[Bioperl-l] Bio::DB::GFF::Aggregator problem, new wormbase models.
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
And one feature, with the UTRs "aggregated" together with the curated CDS's,
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.
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.
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