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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, \
    def test_tn93_from_matrix(self):
        """compute TN93 distances"""
        calc = TN93Pair(DNA, alignment=self.alignment)
        calc.run(show_progress=False)
        self.assertEquals(calc.Lengths['s1', 's2'], 10)
    def test_distance_pair(self):
        """get distances dict"""
        calc = TN93Pair(DNA, alignment=self.alignment)
        calc.run(show_progress=False)
        dists = calc.getPairwiseDistances()

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
    def est_tn93_from_matrix(self):
        """compute TN93 distances"""
        calc = TN93Pair(DNA, alignment=self.alignment)
        calc.run()
        self.assertEquals(calc.Lengths['s1', 's2'], 10)
    def est_distance_pair(self):
        """get distances dict"""
        calc = TN93Pair(DNA, alignment=self.alignment)
        calc.run()
        dists = calc.getPairwiseDistances()