[BioSQL-l] BioSQL and GBrowse

[Michael Cipriano]

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