[Bioperl-l] Taxonomy and entrez

Chris Fields cjfields at uiuc.edu
Mon Sep 4 20:31:26 EDT 2006


On Sep 4, 2006, at 5:22 PM, Sendu Bala wrote:
...

>
> binomial() is there for backward compatibility, as is the entire
> Bio::Species class. It allows people to (hopefully) get the same  
> strings
> they are used to getting.
>
> FYI, binomial() is indeed implemented using traversals of the lineage
> tree. It just does some fantastic and surprising things to give us  
> that
> old Bio::Species flavour we all know and love (?).

Heh, not so much.  Anyway, I didn't notice the 'argument' form of  
binomial().  My bad!

Still, I have to say, having a 'trinomial' or full name accessible  
via the binomial() doesn't make too much sense.  Oh well, that's part  
of the reason we're switching.

...

> I'm not promoting it. I stated that you didn't need to use  
> Bio::Species.
> I mentioned it in case the OP wanted the familiarity of  
> Bio::Species and
> the behaviour of its old methods.

Right, but you didn't indicate that Bio::Species is deprecated,  
either.  If I'm told that something can be accomplished two different  
ways (Bio::Taxon, Bio::Species), I would expect it to stay that way.   
This isn't quite true with Bio::Species, which is slated to be  
deprecated soon.

Not a big deal, but something to remember.

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





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