[Bioperl-l] Bio::DB::Taxonomy root not present
hlapp at drycafe.net
Thu Jul 7 22:28:21 UTC 2011
On Jul 7, 2011, at 3:22 PM, Brian Osborne wrote:
> It's also true that having 5 trees instead of 1 is incorrect
That's a strong statement and I'm not sure I agree with this - let's
keep in mind that these are taxonomies, not phylogenetic trees of all
of life. Not every taxonomy has a node for "all of life" or for LUCA.
For example, ITIS, one of the most widely used taxonomies if you're
not dealing strictly with molecular data, does not - there is one
"tree" for each kingdom of life. (Not that I want to recommend that as
a good thing.)
I agree with your programming awkwardness argument, though I would
add that looking for a specific label of a node to identify the root
is always a bad (because fragile) thing to do. A better way to
identify a root node would be parent undefined, or being the same as
the node itself. If the code did that for each the 5 or so children of
'root', then the fake root could be removed.
At the very least code in Bio::DB::Taxonomy or anywhere else should
not assume that there is a single root for a taxonomy. Because there
are taxonomies for which this really isn't the case.
: Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
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