[BioSQL-l] Problem with add feature under BioSQL

[Michael Cipriano]

Hi,

Yes, I only see the problem with gbrowse, though it could come up
anytime someone wants connect with Das using Bio::DB::Das::BioSQL and
needs the overlap function (or other range functions) in the Segment
object.

-Michael

On Wed, 2006-05-31 at 14:33 -0400, Hilmar Lapp wrote:
> This should be a Gbrowse problem, not in Biosql or bioperl-db unless  
> I'm missing something? Just trying to make sure ...
> 
> 	-hilmar
> 
> On May 30, 2006, at 6:26 PM, Michael Cipriano wrote:
> 
> > Hello,
> >
> > I have found a problem with adding features via gbrowse_img with the
> > add=xxx tag. I am using the CVS version of GGB, bioperl-live and  
> > BioSQL
> > schema on mysql.
> >
> > When using the add=xxx tag, it will produce a fatal error (with
> > BioSQL/Das interface). There error shown in the error log is:
> > link:
> > /cgi-bin/gbrowse_img/bacteria/? 
> > name=NC_000964:1..2000;width=600;type=CDS;add=NC_000964+myhit+9..999;
> >
> > ERROR from apache error_log:
> > [Tue May 30 12:17:16 2006] [error] [client 131.243.56.104] Can't  
> > locate
> > object method "overlaps" via package "Bio::DB::Das::BioSQL::Segment"
> > at /var/www/cgi-bin/gbrowse_img line 502.
> > [Tue May 30 12:17:16 2006] [error] [client 131.243.56.104]  
> > Premature end
> > of script headers: gbrowse_img
> >
> > This is from this section of code at line ~506:
> >
> >     unless ($segments{$refname}) {
> >       my @segments = map {
> >         eval{$_->absolute(0)}; $_  # so that rel2abs works properly
> > later
> >       }
> >         grep { $current_segment->overlaps($_) } get_segments($db,
> > $refname);
> >       return unless @segments;
> >       $segments{$refname} = $segments[0];
> >     }
> >
> >
> > The overlaps function is not defined in the
> > Bio::DB::Das::BioSQL::Segment or any of the objects it inherits.
> >
> > The fix was the inclusion of Bio::RangeI in the @ISA variable (shown
> > below) in the file Bio/DB/Das/BioSQL/Segment.pm
> >
> >
> > #@ISA = qw(Bio::Root::Root Bio::SeqI Bio::Das::SegmentI); #OLD BROKEN
> > @ISA = qw(Bio::Root::Root Bio::RangeI Bio::SeqI Bio::Das::SegmentI);
> >
> >
> > I am not sure if this will have any other consequences other then  
> > fixing
> > the bug I mentioned (and possibly fixing something else).
> >
> > Can anyone tell me if this will introduce any new bugs, and if not,  
> > can
> > someone commit this change.
> >
> > Thanks,
> > Michael Cipriano
> > Developer - LBNL
> >
> >
> > _______________________________________________
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> > BioSQL-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/biosql-l
> >
>