[Bioperl-l] Bio::Species/Bio::Taxonomy changes

[Hilmar Lapp]

On Jul 23, 2006, at 4:53 PM, Chris Fields wrote:

> I also propose (I'll probably get yelled at here) NOT actively
> supporting additional parsing of species, subspecies, etc directly
> from a file w/o a DB lookup.  As in, leave species, subspecies, genus
> parsing from the flatfile as is (no longer support it) or remove it
> completely and leave them unset.

Note that most (as in: most used, not most taxa) cases are actually  
straightforward. I don't think removing what's there is desirable,  
just everyone needs to understand that it will recognize only a  
limited number of syntactical variations, and beyond that if you want  
correct taxon attributes you will a database (be it flatfile, eutil,  
whatever) lookup.

> If people want to
> have reliable $species->species or $species-genus for taxonomy
> information, they will need to have the db_handle() set for the
> Bio::Taxonomy::Node object and have an Node-based method to reset
> species, genus, etc to the tax database information (maybe
> reset_taxon or something along those lines).

That's what I've saying all along.

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