[Bioperl-l] Bio::DB::GFF::Aggregator problem, new wormbase models.

Philip MacMenamin pm66 at nyu.edu
Tue Feb 17 15:18:23 EST 2004

I cannot get things to aggregate properly in the new wormbase models. 
Previously this worked:
$aggregator = Bio::DB::GFF::Aggregator->new(-method    => 'test',
					       -sub_parts => ['UTR','CDS:curated']
(Or I could of more simply used the 'processed_transcript' aggregator that 
Linoln wrote.)

And one feature, with the UTRs "aggregated" together with the curated CDS's, 
was returned:
test:5_UTR(AH6.5), start->9524078 end->9526248
This could be fed to some kind of glyph, and would draw a nice picture of 
UTRs hanging off a coding seq.

[--------------]    [----------]  [---->
(You have to use your imaginatio a bit here)

With the new models of wormbase, this is not the case, so I am re-writing 
code to accomadate these changes. 

Now I am returned for example 3 features: a 3 prime UTR, a prime, and a CDS.
test:UTR(5_UTR:AH6.5)9524078 9524086
test:UTR(3_UTR:AH6.5)9525782 9526248
test:curated(AH6.5)9524087 9525781

The glyph then draws these things on two planes.
[]				[------->
 [---------]  [------------] [----------]

My assumption is that a single feature can be rendered as a single glyph. And 
if you have >1 feature, then >1 glyphs are needed. Therefore, I assume the 
problem stems from my failure to aggregate UTR and CDS features.

I have noticed that the new SQL GFF Db used to have two fmethods for UTRs, 
one for both 3 and 5 primes. The new one has only one. There are other 
changes of course, but I think this is important.

So, essentially I want to draw UTRs with CDS's attached... with the new 
wormbase models. If anyone knows how to do this, i'd like to hear from them.

Thanks :)

Philip MacMenamin

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