[Bioperl-l] Aggressive aggregation?
chad at dieselwurks.com
Thu Mar 10 12:21:01 EST 2005
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 ?
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