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src/p/y/pycogent-HEAD/tests/test_evolve/test_pairwise_distance.py   pycogent(Download)
    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)
 
        # same answer when using ambiguous alignment
        calc.run(self.ambig_alignment, show_progress=False)
        self.assertFloatEqual(calc.Dists['s1', 's2'], 0.2554128119)
 
        # but different answer if subsequent alignment is different
        calc.run(self.diff_alignment, show_progress=False)
    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)
    def est_tn93_from_matrix(self):
        """compute TN93 distances"""
        calc = TN93Pair(DNA, alignment=self.alignment)
        calc.run()
        self.assertEquals(calc.Lengths['s1', 's2'], 10)
 
        # same answer when using ambiguous alignment
        calc.run(self.ambig_alignment)
        self.assertFloatEqual(calc.Dists['s1', 's2'], 0.2554128119)
 
        # but different answer if subsequent alignment is different
        calc.run(self.diff_alignment)
    def est_distance_pair(self):
        """get distances dict"""
        calc = TN93Pair(DNA, alignment=self.alignment)
        calc.run()
        dists = calc.getPairwiseDistances()