em_test.py 文件源码

def setUp(self):
        parser = argparse.ArgumentParser()
        self.args = parser.parse_args([])
        self.args.init_alpha = 1.0
        self.args.tolerance  = 0.0001
        self.args.max_iter   = 1000
        self.args.n_multi    = 1
        self.args.verbose    = False

        phy_in = ['I, A1G ,,',
                  ',H, A3T A5T ,,',
                  ',,F, A6T ,,',
                  ',,,B, A8T ,,',
                  ',,,C, T5A ,,',
                  ',,G, A7T ,,',
                  ',,,D, A9T ,,',
                  ',,,E, A4T ,,',
                  ',A, A2T A4T ,,']
        phy = phylotree.Phylotree(phy_in)
        ref = "AAAAAAAAA"
        reads = list(["1:A,2:T,3:A", "2:T,3:A", "3:A,4:T,5:T", "5:T,6:A",
                      "6:A,7:T", "6:A,7:T,8:A", "7:T,8:A", "4:T,5:T",
                      "1:A,2:T,3:T,4:T", "5:A,6:T,7:A,8:A"])
        haps = list('ABCDEFGHI')
        self.input_mat = preprocess.build_em_matrix(ref, phy, reads,
                                                    haps, self.args)
        self.wts = numpy.ones(len(reads))

        self.true_props = numpy.array(
                            [0.0, 0.8, 0.0, 0.0, 0.2, 0.0, 0.0, 0.0, 0.0])
        inf = float('Inf')
        self.true_haps = numpy.full_like(self.input_mat, -inf)
        self.true_haps[0:8, 1] = 0.0
        self.true_haps[8:10, 4] = 0.0