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src/p/y/pycogent-HEAD/tests/test_evolve/test_pairwise_distance.py   pycogent(Download)
from cogent.util.unit_test import TestCase, main
from cogent import LoadSeqs, DNA, RNA, PROTEIN
from cogent.evolve.pairwise_distance import get_moltype_index_array, \
    seq_to_indices, _fill_diversity_matrix, \
    _jc69_from_matrix, JC69Pair, _tn93_from_matrix, TN93Pair, LogDetPair, \
        matrix = numpy.zeros((4,4), float)
        _fill_diversity_matrix(matrix, s1, s2)
        total, p, dist, var = _jc69_from_matrix(matrix)
        self.assertEquals(total, 10.0)
        self.assertEquals(p, 0.2)

src/c/o/cogent-1.5.3/tests/test_evolve/test_pairwise_distance.py   cogent(Download)
from cogent.util.unit_test import TestCase, main
from cogent import LoadSeqs, DNA, RNA, PROTEIN
from cogent.evolve.pairwise_distance import get_moltype_index_array, \
    seq_to_indices, _fill_diversity_matrix, \
    _jc69_from_matrix, JC69Pair, _tn93_from_matrix, TN93Pair, LogDetPair
        matrix = numpy.zeros((4,4), float)
        _fill_diversity_matrix(matrix, s1, s2)
        total, p, dist, var = _jc69_from_matrix(matrix)
        self.assertEquals(total, 10.0)
        self.assertEquals(p, 0.2)