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src/c/o/cogent-1.5.3/cogent/evolve/coevolution.py   cogent(Download)
from cogent.core.profile import Profile
from cogent.core.alphabet import CharAlphabet, Alphabet
from cogent.maths.stats.distribution import binomial_exact
from cogent.maths.stats.special import ROUND_ERROR
from cogent.parse.record import FileFormatError
        try:
            results.append(\
             binomial_exact(pos_freq,scaled_aln_size,natural_prob))
        # Because of the scaling of alignments to scaled_aln_size, pos_freq is
        # a float rather than an int. So, if a position is perfectly conserved,
        # pos_freq as a float could be greater than scaled_aln_size. 
        # In this case I cast it to an int. I don't like this alignment 
        # scaling stuff though. 
        except ValueError, e:
            results.append(binomial_exact(int(pos_freq),\

src/p/y/pycogent-HEAD/cogent/evolve/coevolution.py   pycogent(Download)
from cogent.core.profile import Profile
from cogent.core.alphabet import CharAlphabet, Alphabet
from cogent.maths.stats.distribution import binomial_exact
from cogent.maths.stats.special import ROUND_ERROR
from cogent.parse.record import FileFormatError
        try:
            results.append(\
             binomial_exact(pos_freq,scaled_aln_size,natural_prob))
        # Because of the scaling of alignments to scaled_aln_size, pos_freq is
        # a float rather than an int. So, if a position is perfectly conserved,
        # pos_freq as a float could be greater than scaled_aln_size. 
        # In this case I cast it to an int. I don't like this alignment 
        # scaling stuff though. 
        except ValueError, e:
            results.append(binomial_exact(int(pos_freq),\

src/c/o/cogent-1.5.3/tests/test_maths/test_stats/test_distribution.py   cogent(Download)
 
from cogent.util.unit_test import TestCase, main
from cogent.maths.stats.distribution import z_low, z_high, zprob, chi_low, \
    chi_high, t_low, t_high, tprob, poisson_high, poisson_low, poisson_exact, \
    binomial_high, binomial_low, binomial_exact, f_low, f_high, fprob, \
        for (key, value) in expected.items():
            min_val, max_val = value
            assert min_val < binomial_exact(*key) < max_val
            #self.assertFloatEqualRel(binomial_exact(*key), value, 1e-4)
 

src/p/y/pycogent-HEAD/tests/test_maths/test_stats/test_distribution.py   pycogent(Download)
 
from cogent.util.unit_test import TestCase, main
from cogent.maths.stats.distribution import z_low, z_high, zprob, chi_low, \
    chi_high, t_low, t_high, tprob, poisson_high, poisson_low, poisson_exact, \
    binomial_high, binomial_low, binomial_exact, f_low, f_high, fprob, \
        for (key, value) in expected.items():
            min_val, max_val = value
            assert min_val < binomial_exact(*key) < max_val
            #self.assertFloatEqualRel(binomial_exact(*key), value, 1e-4)
 

src/p/y/pycogent-HEAD/tests/test_evolve/test_coevolution.py   pycogent(Download)
from cogent.core.profile import Profile
from cogent.core.alphabet import CharAlphabet, Alphabet
from cogent.maths.stats.distribution import binomial_exact
from cogent.core.alignment import DenseAlignment
from cogent.seqsim.tree import RandomTree

src/c/o/cogent-1.5.3/tests/test_evolve/test_coevolution.py   cogent(Download)
from cogent.core.profile import Profile
from cogent.core.alphabet import CharAlphabet, Alphabet
from cogent.maths.stats.distribution import binomial_exact
from cogent.core.alignment import DenseAlignment
from cogent.seqsim.tree import RandomTree