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#!/usr/bin/env python
import numpy
import time
from cogent import DNA
from cogent.align.align import classic_align_pairwise, make_dna_scoring_dict
__author__ = "Peter Maxwell"
__copyright__ = "Copyright 2007-2012, The Cogent Project"
__credits__ = ["Peter Maxwell"]
__license__ = "GPL"
__version__ = "1.5.3"
__maintainer__ = "Peter Maxwell"
__email__ = "pm67nz@gmail.com"
__status__ = "Production"
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.makeSequence('AAAATGCTTA' * r)
seq1 = DNA.makeSequence('AATTTTGCTG' * r)
t0 = time.time()
aln = classic_align_pairwise(seq1, seq2, S, 10, 2, local=False, **kw)
t = time.time() - t0
return (len(seq1)*len(seq2))/t
print t
if __name__ == '__main__':
d = 2
e = 1
options = [(False, False), (True, False), (False, True)]
template = "%10s " * 4
print " 1000s positions per second"
print template % ("size", "simple", "logs", "scaled")
for r in [50, 100, 200, 500]:
times = [test(r, use_logs=l, use_scaling=s) for (l,s) in options]
print template % tuple([r*10] + [int(t/1000) for t in times])
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