[Biopython-dev] [Bug 2494] _retrieve_taxon in BioSQL.py needs urgent optimization

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=2494





------- Comment #1 from ericgibert at yahoo.fr  2008-04-25 23:54 EST -------
Created an attachment (id=916)
 --> (http://bugzilla.open-bio.org/attachment.cgi?id=916&action=view)
script timing the current SQL and proposed bottom-up 'loop' implementation

results obtained on my dual core PC (Fedora 7 64 bit): (resulting lists are
truncated to help the reading)

go for it:
getTaxonSQLsimplex took 370.300 ms
[1L, 2759L, 6072L, ......  229390L, 229391L]
getTaxonSQL took 6846.810 ms
['Eukaryota', 'Metazoa', '......  'Nannophya', 'Nannophya pygmaea']
getTaxonSQLall took 6772.037 ms
['root', 'cellular organisms', '... 'Odonata', 'Anisoptera/Anisozygoptera
group''Nannophya', 'Nannophya pygmaea']
getTaxonLoop took 14.559 ms
['cellular organisms',... 'Nannophya', 'Nannophya pygmaea']

Conclusion: many runs have shown that the Loop function is always under 15ms
while the current SQL will be more than 6500ms.


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