[Bioperl-l] Taxonomy and entrez
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
> 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
> 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
> 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
Not a big deal, but something to remember.
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign
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