[Bioperl-l] Aggressive aggregation?

[Chad Matsalla]

On Wed, 9 Mar 2005, Aaron J. Mackey wrote:
> > chr1 aafcest     HSP   200   275   .     -     .     Target
> > "Sequence:chad1" 200 275
> > chr1 aafcest     HSP   300   450   .     -     .     Target
> > "Sequence:chad1" 300 450
> > chr1 aafcest     match 200   450   .     -     .     Target
> > "Sequence:chad1" 200 450
>
>
> These need to be Target "Sequence:chad1-1" and "Sequence:chad1-2" or
> some such.  This also means that if you're saving the ESTs in the
> database (for sequence alignment display), you'll have to save them
> redundantly under chad1-1, chad1-2, etc.

This is horrible. I want to fix this.

> Now, you could write a custom aggregator that de-aggregated multiple
> chad1 "match" features, assigning the contained HSPs to each, but there
> is no such "default" behavior.  Let me know if there's general interest
> for this ...

I think there is, and I volunteer to write it. I'm new to the Bio::DB
subsystem but I'm eager to dive in. Can you help me by providing a
general flowchart on what you'd do to create this? What should the
Aggregator be called? Hmm. Bio::DB::GFF::Aggregator::manymatch ?

Chad Matsalla