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biocore / deblur

Deblur is a greedy deconvolution algorithm based on known read error profiles.
BSD 3-Clause "New" or "Revised" License
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Use lookup table for translate the sequence to np array #6

Closed josenavas closed 8 years ago

josenavas commented 9 years ago

See here

wasade commented 9 years ago

Note, it is essentially the same as using a lookup array in C. The advantage is that all lookups are O(1) as it is indexing into an array. Hashing is O(1) as well, except the hash computation is an appreciable difference. Additionally, you can likely do bulk numpy ops which tend to be faster than pure Python

On Thu, Mar 12, 2015 at 10:17 AM, josenavas notifications@github.com wrote:

See here https://github.com/biocore/scikit-bio/pull/53#discussion-diff-9171472

— Reply to this email directly or view it on GitHub https://github.com/biocore/deblur/issues/6.

wasade commented 8 years ago

Currently performance of the code is pretty good. This might be useful to do in the future, but I think we should table it for now.