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
def setUp(self): phy_in = [ 'I, A1G ,,', ',H, A3T A5T ,,', ',,F, A6T ,,', ',,,B, A8T ,,', ',,,C, T5A ,,', ',,G, A7T ,,', ',,,D, A9T ,,', ',,,E, A4T ,,', ',A, A2T A4T ,,' ] self.phy = phylotree.Phylotree(phy_in) self.ref = "AAAAAAAAA"
def setUp(self): phy_in = [ 'I, A1G ,,', ',H, A3T A5T ,,', ',,F, A6T ,,', ',,,B, A8T ,,', ',,,C, T5A! ,,', ',,G, A7T ,,', ',,,D, (A9T) ,,', ',,,E, A4t ,,', ',A, A2T a4t ,,' ] self.ref = "AAAAAAAAA" self.phy = phylotree.Phylotree(phy_in, refseq=self.ref)
def test_include_anonymous_haplogroups(self): phy_in = [ 'I, A1G ,,', ',H, A3T A5T ,,', ',,, A6T ,,', ',,,B, A8T ,,', ',,,C, T5A! ,,', ',,G, A7T ,,', ',,,D, (A9T) ,,', ',,,E, A4t ,,', ',A, A2T a4t ,,' ] phy = phylotree.Phylotree(phy_in, anon_haps=True) self.assertTrue('H[1]' in phy.hap_var)
def setUp(self): parser = argparse.ArgumentParser() self.args = parser.parse_args([]) 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 ,,' ] self.phy = phylotree.Phylotree(phy_in) self.ref = "AAAAAAAAA" self.haps = list("ABCDEFGHI")
def test_ignore_anonymous_haplogroups(self): phy_in = [ 'I, A1G ,,', ',H, A3T A5T ,,', ',,, A6T ,,', ',,,B, A8T ,,', ',,,C, T5A! ,,', ',,G, A7T ,,', ',,,D, (A9T) ,,', ',,,E, A4t ,,', ',A, A2T a4t ,,' ] phy = phylotree.Phylotree(phy_in, anon_haps=False) self.assertFalse('F' in phy.hap_var) self.assertTrue('B' in phy.hap_var) self.assertTrue('C' in phy.hap_var) self.assertEqual(self.phy.hap_var['B'], ['A1G', 'A3T', 'A5T', 'A6T', 'A8T']) self.assertEqual(self.phy.hap_var['C'], ['A1G', 'A3T', 'T5A', 'A6T'])
def setUp(self): parser = argparse.ArgumentParser() self.args = parser.parse_args([]) self.args.verbose = False self.args.min_reads = 1 self.args.min_var_reads = 1 self.args.frac_var_reads = 0.02 self.args.var_fraction = 0.5 self.args.var_count = None self.args.var_check = False self.args.contributors = None phy_in = [ 'I, A1G ,,', ',H, A3T A5T ,,', ',,F, A6T ,,', ',,,B, A8T ,,', ',,,C, T5A ,,', ',,G, A7T ,,', ',,,D, A9T ,,', ',,,E, A4T ,,', ',A, A2T A4T ,,' ] self.ref = "AAAAAAAAA" self.phy = phylotree.Phylotree(phy_in, refseq=self.ref) self.cons = [['A', 0.4], ['E', 0.3]] self.obs = observe.ObservedBases() self.obs.obs_tab[1]['T'] = 1 self.obs.obs_tab[3]['T'] = 2 self.obs.obs_tab[0]['G'] = 1 self.obs.obs_tab[6]['T'] = 1 self.obs.obs_tab[2]['T'] = 1 self.obs.obs_tab[4]['T'] = 1 self.wts = numpy.array([1, 1, 1]) self.haps = list('ABCDEFGHI') self.props = numpy.array( [0.40, 0.01, 0.01, 0.01, 0.3, 0.01, 0.01, 0.01, 0.01]) self.mix_mat = numpy.array( [[0.91, 0.01, 0.01, 0.01, 0.01, 0.01, 0.01, 0.01, 0.01], [0.91, 0.01, 0.01, 0.01, 0.01, 0.01, 0.01, 0.01, 0.01], [0.01, 0.01, 0.01, 0.01, 0.91, 0.01, 0.01, 0.01, 0.01]]) self.em_results = (self.props, self.mix_mat)