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

[Jason Stajich]

I'm sure Lincoln will answer better in full, but have you tried the
processed_transcript aggregator instead?

There is a wormbase_gene aggregator as part of Gbrowse as well?

>From Bio::DB::GFF::Aggregator::wormbase_gene which is part of Gbrowse

=head1 DESCRIPTION

Bio::DB::GFF::Aggregator::wormbase_gene is one of the default
aggregators, and was written to be compatible with the C elegans GFF
files.  It aggregates raw "CDS", "5'UTR", "3'UTR", "polyA"
and "TSS" features into "transcript" features.  For compatibility with
the idiosyncrasies of the Sanger GFF format, it expects that the full
range of the transcript is contained in a main feature of type
"Sequence".


-jason
On Tue, 23 Dec 2003, 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.
>

--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu