[Bioperl-l] wormbase115/Bio::DB::GFF::Aggregator wormbase_transcript problem

[Philip MacMenamin]

Hi, 
Previously I ran the following code to draw a curated gene with UTRs 
hanging on the ends (attached):

my $aggregator = Bio::DB::GFF::Aggregator->new(-method => 'transcript',
					   -sub_parts => ['UTR:UTR','exon:curated','CDS:curated']
					  );
my $db = new Bio::DB::GFF(-adaptor=>'dbi::mysqlopt',
			      -dsn=>'dbi:mysql:wormbase115Mod;host=localhost',
			      -user=>'philip',
			      -pass=> $passwd,
			      -aggregator =>$aggregator
			     ) or die();
my @all_transcripts = $searchSeg->features('transcript');
if (scalar @all_transcripts )
{
	$panel->add_track(wormbase_transcript=>\@all_transcripts,
			  -bgcolor      => 'wheat',
			  -fgcolor      => 'black',
			  -forwardcolor => 'blue',
			  -reversecolor => 'blue',
			  -spacing => 0,
			  -utr_color    => '#D0D0D0',
			  -font2color   => 'blue',
			  -height       => 10,
			  -description  => 1,
			  -label        => 1,
			  -key          => "Curated genes");
}

This worked fine. 

With the latest release of wormbase this code does not work. 
So I have changed the -sub_parts arg for the Aggregator object to 
 -sub_parts => ['UTR:UTR','exon:curated','CDS:curated']
which gets rid of some things that I dont want. However, I cannot get it to 
draw the UTRs actually hanging on the ends of the gene, it stacks/bumps them 
now. They do not over lap in their start /stop co-ords.

???
Thanks. 
-- 
Philip MacMenamin