[Biopython] Bio.trie

[Andrew Dalke]

On Dec 29, 2010, at 4:24 AM, Michiel de Hoon wrote:
> We would like to know though how many users Bio.trie has, so we can decide whether it is worthwhile to update this module. If you are using Bio.trie, please let us know (preferably via the mailing list). If there are no current users, I suggest that we deprecate and later remove this module from Biopython.

I am not a user but the other day I was looking through the Python bug list and came across:

   http://bugs.python.org/issue9520

   The best existing implementation I've been able to find so far
   is one in the BioPython. Compared to defaultdict(int) on the
   task of counting words. Dataset 123,981,712 words (6,504,484
   unique), 1..21 characters long:
     * bio.tree - 459 Mb/0.13 Hours, good O(1) behavior
     * defaultdict(int) - 693 Mb/0.32 Hours, poor, almost O(N) behavior



				Andrew
				dalke at dalkescientific.com