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)
