[BioSQL-l] Problem with add feature under BioSQL

[Hilmar Lapp]

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
>
>
> _______________________________________________
> BioSQL-l mailing list
> BioSQL-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biosql-l
>

-- 
===========================================================
: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
===========================================================