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

[Philip MacMenamin]

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

I hadnt. But I just did, and this one makes all the gene with the introns,
the UTRs and the exons one solid bar. All on the same plane, like I would
like, but not differentiating intron, exon or UTR.

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

This doesnt seem to do the right thing either.

if left alone the Bio::DB::GFF::Aggregator::transcript seems to leave out the
UTRs entirely.
my $aggregator = Bio::DB::GFF::Aggregator->new(-method => 'transcript',
					   -sub_parts => ['UTR:UTR','exon:curated','CDS:curated']
					  );

I know that the wormbase GFF files are differant, and this seems to be the
cause of this lack of UTRs in the orig Bio::DB::GFF::Aggregator::transcript.
Maybe the Aggregator above works fine, its just that the way that I am
drawing it is off?
ie:
      if (scalar @all_transcripts )
      {
	$panel->add_track(wormbase_transcript=>\@all_transcripts,
	etc.
      }

-- 
Philip MacMenamin