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

[Lincoln Stein]

Hi Philip,

The gene model methods are being overhauled in wormbase.  Can you put 
this problem on hold until after the first of the year?  The changes 
will have stabilized by then and I'll have a good answer for you.

Lincoln

On Tuesday 23 December 2003 11:01 am, Philip MacMenamin wrote:
> 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.