[BioSQL-l] BioSQL and GBrowse

[Michael Cipriano]

Ok, I installed the CVS version rather then the release version and
everything seems to be working now, so if anyone else gets this problem,
that is the simple solution.

-Michael

On Tue, 2006-03-07 at 09:39 -0800, Michael Cipriano wrote:
> Hello,
> 
> I'm not sure if this is a GBrowse problem, or a GBrowse on BioSQL
> problem, so tell me if I should post this to the GBrowse list.
> 
> I have a BioSQL database with bacterial genome sequences loaded from
> genbank files.  I can browse around the database just fine, but when I
> try and use gbrowse_img, the image is messed up.
> 
> Take a look at these two links, they should show basicaly the same
> thing, but the gbrowse_img link shows the features all piled up at the
> left side of the image, and they are barely visible.
> 
> 
> http://alien.lbl.gov/cgi-bin/gbrowse/bacteria/?start=1277180;stop=1278571;ref=NC_000913;width=800;version=100;label=CDS-Genes;
> http://alien.lbl.gov/cgi-bin/gbrowse_img/bacteria?name=NC_000913:1277180..1278571;type=CDS+Genes;width=800
> 
> The weird thing is that I can sometimes get the images to work partialy,
> but mostly on the most 5' end of the genome, in the low numbers. For
> instance:
> 
> http://alien.lbl.gov/cgi-bin/gbrowse/bacteria/?start=1000;stop=5000;ref=NC_000913;width=800;version=100;label=CDS-Genes;id=3ed54d66a36f50ddbe3c9cade69202e3
> http://alien.lbl.gov/cgi-bin/gbrowse_img/bacteria?name=NC_000913:1000..5000;type=CDS+Genes;width=800;
> 
> This shows more of the image in the gbrowse_img portion, but it is about
> 1kb off, so I think that the larger the position, the larger the stop
> position is being displayed? This is purely conjecture, but it seems a
> little weird. 
> 
> Here is part of my gbrowse conf file (below).  I will note that I have
> installed many configurations of gbrowse, but this is my first one using
> BioSQL. This does seem to be a biosql only problem, as the included
> in-memory GFF database shows the correct image. 
> 
> Any help would be appreciated.
> 
> Thanks,
> Michael Cipriano
> 
> 
> 
> Versions from the top of the files:
> 
> gbrowse_img:
> $VERSION   = 1.64;
> # $Id: gbrowse_img.PLS,v 1.27.4.8.2.4 2005/11/11 22:00:39 lstein Exp $
> 
> gbrowse:
> $VERSION   = 1.64;
> $BIOGRAPHICS_VERSION   = 1.65;
> # $Id: gbrowse.PLS,v 1.119.4.57.2.10 2005/11/15 19:20:40 lstein Exp $
> 
> 
> Here is the CDS stanza from gbrowse.
> 
> [CDS]
> feature      = CDS
> glyph        = transcript2
> bgcolor      = turquoise
> fgcolor      = black
> height       = 10
> connector    = solid
> label        = sub {
>         my $feature = shift;
>         my @notes;
>         if ($feature->primary_tag eq "CDS")
>         {
>                 foreach (qw(product gene))
>                 {
>                         next unless $feature->has_tag($_);
>                         @notes = $feature->each_tag_value($_);
>                         last;
>                 }
>                 return $notes[0];
>         } else
>         {
>                 return $feature->display_name;
>         }
>  }
> 
> description  = sub {
>         my $feature = shift;
>         my @notes;
>         if ($feature->primary_tag eq "CDS")
>         {
>                 foreach (qw(note))
>                 {
>                         next unless $feature->has_tag($_);
>                         @notes = $feature->each_tag_value($_);
>                         last;
>                 }
>                 return unless @notes;
>                 substr($notes[0],30) = '...' if length $notes[0] > 30;
>                 return $notes[0];
>         } else
>         {
>                 my $description;
>                 foreach ($feature->all_tags)
>                 {
>                         my @values = $feature->each_tag_value($_);
>                         $description .= $_ eq 'note' ? "@values" :
> "$_=@values; ";
>                 }
>                 $description =~ s/; $//; # get rid of last
>                 return $description;
>         }
>   }
> link         = sub {
>                         my $feature = shift;
>                         my $pk = $feature->primary_key();
>                         return
> "/cgi-bin/regtransbase?page=geneinfo&seqfeature_id=$pk";
>   }
> key          = Predicted transcripts
> 
> 
> 
> 
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