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pybbhash

This is a Python (Cython) wrapper for the BBHash codebase for building minimal perfect hash functions.

Right now, this is being used for some k-mer-based hashing foo that we have in khmer. As such, I am focused on building MPHF for 64-bit hashes and am wrapping only that bit of the interface; the rest should be ~straightforward (hah!).

Big TODO items

The two remaining Big Items are:

  • I would like to be able to use generic Python iterators in the PyMPHF construction. Right now there is a round of memory-inefficient copying of hashes, which is bad when you have a lot of k-mers!

  • I would like to be able to save to/load from strings, not just files.

I also need to investigate thread safety.

Usage:

import bbhash

# some collection of 64-bit (or smaller) hashes
uint_hashes = [10, 20, 50, 80]

num_threads = 1 # hopefully self-explanatory :)
gamma = 1.0     # internal gamma parameter for BBHash

mph = bbhash.PyMPHF(uint_hashes, len(uint_hashes), num_threads, gamma)

for val in uint_hashes:
    print('{} now hashes to {}'.format(val, mph.lookup(val)))

# can also use 'mph.save(filename)' and 'mph = bbhash.load_mphf(filename)'.

CTB 1/2018