def test_smooth(self):
# See test_kdistlib.test_ProfileDistance_dynamic_smooth
counts_left = Counter([
'AC', 'AG', 'AT', 'CA', 'CC', 'CG', 'CT', 'GA', 'GC', 'GG', 'GT',
'TA', 'TG', 'TT'
])
counts_right = Counter([
'AC', 'AT', 'CA', 'CC', 'CG', 'CT', 'GA', 'GC', 'GG', 'GT', 'TA',
'TC', 'TG', 'TT'
])
filename_left = self.empty()
filename_right = self.empty()
with utils.open_profile(self.profile(counts_left, 2)) as handle_left:
with utils.open_profile(self.profile(counts_right,
2)) as handle_right:
with utils.open_profile(filename_left, 'w') as out_left:
with utils.open_profile(filename_right, 'w') as out_right:
kmer.smooth(handle_left,
handle_right,
out_left,
out_right,
summary='min')
counts_left = Counter([
'AA', 'AA', 'AA', 'CA', 'CC', 'CG', 'CT', 'GA', 'GC', 'GG', 'GT',
'TA', 'TA', 'TA'
])
counts_right = Counter([
'AA', 'AA', 'CA', 'CC', 'CG', 'CT', 'GA', 'GC', 'GG', 'GT', 'TA',
'TA', 'TA', 'TA'
])
utils.test_profile_file(filename_left, counts_left, 2)
utils.test_profile_file(filename_right, counts_right, 2)
def test_smooth_custom_name(self):
# See test_kdistlib.test_ProfileDistance_dynamic_smooth
counts_left = Counter(['AC', 'AG', 'AT', 'CA', 'CC', 'CG', 'CT', 'GA', 'GC', 'GG', 'GT', 'TA', 'TG', 'TT'])
counts_right = Counter(['AC', 'AT', 'CA', 'CC', 'CG', 'CT', 'GA', 'GC', 'GG', 'GT', 'TA', 'TC', 'TG', 'TT'])
filename_left = self.empty()
filename_right = self.empty()
with utils.open_profile(self.profile(counts_left, 2)) as handle_left:
with utils.open_profile(self.profile(counts_right, 2)) as handle_right:
with utils.open_profile(filename_left, 'w') as out_left:
with utils.open_profile(filename_right, 'w') as out_right:
kmer.smooth(handle_left, handle_right, out_left, out_right, custom_summary='numpy.max')