Python goldman_q_dna_triple Examples

Example #1

    def test_goldman_q_dna_triple(self):
        """Should return expected rate matrix"""
        seq1 = "ATGCATGCATGC"
        seq2 = "AAATTTGGGCCC"
        outgroup = "AATTGGCCAATT"

        expected = array([[-(1 / 2.0), (1 / 2.0), 0, 0], [0, 0, 0, 0],
                          [(1 / 3.0), 0, -(1 / 3.0), 0], [0, 0, 0, 0]])
        observed = goldman_q_dna_triple(seq1, seq2, outgroup)
        self.assertFloatEqual(observed, expected)

Example #2

File: test_usage.py Project: GavinHuttley/pycogent

    def test_goldman_q_dna_triple(self):
        """Should return expected rate matrix"""
        seq1 = "ATGCATGCATGC"
        seq2 = "AAATTTGGGCCC"
        outgroup = "AATTGGCCAATT"

        expected = array([[-(1/2.0), (1/2.0), 0, 0],
                          [0, 0, 0, 0],
                          [(1/3.0), 0, -(1/3.0), 0],
                          [0, 0, 0, 0]])
        observed = goldman_q_dna_triple(seq1, seq2, outgroup)
        self.assertFloatEqual(observed, expected)