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timeu/h5py_iterate.py

Created January 22, 2016 09:08
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h5py_iterate.py
h5 = h5py.File('my_file','r')
snps = h5['snps']
start = 0
end = END_OF_CHROMOSOME
# how many SNPs you want
chunk_size = 1000
for i in xrange(start,end,chunk_size):
stop_ix = min(i+chunk_size,end)
# this will return an array of 1000 snps
chunked_snps = snps[i:stop_ix]
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