e they are
> being fed from two different mysql databases.
>
> when the database has all the tracks then it seems to generate pictures, but
> when i only load one feature eg. qtl, then it doesnt show anything..
> This is what my conf file looks like:
>
> [GENERAL]
>
> database     = general
>
>
>
> autocomplete = 1
>
> search options = default +autocomplete +wildcard
>
>
>
> # turn on remote rendering-- see [TRACK DEFAULTS] for the hosts
>
> # and ports the rendering slaves run on.
>
> renderfarm    = 1
>
>
>
> # just the basic track dumper plugin was in before..now added new plugins
>
> plugins = TrackDumper Aligner BatchDumper Submitter OligoFinder FilterTest
> AttributeHiliter
>
>
>
> #balloon tips acknowledge:
>
> balloon tips = 1
>
>
>
> # list of tracks to turn on by default
>
> default features = miRNA_Track
>
>
>
> # size of the region
>
> max segment     = 1000000000
>
> default segment = 50000
>
>
>
> # examples to show in the introduction
>
> examples = Odz3
>
>
>
> # feature to show on startup
>
> initial landmark = Chr16
>
>
>
> #to generalise searches. the search results will include both gene and
> protein keywords and will not require specific Gene:xxx or protein:xxx it
> will search xxx through gene and protein in order of them appearing in the
> line just below.
>
> automatic classes = RGD Gene
>
>
>
> #init codes work like functions built into the code:
>
> init_code         = sub bring_bubble{
>
>                      ------some code--------
>
>                      --------more code------
>
> }
>
> ########################
>
> # databases being used #
>
> ########################
>
> [general:database]
>
> db_adaptor    = Bio::DB::SeqFeature::Store
>
> db_args       = -adaptor DBI::mysql
>
>               -dsn     DBI:mysql:database=DBNAME;host=HOSTNAME.hmgc.mcw.edu
>
>               -user    USERNAME
>
>               -pass    PASSWORD
>
> ########################
>
> # Default glyph settings
>
> ########################
>
> [TRACK DEFAULTS]
>
> database      = general
>
> glyph         = generic
>
> height        = 10
>
> bgcolor       = lightgrey
>
> fgcolor       = black
>
> font2color    = blue
>
> label density = 25
>
> bump density  = 100
>
>
>
> # where to link to when user clicks in detailed view
>
> link          = AUTO
>
>
>
> #################################
>
> # Individual Track glyph settings
>
> #################################
>
>
>
> [miRNA_Track]
>
> category      = GENOMIC FEATURES
>
> feature       = miRNA:miRBase
>
> glyph         = dot
>
> fgcolor       = blue
>
> bgcolor       = lightblue
>
> linewidth    = 2
>
> height       = 6
>
> label        = sub{
>
>                      my $feature=shift;
>
>                      my ($miRna)=$feature->display_name;
>
>                      return $miRna;
>
>               }
>
> key           = miRNAs
>
> link          = sub {
>
>                      my $feature=shift;
>
>                      my ($miRnaID)=$feature->load_id;
>
>                      return
> "http://microrna.sanger.ac.uk/cgi-bin/sequences/mirna_entry.pl?id=$miRnaID";
>
>               }
>
> balloon hover = sub {bring_bubble(shift)}
>
> balloon sticky = 1
>
> citation      = This track shows rat microRNAs (miRNAs) derived from the <a
> href="http://microrna.sanger.ac.uk/"> Sanger Institute\'s miRBase</a>.
> miRBase is the repository for microRNA data, incorporating the database and
> gene naming roles previously provided by the miRNA Registry. Hovering over a
> feature provides annotation including miRBase ID and source. Clicking on a
> feature or selecting the miRBase ID links to the miRBase miRNA Report pages.
>
>
>
> [miRNA_Track:overview]
>
> feature       = miRNA:miRBase
>
> glyph         = dot
>
> fgcolor       = blue
>
> bgcolor       = lightblue
>
> linewidth    = 2
>
> height       = 6
>
> label        = sub{
>
>                      my $feature=shift;
>
>                      my ($miRna)=$feature->display_name;
>
>                      return $miRna;
>
>               }
>
> key           = miRNAs Overview
>
> link          = sub {
>
>                      my $feature=shift;
>
>                      my ($miRnaID)=$feature->load_id;
>
>                      return
> "http://microrna.sanger.ac.uk/cgi-bin/sequences/mirna_entry.pl?id=$miRnaID";
>
>               }
>
> citation      = This track shows rat microRNAs (miRNAs) derived from the <a
> href="http://microrna.sanger.ac.uk/"> Sanger Institute\'s miRBase</a>.
> miRBase is the repository for microRNA data, incorporating the database and
> gene naming roles previously provided by the miRNA Registry. Hovering over a
> feature provides annotation including miRBase ID and source. Clicking on a
> feature or selecting the miRBase ID links to the miRBase miRNA Report pages.
>
>
>
> [QTLS]
>
> glyph        = saw_teeth
>
> category      = GENOMIC FEATURES
>
> feature       = QTL:RGD
>
> height       = 5
>
> linewidth     = 3
>
> bgcolor       = maroon
>
> fgcolor       = orange
>
> label        = sub{
>
>                      my $feature=shift;
>
>                      my ($qtlid)=$feature->load_id;
>
>                      my @qtlarr=split(/:/, $qtlid);
>
>                      return "QTL:$qtlarr[1]";
>
>               }
>
> description   = sub{
>
>                      my $feature=shift;
>
>                      my ($desc)=$feature->attributes('Dbxref');
>
>                      my @desc_arr=split(/:/, $desc);
>
>                      return "RGDID:".$desc_arr[1];
>
>
>
>               }
>
> link         = sub {
>
>                      my $feature=shift;
>
>                      my ($link)=$feature->attributes('Dbxref');
>
>                      if ($link=~/RGD:(\d+)/) {
>
>                             my $rgdid=$1;
>
>                             return
> "http://rgd.mcw.edu/objectSearch/qtlReport.jsp?rgd_id=$rgdid";
>
>                      }
>
>               }
>
> balloon hover  = sub {bring_bubble(shift)}
>
> balloon sticky = 1
>
> key           = RGD QTLs
>
> citation      = This track shows <a href="http://www.rgd.mcw.edu/qtls/"> RGD
> Rat Quantitative Trait Loci (QTL)</a>. In some cases the boundaries of the
> QTL have been estimated as explained in <a
> href="ftp://rgd.mcw.edu/pub/data_release/QTLS_README"> QTLs Readme file</a>.
> Hovering over a feature provides additional annotation including the name,
> symbol, LOD (where available), p-value (where available), mapping method,
> and RGD ID, which links to the RGD QTL report page. Clicking on a feature
> also links to its RGD report page.
>
>
>
> [PGA]
>
> category      = PGA
>
> feature       = PGA:ENU_BN PGA:ENU_FHH PGA:SB_F344
>
> glyph         = diamond
>
> bgcolor       = purple
>
> fgcolor       = pink
>
> key           = PGA
>
> balloon hover  = sub {bring_bubble(shift)}
>
> balloon sticky = 1
>
> select        = source 'SB_F344' 'ENU_FHH' 'ENU_BN'
>
> label         = sub {
>
>                   my $feature=shift;
>
>                   my ($pga_label)= $feature->display_name;
>
>                   return $pga_label
>
>                 }
>
> description   = sub {
>
>                   my $feature=shift;
>
>                   my ($pga_desc)= $feature->attributes("Id");
>
>                   return $pga_desc;
>
>                 }
>
> link           = sub {
>
>                   my $feature=shift;
>
>                   my ($pga_id)=$feature->attributes("Id");
>
>                   $pga_id=~s/RGD://;
>
>                   return
> "http://rgd.mcw.edu/tools/strains/strains_view.cgi?id=$pga_id";
>
>                   }
>
> citation      = This track includes the genomic locations of the <a
> href="http://pga.mcw.edu/"> PhysGen PGA</a> mutant strains developed using
> ENU mutagenesis or the Sleeping Beauty transposon strategy. Hovering over a
> feature provides additional annotation including the Gene Name, RGD Strain
> ID, Strain and Source (ENU_FHH, ENU_BN, SB_F344). Clicking on a feature or
> selecting the RGD Strain ID links to the strain report pages at RGD.
>
>
>
> [CNV]
>
> category     = ANNOTATED VARIANTS
>
> feature       = CNV:Hubrecht_Institute
>
> glyph        = span
>
> fgcolor       = sub {bring_cnv_color(shift)}
>
> bgcolor             = black
>
> font2color    = pink1
>
> linewidth     = 3
>
> height        = 5
>
> label       = sub{
>
>                      my $cnv_feat = shift;
>
>                      my ($cnvID)=$cnv_feat->attributes('Dbxref');
>
>                      return "$cnvID";
>
>
>
>               }
>
> description   = sub{
>
>                      my $cnv_feat = shift;
>
>                      my ($type)=$cnv_feat->attributes('type');
>
>                      return "TYPE:$type";
>
>
>
>               }
>
> balloon hover = sub {bring_bubble(shift)}
>
> balloon sticky= 1
>
> key           =CNVs
>
> link   = sub{
>
>                      my $cnv_feat = shift;
>
>                      my ($cnvID)=$cnv_feat->attributes('Dbxref');
>
>                      $cnvID =~s/cnv_//i;
>
>                      return
> "http://h094.niob.knaw.nl/RatCNVs/cgi-bin/cnv.pl?id=$cnvID";
>
>
>
>               }
>
> citation      = <a href="http://h094.niob.knaw.nl/RatCNVs/"> Copy Number
> Variants (CNVs)</a> identified in commonly used laboratory rat strains
> through combination of computational approaches and experimental analysis as
> published in Guryev et al.; Distribution and functional impact of DNA copy
> number variation in the rat. Nature Genetics 40, 538 - 545 (2008). Hovering
> over a feature provides additional annotation including the CNV ID, Strain,
> Method, Type, and Source. Clicking on a feature or selecting the CNV ID
> links to the Hubrecht Institute\'s CNV pages.<br />CNVs are colored based on
> type as following:<br /><table
> border="1"><tr><th>Type</th><th>Color</th></tr><tr><td>Collapse</td><td>Purple</td></tr><tr><td>Overprediction</td><td>Yellow</td></tr><tr><td>Loss</td><td>Blue</td></tr><tr><td>Loss+Collapse</td><td>Dark
> blue</td></tr><tr><td>Loss+Overprediction</td><td>Light
> blue</td></tr><tr><td>Gain</td><td>Red</td></tr><tr><td>Gain+Collapse</td><td>Dark
> red</td></tr><tr><td>Gain+Overprediction</td><td>Light red</td></tr></table>
>
>
>
>
>
> 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: Lincoln Stein [mailto:[hidden email]]
>
> Sent: Monday, June 21, 2010 10:38 AM
> To: Jayaraman, Pushkala
> Cc: [hidden email]
> Subject: Re: [Gmod-gbrowse] Gbrowse2 tracks not visible..possible bug?
>
>
>
> Hi Pushkala,
>
>
>
> I'm afraid I'll need more information. Is the in-memory Yeast database
> working on the development server? If it is, it probably rules out a
> software problem. What database backend are you using, and how do you load
> it? What operating system are you using?
>
>
>
> When you are unable to upload the "new" data on the Virtual Box, what do you
> mean by "new"?
>
>
>
> Lincoln
>
>
>
> On Mon, Jun 21, 2010 at 8:11 AM, Jayaraman, Pushkala <[hidden email]>
> wrote:
>
> Hello,
>
> I seem to be having problems with Gbrowse showing tracks on screen. This is
> slightly complicated:
>
> 1.       I have set up a fully functional gbrowse2 v2.03 on my Virtual Box
> with saved snapshots.
>
> 2.       I upgraded to Gbrowse 2.08 from SVN stable branch last month and
> set up that on my virtual Box. That seemed to be working too.
>
> 3.       I then had Gbrowse2 installed on our development server. This is
> where problems began,
>
> When I tried to load the exact data that I had displaying successfully on my
> Virtual Box(lets call it Gbrowse_vbox), onto the gbrowse on the server (lets
> call it Gbrowse_serv)I saw that the Gbrowse_serv could not seem to display
> any of the data.
>
> 4.       Dumping the sql database from the vbox onto the server mysql seemed
> to get it to work.
>
> 5.       Recently, I have noticed that loading the new data on gbrowse_vbox
> seems unsuccessful. The apache error logs don't show anythings specific, but
> I do get Segmentation faults and "Use of uninitialized value in
> concatenation or string. (I do not know in what).
>
> 6.       I am just not able to see any of the Overview/Region/Detail panels
> on my screen. When I search for a tem, I sometimes get search results on the
> screen and sometimes just the Blue header that displays "The following 308
> regions match your request "  and then nothing below it in the tracks panel.
>
> 7.       I am able to see the whole page except for the tracks. I can rule
> out the possibility of bad data because It did load and I was able to
> visualize that same data once. I am just not able to load it up again and
> visualize it.
>
>
>
>
>
> Please help..
>
> Pushkala Jayaraman
>
> Programmer/Analyst
>
> Rat Genome Database
>
> Human and Molecular Genetics Center
>
> Medical College of Wisconsin
>
> Email: [hidden email] <mailto:[hidden email]>
>
> Work: 414-955-2229
>
> www.rgd.mcw.edu <http://www.rgd.mcw.edu>
>
>
>
>
> ------------------------------------------------------------------------------
> ThinkGeek and WIRED's GeekDad team up for the Ultimate
> GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
> lucky parental unit.  See the prize list and enter to win:
> http://p.sf.net/sfu/thinkgeek-promo
> _______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
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>
> --
> 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]>
>
>
>
>
>
>
> --
> 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]>
>
> ------------------------------------------------------------------------------
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Re: Gff3 files 'chromosome' feature

Jayaraman, Pushkala
In reply to this post by Scott Cain
I would like to ask one question regarding gff3 files esp. the 'chromosome' entry


Ideally should there be only one 'chromosome' feature for a gff3 file?

For eg.. if I had 1 gff3 file for each chromosome that had all the features pertaining to a gene (mrna, exon, cds, intron, pseudogene..etc)
And I had the chromosome feature in that file. Then,
Can I have multiple entries of 'chromosome' with
start = start of first contig
and
stop = stop of first contig
and then repeat this for the next contig..depending on the number of contigs that make up that chromosome?

Or must I only have one entry for 'chromosome' wherein I have the:
start = start of the first contig that makes up that chromosome
and
stop = stop of the last contig that makes up that chromosome?

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


-----Original Message-----
From: Scott Cain [mailto:[hidden email]]
Sent: Monday, June 21, 2010 11:47 AM
To: Jayaraman, Pushkala
Cc: Lincoln Stein; [hidden email]
Subject: Re: [Gmod-gbrowse] Gbrowse2 tracks not visible..possible bug?

Pushkala,

You need "Name=Chr15" in column nine of that first line; that is what
identifies it as being Chr15.

Scott


On Mon, Jun 21, 2010 at 12:42 PM, Jayaraman, Pushkala
<[hidden email]> wrote:

> Hello Lincoln,
>
> This is what I get:
>
>
>
> mysql> select * from name where name like 'chr%';
>
> +-------+--------+--------------+
>
> | id    | name   | display_name |
>
> +-------+--------+--------------+
>
> | 29168 | Chrm3  |            1 |
>
> | 29169 | Chrm3  |            1 |
>
> | 29172 | Chrm3  |            1 |
>
> |  2076 | Chrna2 |            1 |
>
> |  2078 | Chrna2 |            1 |
>
> |  2080 | Chrna2 |            1 |
>
> |  2082 | Chrna2 |            1 |
>
> |  2084 | Chrna2 |            1 |
>
> |  2086 | Chrna2 |            1 |
>
> |  2088 | Chrna2 |            1 |
>
> |  2089 | Chrna2 |            1 |
>
> +-------+--------+--------------+
>
> 11 rows in set (0.00 sec)
>
>
>
> Why am I not getting any of the chromosome names?
>
>
>
>
>
> When I do "head nameof_gff3_file.gff3" I get:
>
>
>
> Chr15   GenBank chromosome      24425085        28088033        .       +
>    .       ID=NW_047453;Alias=15;Dbxref=taxon:10116;Note=Rattus norvegicus
> chromosome 15 genomic cont
>
> ig%2C reference assembly (based on RGSC v3.4).,GENOME ANNOTATION REFSEQ:
> Features on this sequence have been produced for build 4 version 1 of the
> NCBI's genome annotation [see d
>
> ocumentation]. The DNA sequence is version 3.4 'November 2004 Update' of the
> Rat genome assembly,produced by the Baylor College of Medicine Human Genome
> Sequencing Center (BCM- H
>
> GSC) as part of the Rat Genome Sequencing Consortium (RGSC). This supersedes
> all prior versions of the Rat assembly (2.0,2.1,3.0,3.1 3.2 and 3.3) (see
> http://www.hgsc.bcm.tmc.edu
>
> /projects/rat/). ;chromosome=15;comment1=GENOME ANNOTATION REFSEQ: Features
> on this sequence have been produced for build 4 version 1 of the NCBI's
> genome annotation [see documen
>
> tation]. The DNA sequence is version 3.4 'November 2004 Update' of the Rat
> genome assembly%2C produced by the Baylor College of Medicine Human Genome
> Sequencing Center (BCM- HGSC
>
> ) as part of the Rat Genome Sequencing Consortium (RGSC). This supersedes
> all prior versions of the Rat assembly (2.0%2C 2.1%2C 3.0%2C 3.1 3.2 and
> 3.3) (see http://www.hgsc.bcm.tmc.edu/projects/rat/).
> ;date=03-JUL-2006;mol_type=genomic DNA;organism=Rattus
> norvegicus;strain=BN/SsNHsdMCW;
>
> Chr15   GenBank pseudogene      24427872        24428719        .
> -       .       ID=LOC498499;Dbxref=GeneID:498499;Note=Derived by automated
> computational analysis using gene prediction method: GNOMON. Supporting
> evidence includes similarity to: 98 ESTs%2C 6
> Proteins;gene=LOC498499;pseudo=_no_value;
>
>
>
>
>
> Which clearly shows the chromosome feature right on top.
>
>
>
> 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: Lincoln Stein [mailto:[hidden email]]
> Sent: Monday, June 21, 2010 11:33 AM
> To: Jayaraman, Pushkala
> Cc: [hidden email]
> Subject: Re: [Gmod-gbrowse] Gbrowse2 tracks not visible..possible bug?
>
>
>
> It sounds to me as though you are loading the data correctly. But is there
> any chance that you used -c inadvertently on one of the subsequent loads and
> inadvertently removed the chromosomes? The way to check is:
>
>
>
>  mysql> select * from name where name like 'chr%'
>
>
>
> Lincoln
>
> On Mon, Jun 21, 2010 at 12:19 PM, Jayaraman, Pushkala <[hidden email]>
> wrote:
>
> Hello Lincoln,
>
> Yes,
>
> The yeast, in-memory database is loading well. Also, the data that I had
> loaded into the mysql database about a month ago (before I updated gbrowse
> through svn) is also seems to be rendering tracks on my VirtualBox as well
> as the server(I create a dump of the dabatase that I used on the VBox and
> uploaded that same database on the server and it works well)..
>
>
>
> I am using a mysql database backend. This is how I load the data
>
>  bp_seqfeature_load.pl -a DBI::mysql -d
> "DBI:mysql:database=DBNAME;host=HOSTNAME" -c -f filename.gff3
>
>
>
> I do not use -c each time. But I seem to have to use it the first time after
> I newly create a DB. Else it complains about not finding the tables. So it
> gives out errors like 'cannot load data into .locationlist table or view
> does not exist'.
>
> But when I use the -c feature, it seems to load it in pretty well. After
> that, I do not have to use the -c feature when I am adding data into the
> database.
>
>
> As you can see in the above two attached pictures, both are feb by very
> similar conf files except for their name. I simply made a copy of the conf
> file and renamed one. the data source though, is different. i.e they are
> being fed from two different mysql databases.
>
> when the database has all the tracks then it seems to generate pictures, but
> when i only load one feature eg. qtl, then it doesnt show anything..
> This is what my conf file looks like:
>
> [GENERAL]
>
> database     = general
>
>
>
> autocomplete = 1
>
> search options = default +autocomplete +wildcard
>
>
>
> # turn on remote rendering-- see [TRACK DEFAULTS] for the hosts
>
> # and ports the rendering slaves run on.
>
> renderfarm    = 1
>
>
>
> # just the basic track dumper plugin was in before..now added new plugins
>
> plugins = TrackDumper Aligner BatchDumper Submitter OligoFinder FilterTest
> AttributeHiliter
>
>
>
> #balloon tips acknowledge:
>
> balloon tips = 1
>
>
>
> # list of tracks to turn on by default
>
> default features = miRNA_Track
>
>
>
> # size of the region
>
> max segment     = 1000000000
>
> default segment = 50000
>
>
>
> # examples to show in the introduction
>
> examples = Odz3
>
>
>
> # feature to show on startup
>
> initial landmark = Chr16
>
>
>
> #to generalise searches. the search results will include both gene and
> protein keywords and will not require specific Gene:xxx or protein:xxx it
> will search xxx through gene and protein in order of them appearing in the
> line just below.
>
> automatic classes = RGD Gene
>
>
>
> #init codes work like functions built into the code:
>
> init_code         = sub bring_bubble{
>
>                      ------some code--------
>
>                      --------more code------
>
> }
>
> ########################
>
> # databases being used #
>
> ########################
>
> [general:database]
>
> db_adaptor    = Bio::DB::SeqFeature::Store
>
> db_args       = -adaptor DBI::mysql
>
>               -dsn     DBI:mysql:database=DBNAME;host=HOSTNAME.hmgc.mcw.edu
>
>               -user    USERNAME
>
>               -pass    PASSWORD
>
> ########################
>
> # Default glyph settings
>
> ########################
>
> [TRACK DEFAULTS]
>
> database      = general
>
> glyph         = generic
>
> height        = 10
>
> bgcolor       = lightgrey
>
> fgcolor       = black
>
> font2color    = blue
>
> label density = 25
>
> bump density  = 100
>
>
>
> # where to link to when user clicks in detailed view
>
> link          = AUTO
>
>
>
> #################################
>
> # Individual Track glyph settings
>
> #################################
>
>
>
> [miRNA_Track]
>
> category      = GENOMIC FEATURES
>
> feature       = miRNA:miRBase
>
> glyph         = dot
>
> fgcolor       = blue
>
> bgcolor       = lightblue
>
> linewidth    = 2
>
> height       = 6
>
> label        = sub{
>
>                      my $feature=shift;
>
>                      my ($miRna)=$feature->display_name;
>
>                      return $miRna;
>
>               }
>
> key           = miRNAs
>
> link          = sub {
>
>                      my $feature=shift;
>
>                      my ($miRnaID)=$feature->load_id;
>
>                      return
> "http://microrna.sanger.ac.uk/cgi-bin/sequences/mirna_entry.pl?id=$miRnaID";
>
>               }
>
> balloon hover = sub {bring_bubble(shift)}
>
> balloon sticky = 1
>
> citation      = This track shows rat microRNAs (miRNAs) derived from the <a
> href="http://microrna.sanger.ac.uk/"> Sanger Institute\'s miRBase</a>.
> miRBase is the repository for microRNA data, incorporating the database and
> gene naming roles previously provided by the miRNA Registry. Hovering over a
> feature provides annotation including miRBase ID and source. Clicking on a
> feature or selecting the miRBase ID links to the miRBase miRNA Report pages.
>
>
>
> [miRNA_Track:overview]
>
> feature       = miRNA:miRBase
>
> glyph         = dot
>
> fgcolor       = blue
>
> bgcolor       = lightblue
>
> linewidth    = 2
>
> height       = 6
>
> label        = sub{
>
>                      my $feature=shift;
>
>                      my ($miRna)=$feature->display_name;
>
>                      return $miRna;
>
>               }
>
> key           = miRNAs Overview
>
> link          = sub {
>
>                      my $feature=shift;
>
>                      my ($miRnaID)=$feature->load_id;
>
>                      return
> "http://microrna.sanger.ac.uk/cgi-bin/sequences/mirna_entry.pl?id=$miRnaID";
>
>               }
>
> citation      = This track shows rat microRNAs (miRNAs) derived from the <a
> href="http://microrna.sanger.ac.uk/"> Sanger Institute\'s miRBase</a>.
> miRBase is the repository for microRNA data, incorporating the database and
> gene naming roles previously provided by the miRNA Registry. Hovering over a
> feature provides annotation including miRBase ID and source. Clicking on a
> feature or selecting the miRBase ID links to the miRBase miRNA Report pages.
>
>
>
> [QTLS]
>
> glyph        = saw_teeth
>
> category      = GENOMIC FEATURES
>
> feature       = QTL:RGD
>
> height       = 5
>
> linewidth     = 3
>
> bgcolor       = maroon
>
> fgcolor       = orange
>
> label        = sub{
>
>                      my $feature=shift;
>
>                      my ($qtlid)=$feature->load_id;
>
>                      my @qtlarr=split(/:/, $qtlid);
>
>                      return "QTL:$qtlarr[1]";
>
>               }
>
> description   = sub{
>
>                      my $feature=shift;
>
>                      my ($desc)=$feature->attributes('Dbxref');
>
>                      my @desc_arr=split(/:/, $desc);
>
>                      return "RGDID:".$desc_arr[1];
>
>
>
>               }
>
> link         = sub {
>
>                      my $feature=shift;
>
>                      my ($link)=$feature->attributes('Dbxref');
>
>                      if ($link=~/RGD:(\d+)/) {
>
>                             my $rgdid=$1;
>
>                             return
> "http://rgd.mcw.edu/objectSearch/qtlReport.jsp?rgd_id=$rgdid";
>
>                      }
>
>               }
>
> balloon hover  = sub {bring_bubble(shift)}
>
> balloon sticky = 1
>
> key           = RGD QTLs
>
> citation      = This track shows <a href="http://www.rgd.mcw.edu/qtls/"> RGD
> Rat Quantitative Trait Loci (QTL)</a>. In some cases the boundaries of the
> QTL have been estimated as explained in <a
> href="ftp://rgd.mcw.edu/pub/data_release/QTLS_README"> QTLs Readme file</a>.
> Hovering over a feature provides additional annotation including the name,
> symbol, LOD (where available), p-value (where available), mapping method,
> and RGD ID, which links to the RGD QTL report page. Clicking on a feature
> also links to its RGD report page.
>
>
>
> [PGA]
>
> category      = PGA
>
> feature       = PGA:ENU_BN PGA:ENU_FHH PGA:SB_F344
>
> glyph         = diamond
>
> bgcolor       = purple
>
> fgcolor       = pink
>
> key           = PGA
>
> balloon hover  = sub {bring_bubble(shift)}
>
> balloon sticky = 1
>
> select        = source 'SB_F344' 'ENU_FHH' 'ENU_BN'
>
> label         = sub {
>
>                   my $feature=shift;
>
>                   my ($pga_label)= $feature->display_name;
>
>                   return $pga_label
>
>                 }
>
> description   = sub {
>
>                   my $feature=shift;
>
>                   my ($pga_desc)= $feature->attributes("Id");
>
>                   return $pga_desc;
>
>                 }
>
> link           = sub {
>
>                   my $feature=shift;
>
>                   my ($pga_id)=$feature->attributes("Id");
>
>                   $pga_id=~s/RGD://;
>
>                   return
> "http://rgd.mcw.edu/tools/strains/strains_view.cgi?id=$pga_id";
>
>                   }
>
> citation      = This track includes the genomic locations of the <a
> href="http://pga.mcw.edu/"> PhysGen PGA</a> mutant strains developed using
> ENU mutagenesis or the Sleeping Beauty transposon strategy. Hovering over a
> feature provides additional annotation including the Gene Name, RGD Strain
> ID, Strain and Source (ENU_FHH, ENU_BN, SB_F344). Clicking on a feature or
> selecting the RGD Strain ID links to the strain report pages at RGD.
>
>
>
> [CNV]
>
> category     = ANNOTATED VARIANTS
>
> feature       = CNV:Hubrecht_Institute
>
> glyph        = span
>
> fgcolor       = sub {bring_cnv_color(shift)}
>
> bgcolor             = black
>
> font2color    = pink1
>
> linewidth     = 3
>
> height        = 5
>
> label       = sub{
>
>                      my $cnv_feat = shift;
>
>                      my ($cnvID)=$cnv_feat->attributes('Dbxref');
>
>                      return "$cnvID";
>
>
>
>               }
>
> description   = sub{
>
>                      my $cnv_feat = shift;
>
>                      my ($type)=$cnv_feat->attributes('type');
>
>                      return "TYPE:$type";
>
>
>
>               }
>
> balloon hover = sub {bring_bubble(shift)}
>
> balloon sticky= 1
>
> key           =CNVs
>
> link   = sub{
>
>                      my $cnv_feat = shift;
>
>                      my ($cnvID)=$cnv_feat->attributes('Dbxref');
>
>                      $cnvID =~s/cnv_//i;
>
>                      return
> "http://h094.niob.knaw.nl/RatCNVs/cgi-bin/cnv.pl?id=$cnvID";
>
>
>
>               }
>
> citation      = <a href="http://h094.niob.knaw.nl/RatCNVs/"> Copy Number
> Variants (CNVs)</a> identified in commonly used laboratory rat strains
> through combination of computational approaches and experimental analysis as
> published in Guryev et al.; Distribution and functional impact of DNA copy
> number variation in the rat. Nature Genetics 40, 538 - 545 (2008). Hovering
> over a feature provides additional annotation including the CNV ID, Strain,
> Method, Type, and Source. Clicking on a feature or selecting the CNV ID
> links to the Hubrecht Institute\'s CNV pages.<br />CNVs are colored based on
> type as following:<br /><table
> border="1"><tr><th>Type</th><th>Color</th></tr><tr><td>Collapse</td><td>Purple</td></tr><tr><td>Overprediction</td><td>Yellow</td></tr><tr><td>Loss</td><td>Blue</td></tr><tr><td>Loss+Collapse</td><td>Dark
> blue</td></tr><tr><td>Loss+Overprediction</td><td>Light
> blue</td></tr><tr><td>Gain</td><td>Red</td></tr><tr><td>Gain+Collapse</td><td>Dark
> red</td></tr><tr><td>Gain+Overprediction</td><td>Light red</td></tr></table>
>
>
>
>
>
> 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: Lincoln Stein [mailto:[hidden email]]
>
> Sent: Monday, June 21, 2010 10:38 AM
> To: Jayaraman, Pushkala
> Cc: [hidden email]
> Subject: Re: [Gmod-gbrowse] Gbrowse2 tracks not visible..possible bug?
>
>
>
> Hi Pushkala,
>
>
>
> I'm afraid I'll need more information. Is the in-memory Yeast database
> working on the development server? If it is, it probably rules out a
> software problem. What database backend are you using, and how do you load
> it? What operating system are you using?
>
>
>
> When you are unable to upload the "new" data on the Virtual Box, what do you
> mean by "new"?
>
>
>
> Lincoln
>
>
>
> On Mon, Jun 21, 2010 at 8:11 AM, Jayaraman, Pushkala <[hidden email]>
> wrote:
>
> Hello,
>
> I seem to be having problems with Gbrowse showing tracks on screen. This is
> slightly complicated:
>
> 1.       I have set up a fully functional gbrowse2 v2.03 on my Virtual Box
> with saved snapshots.
>
> 2.       I upgraded to Gbrowse 2.08 from SVN stable branch last month and
> set up that on my virtual Box. That seemed to be working too.
>
> 3.       I then had Gbrowse2 installed on our development server. This is
> where problems began,
>
> When I tried to load the exact data that I had displaying successfully on my
> Virtual Box(lets call it Gbrowse_vbox), onto the gbrowse on the server (lets
> call it Gbrowse_serv)I saw that the Gbrowse_serv could not seem to display
> any of the data.
>
> 4.       Dumping the sql database from the vbox onto the server mysql seemed
> to get it to work.
>
> 5.       Recently, I have noticed that loading the new data on gbrowse_vbox
> seems unsuccessful. The apache error logs don't show anythings specific, but
> I do get Segmentation faults and "Use of uninitialized value in
> concatenation or string. (I do not know in what).
>
> 6.       I am just not able to see any of the Overview/Region/Detail panels
> on my screen. When I search for a tem, I sometimes get search results on the
> screen and sometimes just the Blue header that displays "The following 308
> regions match your request "  and then nothing below it in the tracks panel.
>
> 7.       I am able to see the whole page except for the tracks. I can rule
> out the possibility of bad data because It did load and I was able to
> visualize that same data once. I am just not able to load it up again and
> visualize it.
>
>
>
>
>
> Please help..
>
> Pushkala Jayaraman
>
> Programmer/Analyst
>
> Rat Genome Database
>
> Human and Molecular Genetics Center
>
> Medical College of Wisconsin
>
> Email: [hidden email] <mailto:[hidden email]>
>
> Work: 414-955-2229
>
> www.rgd.mcw.edu <http://www.rgd.mcw.edu>
>
>
>
>
> ------------------------------------------------------------------------------
> ThinkGeek and WIRED's GeekDad team up for the Ultimate
> GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
> lucky parental unit.  See the prize list and enter to win:
> http://p.sf.net/sfu/thinkgeek-promo
> _______________________________________________
> 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]>
>
>
>
>
>
>
> --
> 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]>
>
> ------------------------------------------------------------------------------
> ThinkGeek and WIRED's GeekDad team up for the Ultimate
> GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
> lucky parental unit.  See the prize list and enter to win:
> http://p.sf.net/sfu/thinkgeek-promo
> _______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>
>



--
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Scott Cain, Ph. D.                                   scott at scottcain dot net
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Re: Gff3 files 'chromosome' feature

Jayaraman, Pushkala

The reason I ask is because,

I have one gff3 file for each chromosome.

Each gff3 file is made up of data present in multiple contigs(ncbi only gives its gff files with contig information and we need to convert that into genomic information using contig-to-chromosome mapping)

 

Although each of my Chromosome entries have a ‘Name=Chr16’ their starts and stops include the start and stop of each contig that is a part of that chromosome. I guess because of this.. only the first entry of ‘chromosome’ is being recognized. I am not able to drag over the entire chromosome in the overview panel..

The picture to the right shows this behavior.

 

The picture to the left shows gbrowse working with the same data, when the database was loaded in May.  

 

I hope I have managed to convey my question clearly..

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

 

 

-----Original Message-----
From: Jayaraman, Pushkala [mailto:[hidden email]]
Sent: Monday, June 21, 2010 1:37 PM
To: [hidden email]
Subject: Re: [Gmod-gbrowse] Gff3 files 'chromosome' feature

 

I would like to ask one question regarding gff3 files esp. the 'chromosome' entry

 

 

Ideally should there be only one 'chromosome' feature for a gff3 file?

 

For eg.. if I had 1 gff3 file for each chromosome that had all the features pertaining to a gene (mrna, exon, cds, intron, pseudogene..etc)

And I had the chromosome feature in that file. Then,

Can I have multiple entries of 'chromosome' with

start = start of first contig

and

stop = stop of first contig

and then repeat this for the next contig..depending on the number of contigs that make up that chromosome?

 

Or must I only have one entry for 'chromosome' wherein I have the:

start = start of the first contig that makes up that chromosome

and

stop = stop of the last contig that makes up that chromosome?

 

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

 

 

-----Original Message-----

From: Scott Cain [mailto:[hidden email]]

Sent: Monday, June 21, 2010 11:47 AM

To: Jayaraman, Pushkala

Cc: Lincoln Stein; [hidden email]

Subject: Re: [Gmod-gbrowse] Gbrowse2 tracks not visible..possible bug?

 

Pushkala,

 

You need "Name=Chr15" in column nine of that first line; that is what

identifies it as being Chr15.

 

Scott

 

 

On Mon, Jun 21, 2010 at 12:42 PM, Jayaraman, Pushkala

<[hidden email]> wrote:

> Hello Lincoln,

> 

> This is what I get:

> 

> 

> 

> mysql> select * from name where name like 'chr%';

> 

> +-------+--------+--------------+

> 

> | id    | name   | display_name |

> 

> +-------+--------+--------------+

> 

> | 29168 | Chrm3  |            1 |

> 

> | 29169 | Chrm3  |            1 |

> 

> | 29172 | Chrm3  |            1 |

> 

> |  2076 | Chrna2 |            1 |

> 

> |  2078 | Chrna2 |            1 |

> 

> |  2080 | Chrna2 |            1 |

> 

> |  2082 | Chrna2 |            1 |

> 

> |  2084 | Chrna2 |            1 |

> 

> |  2086 | Chrna2 |            1 |

> 

> |  2088 | Chrna2 |            1 |

> 

> |  2089 | Chrna2 |            1 |

> 

> +-------+--------+--------------+

> 

> 11 rows in set (0.00 sec)

> 

> 

> 

> Why am I not getting any of the chromosome names?

> 

> 

> 

> 

> 

> When I do "head nameof_gff3_file.gff3" I get:

> 

> 

> 

> Chr15   GenBank chromosome      24425085        28088033        .       +

>    .       ID=NW_047453;Alias=15;Dbxref=taxon:10116;Note=Rattus norvegicus

> chromosome 15 genomic cont

> 

> ig%2C reference assembly (based on RGSC v3.4).,GENOME ANNOTATION REFSEQ:

> Features on this sequence have been produced for build 4 version 1 of the

> NCBI's genome annotation [see d

> 

> ocumentation]. The DNA sequence is version 3.4 'November 2004 Update' of the

> Rat genome assembly,produced by the Baylor College of Medicine Human Genome

> Sequencing Center (BCM- H

> 

> GSC) as part of the Rat Genome Sequencing Consortium (RGSC). This supersedes

> all prior versions of the Rat assembly (2.0,2.1,3.0,3.1 3.2 and 3.3) (see

> http://www.hgsc.bcm.tmc.edu

> 

> /projects/rat/). ;chromosome=15;comment1=GENOME ANNOTATION REFSEQ: Features

> on this sequence have been produced for build 4 version 1 of the NCBI's

> genome annotation [see documen

> 

> tation]. The DNA sequence is version 3.4 'November 2004 Update' of the Rat

> genome assembly%2C produced by the Baylor College of Medicine Human Genome

> Sequencing Center (BCM- HGSC

> 

> ) as part of the Rat Genome Sequencing Consortium (RGSC). This supersedes

> all prior versions of the Rat assembly (2.0%2C 2.1%2C 3.0%2C 3.1 3.2 and

> 3.3) (see http://www.hgsc.bcm.tmc.edu/projects/rat/).

> ;date=03-JUL-2006;mol_type=genomic DNA;organism=Rattus

> norvegicus;strain=BN/SsNHsdMCW;

> 

> Chr15   GenBank pseudogene      24427872        24428719        .

> -       .       ID=LOC498499;Dbxref=GeneID:498499;Note=Derived by automated

> computational analysis using gene prediction method: GNOMON. Supporting

> evidence includes similarity to: 98 ESTs%2C 6

> Proteins;gene=LOC498499;pseudo=_no_value;

> 

> 

> 

> 

> 

> Which clearly shows the chromosome feature right on top.

> 

> 

> 

> 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: Lincoln Stein [mailto:[hidden email]]

> Sent: Monday, June 21, 2010 11:33 AM

> To: Jayaraman, Pushkala

> Cc: [hidden email]

> Subject: Re: [Gmod-gbrowse] Gbrowse2 tracks not visible..possible bug?

> 

> 

> 

> It sounds to me as though you are loading the data correctly. But is there

> any chance that you used -c inadvertently on one of the subsequent loads and

> inadvertently removed the chromosomes? The way to check is:

> 

> 

> 

>  mysql> select * from name where name like 'chr%'

> 

> 

> 

> Lincoln

> 

> On Mon, Jun 21, 2010 at 12:19 PM, Jayaraman, Pushkala <[hidden email]>

> wrote:

> 

> Hello Lincoln,

> 

> Yes,

> 

> The yeast, in-memory database is loading well. Also, the data that I had

> loaded into the mysql database about a month ago (before I updated gbrowse

> through svn) is also seems to be rendering tracks on my VirtualBox as well

> as the server(I create a dump of the dabatase that I used on the VBox and

> uploaded that same database on the server and it works well)..

> 

> 

> 

> I am using a mysql database backend. This is how I load the data

> 

>  bp_seqfeature_load.pl -a DBI::mysql -d

> "DBI:mysql:database=DBNAME;host=HOSTNAME" -c -f filename.gff3

> 

> 

> 

> I do not use -c each time. But I seem to have to use it the first time after

> I newly create a DB. Else it complains about not finding the tables. So it

> gives out errors like 'cannot load data into .locationlist table or view

> does not exist'.

> 

> But when I use the -c feature, it seems to load it in pretty well. After

> that, I do not have to use the -c feature when I am adding data into the

> database.

> 

> 

> As you can see in the above two attached pictures, both are feb by very

> similar conf files except for their name. I simply made a copy of the conf

> file and renamed one. the data source though, is different. i.e they are

> being fed from two different mysql databases.

> 

> when the database has all the tracks then it seems to generate pictures, but

> when i only load one feature eg. qtl, then it doesnt show anything..

> This is what my conf file looks like:

> 

> [GENERAL]

> 

> database     = general

> 

> 

> 

> autocomplete = 1

> 

> search options = default +autocomplete +wildcard

> 

> 

> 

> # turn on remote rendering-- see [TRACK DEFAULTS] for the hosts

> 

> # and ports the rendering slaves run on.

> 

> renderfarm    = 1

> 

> 

> 

> # just the basic track dumper plugin was in before..now added new plugins

> 

> plugins = TrackDumper Aligner BatchDumper Submitter OligoFinder FilterTest

> AttributeHiliter

> 

> 

> 

> #balloon tips acknowledge:

> 

> balloon tips = 1

> 

> 

> 

> # list of tracks to turn on by default

> 

> default features = miRNA_Track

> 

> 

> 

> # size of the region

> 

> max segment     = 1000000000

> 

> default segment = 50000

> 

> 

> 

> # examples to show in the introduction

> 

> examples = Odz3

> 

> 

> 

> # feature to show on startup

> 

> initial landmark = Chr16

> 

> 

> 

> #to generalise searches. the search results will include both gene and

> protein keywords and will not require specific Gene:xxx or protein:xxx it

> will search xxx through gene and protein in order of them appearing in the

> line just below.

> 

> automatic classes = RGD Gene

> 

> 

> 

> #init codes work like functions built into the code:

> 

> init_code         = sub bring_bubble{

> 

>                      ------some code--------

> 

>                      --------more code------

> 

> }

> 

> ########################

> 

> # databases being used #

> 

> ########################

> 

> [general:database]

> 

> db_adaptor    = Bio::DB::SeqFeature::Store

> 

> db_args       = -adaptor DBI::mysql

> 

>               -dsn     DBI:mysql:database=DBNAME;host=HOSTNAME.hmgc.mcw.edu

> 

>               -user    USERNAME

> 

>               -pass    PASSWORD

> 

> ########################

> 

> # Default glyph settings

> 

> ########################

> 

> [TRACK DEFAULTS]

> 

> database      = general

> 

> glyph         = generic

> 

> height        = 10

> 

> bgcolor       = lightgrey

> 

> fgcolor       = black

> 

> font2color    = blue

> 

> label density = 25

> 

> bump density  = 100

> 

> 

> 

> # where to link to when user clicks in detailed view

> 

> link          = AUTO

> 

> 

> 

> #################################

> 

> # Individual Track glyph settings

> 

> #################################

> 

> 

> 

> [miRNA_Track]

> 

> category      = GENOMIC FEATURES

> 

> feature       = miRNA:miRBase

> 

> glyph         = dot

> 

> fgcolor       = blue

> 

> bgcolor       = lightblue

> 

> linewidth    = 2

> 

> height       = 6

> 

> label        = sub{

> 

>                      my $feature=shift;

> 

>                      my ($miRna)=$feature->display_name;

> 

>                      return $miRna;

> 

>               }

> 

> key           = miRNAs

> 

> link          = sub {

> 

>                      my $feature=shift;

> 

>                      my ($miRnaID)=$feature->load_id;

> 

>                      return

> "http://microrna.sanger.ac.uk/cgi-bin/sequences/mirna_entry.pl?id=$miRnaID";

> 

>               }

> 

> balloon hover = sub {bring_bubble(shift)}

> 

> balloon sticky = 1

> 

> citation      = This track shows rat microRNAs (miRNAs) derived from the <a

> href="http://microrna.sanger.ac.uk/"> Sanger Institute\'s miRBase</a>.

> miRBase is the repository for microRNA data, incorporating the database and

> gene naming roles previously provided by the miRNA Registry. Hovering over a

> feature provides annotation including miRBase ID and source. Clicking on a

> feature or selecting the miRBase ID links to the miRBase miRNA Report pages.

> 

> 

> 

> [miRNA_Track:overview]

> 

> feature       = miRNA:miRBase

> 

> glyph         = dot

> 

> fgcolor       = blue

> 

> bgcolor       = lightblue

> 

> linewidth    = 2

> 

> height       = 6

> 

> label        = sub{

> 

>                      my $feature=shift;

> 

>                      my ($miRna)=$feature->display_name;

> 

>                      return $miRna;

> 

>               }

> 

> key           = miRNAs Overview

> 

> link          = sub {

> 

>                      my $feature=shift;

> 

>                      my ($miRnaID)=$feature->load_id;

> 

>                      return

> "http://microrna.sanger.ac.uk/cgi-bin/sequences/mirna_entry.pl?id=$miRnaID";

> 

>               }

> 

> citation      = This track shows rat microRNAs (miRNAs) derived from the <a

> href="http://microrna.sanger.ac.uk/"> Sanger Institute\'s miRBase</a>.

> miRBase is the repository for microRNA data, incorporating the database and

> gene naming roles previously provided by the miRNA Registry. Hovering over a

> feature provides annotation including miRBase ID and source. Clicking on a

> feature or selecting the miRBase ID links to the miRBase miRNA Report pages.

> 

> 

> 

> [QTLS]

> 

> glyph        = saw_teeth

> 

> category      = GENOMIC FEATURES

> 

> feature       = QTL:RGD

> 

> height       = 5

> 

> linewidth     = 3

> 

> bgcolor       = maroon

> 

> fgcolor       = orange

> 

> label        = sub{

> 

>                      my $feature=shift;

> 

>                      my ($qtlid)=$feature->load_id;

> 

>                      my @qtlarr=split(/:/, $qtlid);

> 

>                      return "QTL:$qtlarr[1]";

> 

>               }

> 

> description   = sub{

> 

>                      my $feature=shift;

> 

>                      my ($desc)=$feature->attributes('Dbxref');

> 

>                      my @desc_arr=split(/:/, $desc);

> 

>                      return "RGDID:".$desc_arr[1];

> 

> 

> 

>               }

> 

> link         = sub {

> 

>                      my $feature=shift;

> 

>                      my ($link)=$feature->attributes('Dbxref');

> 

>                      if ($link=~/RGD:(\d+)/) {

> 

>                             my $rgdid=$1;

> 

>                             return

> "http://rgd.mcw.edu/objectSearch/qtlReport.jsp?rgd_id=$rgdid";

> 

>                      }

> 

>               }

> 

> balloon hover  = sub {bring_bubble(shift)}

> 

> balloon sticky = 1

> 

> key           = RGD QTLs

> 

> citation      = This track shows <a href="http://www.rgd.mcw.edu/qtls/"> RGD

> Rat Quantitative Trait Loci (QTL)</a>. In some cases the boundaries of the

> QTL have been estimated as explained in <a

> href="ftp://rgd.mcw.edu/pub/data_release/QTLS_README"> QTLs Readme file</a>.

> Hovering over a feature provides additional annotation including the name,

> symbol, LOD (where available), p-value (where available), mapping method,

> and RGD ID, which links to the RGD QTL report page. Clicking on a feature

> also links to its RGD report page.

> 

> 

> 

> [PGA]

> 

> category      = PGA

> 

> feature       = PGA:ENU_BN PGA:ENU_FHH PGA:SB_F344

> 

> glyph         = diamond

> 

> bgcolor       = purple

> 

> fgcolor       = pink

> 

> key           = PGA

> 

> balloon hover  = sub {bring_bubble(shift)}

> 

> balloon sticky = 1

> 

> select        = source 'SB_F344' 'ENU_FHH' 'ENU_BN'

> 

> label         = sub {

> 

>                   my $feature=shift;

> 

>                   my ($pga_label)= $feature->display_name;

> 

>                   return $pga_label

> 

>                 }

> 

> description   = sub {

> 

>                   my $feature=shift;

> 

>                   my ($pga_desc)= $feature->attributes("Id");

> 

>                   return $pga_desc;

> 

>                 }

> 

> link           = sub {

> 

>                   my $feature=shift;

> 

>                   my ($pga_id)=$feature->attributes("Id");

> 

>                   $pga_id=~s/RGD://;

> 

>                   return

> "http://rgd.mcw.edu/tools/strains/strains_view.cgi?id=$pga_id";

> 

>                   }

> 

> citation      = This track includes the genomic locations of the <a

> href="http://pga.mcw.edu/"> PhysGen PGA</a> mutant strains developed using

> ENU mutagenesis or the Sleeping Beauty transposon strategy. Hovering over a

> feature provides additional annotation including the Gene Name, RGD Strain

> ID, Strain and Source (ENU_FHH, ENU_BN, SB_F344). Clicking on a feature or

> selecting the RGD Strain ID links to the strain report pages at RGD.

> 

> 

> 

> [CNV]

> 

> category     = ANNOTATED VARIANTS

> 

> feature       = CNV:Hubrecht_Institute

> 

> glyph        = span

> 

> fgcolor       = sub {bring_cnv_color(shift)}

> 

> bgcolor             = black

> 

> font2color    = pink1

> 

> linewidth     = 3

> 

> height        = 5

> 

> label       = sub{

> 

>                      my $cnv_feat = shift;

> 

>                      my ($cnvID)=$cnv_feat->attributes('Dbxref');

> 

>                      return "$cnvID";

> 

> 

> 

>               }

> 

> description   = sub{

> 

>                      my $cnv_feat = shift;

> 

>                      my ($type)=$cnv_feat->attributes('type');

> 

>                      return "TYPE:$type";

> 

> 

> 

>               }

> 

> balloon hover = sub {bring_bubble(shift)}

> 

> balloon sticky= 1

> 

> key           =CNVs

> 

> link   = sub{

> 

>                      my $cnv_feat = shift;

> 

>                      my ($cnvID)=$cnv_feat->attributes('Dbxref');

> 

>                      $cnvID =~s/cnv_//i;

> 

>                      return

> "http://h094.niob.knaw.nl/RatCNVs/cgi-bin/cnv.pl?id=$cnvID";

> 

> 

> 

>               }

> 

> citation      = <a href="http://h094.niob.knaw.nl/RatCNVs/"> Copy Number

> Variants (CNVs)</a> identified in commonly used laboratory rat strains

> through combination of computational approaches and experimental analysis as

> published in Guryev et al.; Distribution and functional impact of DNA copy

> number variation in the rat. Nature Genetics 40, 538 - 545 (2008). Hovering

> over a feature provides additional annotation including the CNV ID, Strain,

> Method, Type, and Source. Clicking on a feature or selecting the CNV ID

> links to the Hubrecht Institute\'s CNV pages.<br />CNVs are colored based on

> type as following:<br /><table

> border="1"><tr><th>Type</th><th>Color</th></tr><tr><td>Collapse</td><td>Purple</td></tr><tr><td>Overprediction</td><td>Yellow</td></tr><tr><td>Loss</td><td>Blue</td></tr><tr><td>Loss+Collapse</td><td>Dark

> blue</td></tr><tr><td>Loss+Overprediction</td><td>Light

> blue</td></tr><tr><td>Gain</td><td>Red</td></tr><tr><td>Gain+Collapse</td><td>Dark

> red</td></tr><tr><td>Gain+Overprediction</td><td>Light red</td></tr></table>

> 

> 

> 

> 

> 

> 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: Lincoln Stein [mailto:[hidden email]]

> 

> Sent: Monday, June 21, 2010 10:38 AM

> To: Jayaraman, Pushkala

> Cc: [hidden email]

> Subject: Re: [Gmod-gbrowse] Gbrowse2 tracks not visible..possible bug?

> 

> 

> 

> Hi Pushkala,

> 

> 

> 

> I'm afraid I'll need more information. Is the in-memory Yeast database

> working on the development server? If it is, it probably rules out a

> software problem. What database backend are you using, and how do you load

> it? What operating system are you using?

> 

> 

> 

> When you are unable to upload the "new" data on the Virtual Box, what do you

> mean by "new"?

> 

> 

> 

> Lincoln

> 

> 

> 

> On Mon, Jun 21, 2010 at 8:11 AM, Jayaraman, Pushkala <[hidden email]>

> wrote:

> 

> Hello,

> 

> I seem to be having problems with Gbrowse showing tracks on screen. This is

> slightly complicated:

> 

> 1.       I have set up a fully functional gbrowse2 v2.03 on my Virtual Box

> with saved snapshots.

> 

> 2.       I upgraded to Gbrowse 2.08 from SVN stable branch last month and

> set up that on my virtual Box. That seemed to be working too.

> 

> 3.       I then had Gbrowse2 installed on our development server. This is

> where problems began,

> 

> When I tried to load the exact data that I had displaying successfully on my

> Virtual Box(lets call it Gbrowse_vbox), onto the gbrowse on the server (lets

> call it Gbrowse_serv)I saw that the Gbrowse_serv could not seem to display

> any of the data.

> 

> 4.       Dumping the sql database from the vbox onto the server mysql seemed

> to get it to work.

> 

> 5.       Recently, I have noticed that loading the new data on gbrowse_vbox

> seems unsuccessful. The apache error logs don't show anythings specific, but

> I do get Segmentation faults and "Use of uninitialized value in

> concatenation or string. (I do not know in what).

> 

> 6.       I am just not able to see any of the Overview/Region/Detail panels

> on my screen. When I search for a tem, I sometimes get search results on the

> screen and sometimes just the Blue header that displays "The following 308

> regions match your request "  and then nothing below it in the tracks panel.

> 

> 7.       I am able to see the whole page except for the tracks. I can rule

> out the possibility of bad data because It did load and I was able to

> visualize that same data once. I am just not able to load it up again and

> visualize it.

> 

> 

> 

> 

> 

> Please help..

> 

> Pushkala Jayaraman

> 

> Programmer/Analyst

> 

> Rat Genome Database

> 

> Human and Molecular Genetics Center

> 

> Medical College of Wisconsin

> 

> Email: [hidden email] <mailto:[hidden email]>

> 

> Work: 414-955-2229

> 

> www.rgd.mcw.edu <http://www.rgd.mcw.edu>

> 

> 

> 

> 

> ------------------------------------------------------------------------------

> ThinkGeek and WIRED's GeekDad team up for the Ultimate

> GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the

> lucky parental unit.  See the prize list and enter to win:

> http://p.sf.net/sfu/thinkgeek-promo

> _______________________________________________

> 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]>

> 

> 

> 

> 

> 

> 

> --

> 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]>

> 

> ------------------------------------------------------------------------------

> ThinkGeek and WIRED's GeekDad team up for the Ultimate

> GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the

> lucky parental unit.  See the prize list and enter to win:

> http://p.sf.net/sfu/thinkgeek-promo

> _______________________________________________

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> [hidden email]

> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

> 

> 

 

 

 

--

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

Scott Cain, Ph. D.                                   scott at scottcain dot net

GMOD Coordinator (http://gmod.org/)                     216-392-3087

Ontario Institute for Cancer Research

 

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Re: Gff3 files 'chromosome' feature

Scott Cain
Hi Pushkala,

I think I understand: you have multiple gff lines for each chromosome
that correspond to the individual contigs, right?  And each of these
has "Name=Chr#"?  You can't do that; you need to have one and one one
gff line for each chromosome (reference sequence).

Scott

On Monday, June 21, 2010, Jayaraman, Pushkala <[hidden email]> wrote:

>
>
>
>
>
>
>
>
>
>
>
>
>
>
> The reason I ask is because,
>
> I have one gff3 file for each chromosome.
>
> Each gff3 file is made up of data present in multiple
> contigs(ncbi only gives its gff files with contig information and we need to
> convert that into genomic information using contig-to-chromosome mapping)
>
>
>
> Although each of my Chromosome entries have a ‘Name=Chr16’
> their starts and stops include the start and stop of each contig that is a part
> of that chromosome. I guess because of this.. only the first entry of ‘chromosome’
> is being recognized. I am not able to drag over the entire chromosome in the
> overview panel..
>
> The picture to the right shows this behavior.
>
>
>
> The picture to the left shows gbrowse working with the
> same data, when the database was loaded in May.
>
>
>
>
>
> I hope I have managed to convey my question clearly..
>
> 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
>
>
>
>
>
> -----Original Message-----
> From: Jayaraman, Pushkala [mailto:[hidden email]]
> Sent: Monday, June 21, 2010 1:37 PM
> To: [hidden email]
> Subject: Re: [Gmod-gbrowse] Gff3 files 'chromosome' feature
>
>
>
> I would like to ask one question regarding gff3 files
> esp. the 'chromosome' entry
>
>
>
>
>
> Ideally should there be only one 'chromosome' feature for
> a gff3 file?
>
>
>
> For eg.. if I had 1 gff3 file for each chromosome that
> had all the features pertaining to a gene (mrna, exon, cds, intron,
> pseudogene..etc)
>
> And I had the chromosome feature in that file. Then,
>
> Can I have multiple entries of 'chromosome' with
>
> start = start of first contig
>
> and
>
> stop = stop of first contig
>
> and then repeat this for the next contig..depending on
> the number of contigs that make up that chromosome?
>
>
>
> Or must I only have one entry for 'chromosome' wherein I
> have the:
>
> start = start of the first contig that makes up that
> chromosome
>
> and
>
> stop = stop of the last contig that makes up that
> chromosome?
>
>
>
> 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
>
>
>
>
>
> -----Original Message-----
>
> From: Scott Cain [mailto:[hidden email]]
>
> Sent: Monday, June 21, 2010 11:47 AM
>
> To: Jayaraman, Pushkala
>
> Cc: Lincoln Stein; [hidden email]
>
> Subject: Re: [Gmod-gbrowse] Gbrowse2 tracks not
> visible..possible bug?
>
>
>
> Pushkala,
>
>
>
> You need "Name=Chr15" in column nine of that
> first line; that is what
>
> identifies it as being Chr15.
>
>
>
> Scott
>
>
>
>
>
> On Mon, Jun 21, 2010 at 12:42 PM, Jayaraman, Pushkala
>
> <[hidden email]> wrote:
>
>> Hello Lincoln,
>
>>
>
>> This is what I get:
>
>>
>
>>
>
>>
>
>> mysql> select * from name where name like 'chr%';
>
>>
>
>> +-------+--------+--------------+
>
>>
>
>> | id    | name   |
> display_name |
>
>>
>
>> +-------+--------+--------------+
>
>>
>
>> | 29168 | Chrm3
> |            1 |
>
>>
>
>> | 29169 | Chrm3
> |            1 |
>
>>
>
>> | 29172 | Chrm3
> |            1 |
>
>>
>
>> |  2076 | Chrna2
> |            1 |
>
>>
>
>> |  2078 | Chrna2
> |            1 |
>
>>
>
>> |  2080 | Chrna2
> |            1 |
>
>>
>
>> |  2082 | Chrna2
> |            1 |
>
>>
>
>> |  2084 | Chrna2
> |            1 |
>
>>
>
>> |  2086 | Chrna2
> |            1 |
>
>>
>
>> |  2088 | Chrna2
> |            1 |
>
>>
>
>> |  2089 | Chrna2
> |            1 |
>
>>
>
>> +-------+--------+--------------+
>
>>
>
>> 11 rows in set (0.00 sec)
>
>>
>
>>
>
>>
>
>> Why am I not getting any of the chromosome names?
>
>>
>
>>
>
>>
>
>>
>
>>
>
>> When I do "head nameof_gff3_file.gff3" I
> get:
>
>>
>
>>
>
>>
>
>> Chr15   GenBank
> chromosome
> 24425085
> 28088033
> .       +
>
>>
>    .
> ID=NW_047453;Alias=15;Dbxref=taxon:10116;Note=Rattus norvegicus
>
>> chromosome 15 genomic cont
>
>>
>
>> ig%2C reference assembly (based on RGSC
> v3.4).,GENOME ANNOTATION REFSEQ:
>
>> Features on this sequence have been produced for
> build 4 version 1 of the
>
>> NCBI's genome annotation [see d
>
>>
>
>> ocumentation]. The DNA sequence is version 3.4
> 'November 2004 Update' of the
>
>> Rat genome assembly,produced by the Baylor College
> of Medicine Human Genome
>
>> Sequencing Center (BCM- H
>
>>
>
>> GSC) as part of the Rat Genome Sequencing Consortium
> (RGSC). This supersedes
>
>> all prior versions of the Rat assembly
> (2.0,2.1,3.0,3.1 3.2 and 3.3) (see
>
>
>
>
>
>
>

--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

------------------------------------------------------------------------------
ThinkGeek and WIRED's GeekDad team up for the Ultimate
GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
lucky parental unit.  See the prize list and enter to win:
http://p.sf.net/sfu/thinkgeek-promo
_______________________________________________
Gmod-gbrowse mailing list
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Reply | Threaded
Open this post in threaded view
|

Re: Gff3 files 'chromosome' feature

Jayaraman, Pushkala
Yes exactly...
:(

Thanks Scott... Could I ask how else do other groups such as PlasmoDB/WormBase etc.. handle the problem of Overlapping contigs.. Have you come across such a problem in the gff3 file?

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


-----Original Message-----
From: Scott Cain [mailto:[hidden email]]
Sent: Monday, June 21, 2010 2:26 PM
To: Jayaraman, Pushkala
Cc: [hidden email]
Subject: Re: [Gmod-gbrowse] Gff3 files 'chromosome' feature

Hi Pushkala,

I think I understand: you have multiple gff lines for each chromosome
that correspond to the individual contigs, right?  And each of these
has "Name=Chr#"?  You can't do that; you need to have one and one one
gff line for each chromosome (reference sequence).

Scott

On Monday, June 21, 2010, Jayaraman, Pushkala <[hidden email]> wrote:

>
>
>
>
>
>
>
>
>
>
>
>
>
>
> The reason I ask is because,
>
> I have one gff3 file for each chromosome.
>
> Each gff3 file is made up of data present in multiple
> contigs(ncbi only gives its gff files with contig information and we need to
> convert that into genomic information using contig-to-chromosome mapping)
>
>
>
> Although each of my Chromosome entries have a 'Name=Chr16'
> their starts and stops include the start and stop of each contig that is a part
> of that chromosome. I guess because of this.. only the first entry of 'chromosome'
> is being recognized. I am not able to drag over the entire chromosome in the
> overview panel..
>
> The picture to the right shows this behavior.
>
>
>
> The picture to the left shows gbrowse working with the
> same data, when the database was loaded in May.
>
>
>
>
>
> I hope I have managed to convey my question clearly..
>
> 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
>
>
>
>
>
> -----Original Message-----
> From: Jayaraman, Pushkala [mailto:[hidden email]]
> Sent: Monday, June 21, 2010 1:37 PM
> To: [hidden email]
> Subject: Re: [Gmod-gbrowse] Gff3 files 'chromosome' feature
>
>
>
> I would like to ask one question regarding gff3 files
> esp. the 'chromosome' entry
>
>
>
>
>
> Ideally should there be only one 'chromosome' feature for
> a gff3 file?
>
>
>
> For eg.. if I had 1 gff3 file for each chromosome that
> had all the features pertaining to a gene (mrna, exon, cds, intron,
> pseudogene..etc)
>
> And I had the chromosome feature in that file. Then,
>
> Can I have multiple entries of 'chromosome' with
>
> start = start of first contig
>
> and
>
> stop = stop of first contig
>
> and then repeat this for the next contig..depending on
> the number of contigs that make up that chromosome?
>
>
>
> Or must I only have one entry for 'chromosome' wherein I
> have the:
>
> start = start of the first contig that makes up that
> chromosome
>
> and
>
> stop = stop of the last contig that makes up that
> chromosome?
>
>
>
> 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
>
>
>
>
>
> -----Original Message-----
>
> From: Scott Cain [mailto:[hidden email]]
>
> Sent: Monday, June 21, 2010 11:47 AM
>
> To: Jayaraman, Pushkala
>
> Cc: Lincoln Stein; [hidden email]
>
> Subject: Re: [Gmod-gbrowse] Gbrowse2 tracks not
> visible..possible bug?
>
>
>
> Pushkala,
>
>
>
> You need "Name=Chr15" in column nine of that
> first line; that is what
>
> identifies it as being Chr15.
>
>
>
> Scott
>
>
>
>
>
> On Mon, Jun 21, 2010 at 12:42 PM, Jayaraman, Pushkala
>
> <[hidden email]> wrote:
>
>> Hello Lincoln,
>
>>
>
>> This is what I get:
>
>>
>
>>
>
>>
>
>> mysql> select * from name where name like 'chr%';
>
>>
>
>> +-------+--------+--------------+
>
>>
>
>> | id    | name   |
> display_name |
>
>>
>
>> +-------+--------+--------------+
>
>>
>
>> | 29168 | Chrm3
> |            1 |
>
>>
>
>> | 29169 | Chrm3
> |            1 |
>
>>
>
>> | 29172 | Chrm3
> |            1 |
>
>>
>
>> |  2076 | Chrna2
> |            1 |
>
>>
>
>> |  2078 | Chrna2
> |            1 |
>
>>
>
>> |  2080 | Chrna2
> |            1 |
>
>>
>
>> |  2082 | Chrna2
> |            1 |
>
>>
>
>> |  2084 | Chrna2
> |            1 |
>
>>
>
>> |  2086 | Chrna2
> |            1 |
>
>>
>
>> |  2088 | Chrna2
> |            1 |
>
>>
>
>> |  2089 | Chrna2
> |            1 |
>
>>
>
>> +-------+--------+--------------+
>
>>
>
>> 11 rows in set (0.00 sec)
>
>>
>
>>
>
>>
>
>> Why am I not getting any of the chromosome names?
>
>>
>
>>
>
>>
>
>>
>
>>
>
>> When I do "head nameof_gff3_file.gff3" I
> get:
>
>>
>
>>
>
>>
>
>> Chr15   GenBank
> chromosome
> 24425085
> 28088033
> .       +
>
>>
>    .
> ID=NW_047453;Alias=15;Dbxref=taxon:10116;Note=Rattus norvegicus
>
>> chromosome 15 genomic cont
>
>>
>
>> ig%2C reference assembly (based on RGSC
> v3.4).,GENOME ANNOTATION REFSEQ:
>
>> Features on this sequence have been produced for
> build 4 version 1 of the
>
>> NCBI's genome annotation [see d
>
>>
>
>> ocumentation]. The DNA sequence is version 3.4
> 'November 2004 Update' of the
>
>> Rat genome assembly,produced by the Baylor College
> of Medicine Human Genome
>
>> Sequencing Center (BCM- H
>
>>
>
>> GSC) as part of the Rat Genome Sequencing Consortium
> (RGSC). This supersedes
>
>> all prior versions of the Rat assembly
> (2.0,2.1,3.0,3.1 3.2 and 3.3) (see
>
>
>
>
>
>
>

--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

------------------------------------------------------------------------------
ThinkGeek and WIRED's GeekDad team up for the Ultimate
GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
lucky parental unit.  See the prize list and enter to win:
http://p.sf.net/sfu/thinkgeek-promo
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
Reply | Threaded
Open this post in threaded view
|

Re: Gff3 files 'chromosome' feature

Scott Cain
Hi Pushkala,

I'm guessing you'll need to write a custom script to do the mapping
from the contig coordinates to chromosomal coordinates.  I don't know
how everybody deals with this sort of thing: sometimes complete
chromosome entries can be found at NCBI.  For WormBase and FlyBase,
they are the owners of the GenBank entries, so they don't have to
worry about converting GenBank entries to GFF3, since they have the
"original" data anyway.

Scott


On Mon, Jun 21, 2010 at 5:11 PM, Jayaraman, Pushkala <[hidden email]> wrote:

> Yes exactly...
> :(
>
> Thanks Scott... Could I ask how else do other groups such as PlasmoDB/WormBase etc.. handle the problem of Overlapping contigs.. Have you come across such a problem in the gff3 file?
>
> 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
>
>
> -----Original Message-----
> From: Scott Cain [mailto:[hidden email]]
> Sent: Monday, June 21, 2010 2:26 PM
> To: Jayaraman, Pushkala
> Cc: [hidden email]
> Subject: Re: [Gmod-gbrowse] Gff3 files 'chromosome' feature
>
> Hi Pushkala,
>
> I think I understand: you have multiple gff lines for each chromosome
> that correspond to the individual contigs, right?  And each of these
> has "Name=Chr#"?  You can't do that; you need to have one and one one
> gff line for each chromosome (reference sequence).
>
> Scott
>
> On Monday, June 21, 2010, Jayaraman, Pushkala <[hidden email]> wrote:
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> The reason I ask is because,
>>
>> I have one gff3 file for each chromosome.
>>
>> Each gff3 file is made up of data present in multiple
>> contigs(ncbi only gives its gff files with contig information and we need to
>> convert that into genomic information using contig-to-chromosome mapping)
>>
>>
>>
>> Although each of my Chromosome entries have a 'Name=Chr16'
>> their starts and stops include the start and stop of each contig that is a part
>> of that chromosome. I guess because of this.. only the first entry of 'chromosome'
>> is being recognized. I am not able to drag over the entire chromosome in the
>> overview panel..
>>
>> The picture to the right shows this behavior.
>>
>>
>>
>> The picture to the left shows gbrowse working with the
>> same data, when the database was loaded in May.
>>
>>
>>
>>
>>
>> I hope I have managed to convey my question clearly..
>>
>> 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
>>
>>
>>
>>
>>
>> -----Original Message-----
>> From: Jayaraman, Pushkala [mailto:[hidden email]]
>> Sent: Monday, June 21, 2010 1:37 PM
>> To: [hidden email]
>> Subject: Re: [Gmod-gbrowse] Gff3 files 'chromosome' feature
>>
>>
>>
>> I would like to ask one question regarding gff3 files
>> esp. the 'chromosome' entry
>>
>>
>>
>>
>>
>> Ideally should there be only one 'chromosome' feature for
>> a gff3 file?
>>
>>
>>
>> For eg.. if I had 1 gff3 file for each chromosome that
>> had all the features pertaining to a gene (mrna, exon, cds, intron,
>> pseudogene..etc)
>>
>> And I had the chromosome feature in that file. Then,
>>
>> Can I have multiple entries of 'chromosome' with
>>
>> start = start of first contig
>>
>> and
>>
>> stop = stop of first contig
>>
>> and then repeat this for the next contig..depending on
>> the number of contigs that make up that chromosome?
>>
>>
>>
>> Or must I only have one entry for 'chromosome' wherein I
>> have the:
>>
>> start = start of the first contig that makes up that
>> chromosome
>>
>> and
>>
>> stop = stop of the last contig that makes up that
>> chromosome?
>>
>>
>>
>> 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
>>
>>
>>
>>
>>
>> -----Original Message-----
>>
>> From: Scott Cain [mailto:[hidden email]]
>>
>> Sent: Monday, June 21, 2010 11:47 AM
>>
>> To: Jayaraman, Pushkala
>>
>> Cc: Lincoln Stein; [hidden email]
>>
>> Subject: Re: [Gmod-gbrowse] Gbrowse2 tracks not
>> visible..possible bug?
>>
>>
>>
>> Pushkala,
>>
>>
>>
>> You need "Name=Chr15" in column nine of that
>> first line; that is what
>>
>> identifies it as being Chr15.
>>
>>
>>
>> Scott
>>
>>
>>
>>
>>
>> On Mon, Jun 21, 2010 at 12:42 PM, Jayaraman, Pushkala
>>
>> <[hidden email]> wrote:
>>
>>> Hello Lincoln,
>>
>>>
>>
>>> This is what I get:
>>
>>>
>>
>>>
>>
>>>
>>
>>> mysql> select * from name where name like 'chr%';
>>
>>>
>>
>>> +-------+--------+--------------+
>>
>>>
>>
>>> | id    | name   |
>> display_name |
>>
>>>
>>
>>> +-------+--------+--------------+
>>
>>>
>>
>>> | 29168 | Chrm3
>> |            1 |
>>
>>>
>>
>>> | 29169 | Chrm3
>> |            1 |
>>
>>>
>>
>>> | 29172 | Chrm3
>> |            1 |
>>
>>>
>>
>>> |  2076 | Chrna2
>> |            1 |
>>
>>>
>>
>>> |  2078 | Chrna2
>> |            1 |
>>
>>>
>>
>>> |  2080 | Chrna2
>> |            1 |
>>
>>>
>>
>>> |  2082 | Chrna2
>> |            1 |
>>
>>>
>>
>>> |  2084 | Chrna2
>> |            1 |
>>
>>>
>>
>>> |  2086 | Chrna2
>> |            1 |
>>
>>>
>>
>>> |  2088 | Chrna2
>> |            1 |
>>
>>>
>>
>>> |  2089 | Chrna2
>> |            1 |
>>
>>>
>>
>>> +-------+--------+--------------+
>>
>>>
>>
>>> 11 rows in set (0.00 sec)
>>
>>>
>>
>>>
>>
>>>
>>
>>> Why am I not getting any of the chromosome names?
>>
>>>
>>
>>>
>>
>>>
>>
>>>
>>
>>>
>>
>>> When I do "head nameof_gff3_file.gff3" I
>> get:
>>
>>>
>>
>>>
>>
>>>
>>
>>> Chr15   GenBank
>> chromosome
>> 24425085
>> 28088033
>> .       +
>>
>>>
>>    .
>> ID=NW_047453;Alias=15;Dbxref=taxon:10116;Note=Rattus norvegicus
>>
>>> chromosome 15 genomic cont
>>
>>>
>>
>>> ig%2C reference assembly (based on RGSC
>> v3.4).,GENOME ANNOTATION REFSEQ:
>>
>>> Features on this sequence have been produced for
>> build 4 version 1 of the
>>
>>> NCBI's genome annotation [see d
>>
>>>
>>
>>> ocumentation]. The DNA sequence is version 3.4
>> 'November 2004 Update' of the
>>
>>> Rat genome assembly,produced by the Baylor College
>> of Medicine Human Genome
>>
>>> Sequencing Center (BCM- H
>>
>>>
>>
>>> GSC) as part of the Rat Genome Sequencing Consortium
>> (RGSC). This supersedes
>>
>>> all prior versions of the Rat assembly
>> (2.0,2.1,3.0,3.1 3.2 and 3.3) (see
>>
>>
>>
>>
>>
>>
>>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
>



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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