[Bioperl-l] Bio::*Taxonomy* changes

[Hilmar Lapp]

On Jul 24, 2006, at 6:15 PM, Sendu Bala wrote:

> I'll tell you what. This will be easier if I just write the code  
> for my
> proposals, including whatever changes would be needed in
> Bio::SeqIO::genbank et al.

Never get in the way of somebody who threatens to code :-) so I  
certainly won't. I think you're on the right track.

My suggestion is, if you have a good picture in front of you of how  
it's going to look like when done, just pretend for a second it is  
done already and give us some code examples that  use the new (to be  
done) API.

As a start, some of the situations it's currently used in:

	- genbank.pm parsing and setting species information for the sequence
	- user asking for the scientific name of the species of the sequence  
(obviously, the call would remain unchanged: $seq->species->binomial 
(). But what happens behind the scene?)
	- genbank.pm writing the SOURCE information for a sequence

Replace genbank.pm with your rich annotation source parser of choice.

Then maybe some advanced uses:

	- from a sequence stream, retain only those of primates
	- like above, but only mitochondrial sequences
	- for an organism, query entrez for all sequences of strains,  
varieties, or subspecies sequences for that organism

Add your own if these sound stupid ...

Just an idea.

	-hilmar

-- 
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: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
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