[BioSQL-l] Problem with add feature under BioSQL

Michael Cipriano mjcipriano at lbl.gov
Tue May 30 18:26:24 EDT 2006


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:

ERROR from apache error_log:
[Tue May 30 12:17:16 2006] [error] [client] 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] 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
        grep { $current_segment->overlaps($_) } get_segments($db,
      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.

Michael Cipriano
Developer - LBNL

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