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#!/usr/bin/env python
import time
import numpy
from cogent3 import DNA
from cogent3.align.align import classic_align_pairwise, make_dna_scoring_dict
def _s2i(s):
return numpy.array(["ATCG".index(c) for c in s])
def test(r=1, **kw):
S = make_dna_scoring_dict(10, -1, -8)
seq2 = DNA.make_seq("AAAATGCTTA" * r)
seq1 = DNA.make_seq("AATTTTGCTG" * r)
t0 = time.clock()
try:
# return_alignment is False in order to emphasise the quadratic part of
# the work.
aln = classic_align_pairwise(
seq1, seq2, S, 10, 2, local=False, return_alignment=False, **kw
)
except ArithmeticError:
return "*"
else:
t = time.clock() - t0
return int((len(seq1) * len(seq2)) / t / 1000)
if __name__ == "__main__":
d = 2
e = 1
options = [(False, False), (True, False), (False, True)]
template = "%10s " * 4
print(" 1000s positions^2 per second")
print(template % ("length", "simple", "logs", "scaled"))
for r in [100, 200, 300, 400, 500]:
times = [test(r, use_logs=l, use_scaling=s) for (l, s) in options]
print(template % tuple([r * 10] + times))
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