def test_check_contrib_phy_vars_ignore_ancestral(self):
# should not find C, T5A is explained by 'A'
# self.cons.append(['C', 0.1])
self.obs.obs_tab[4]['A'] = 1
res = assemble._check_contrib_phy_vars(self.phy, self.obs, self.cons,
self.args)
self.assertEqual(self.cons, res)
def test_check_contrib_phy_vars_rm_shared(self):
# Should remove E, A4T already seen in A, does not count for E.
self.obs.obs_tab[6]['T'] = 0
self.obs.obs_tab[2]['T'] = 0
res = assemble._check_contrib_phy_vars(self.phy, self.obs, self.cons,
self.args)
self.assertEqual(self.cons[0:1], res)
def test_check_contrib_phy_vars_high_min_fraction_requirement(self):
self.args.var_fraction = 0.9
self.cons.append(['C', 0.1])
self.obs.obs_tab[4]['A'] = 1
res = assemble._check_contrib_phy_vars(self.phy, self.obs, self.cons,
self.args)
self.assertEqual(self.cons[0:2], res)
def test_check_contrib_phy_vars_rm_none(self):
self.cons.append(['C', 0.1])
res = assemble._check_contrib_phy_vars(self.phy, self.obs, self.cons,
self.args)
self.assertNotEqual(self.cons, res)
self.assertEqual(self.cons[0:2], res)
def test_check_contrib_phy_vars_check_ancestral(self):
# should pass if A isn't present than 4 can be ancestral evidence
self.cons.append(['C', 0.1])
self.obs.obs_tab[4]['A'] = 1
self.obs.obs_tab[1]['T'] = 0
self.obs.obs_tab[3]['T'] = 0
res = assemble._check_contrib_phy_vars(self.phy, self.obs, self.cons,
self.args)
self.assertEqual(self.cons[1:], res)
def test_check_contrib_phy_vars_high_var_count_requirement(self):
# required number of variants too high.
self.args.var_count = 1
self.args.var_fraction = 0.9
self.cons.append(['C', 0.1])
self.obs.obs_tab[5]['T'] = 1
res = assemble._check_contrib_phy_vars(self.phy, self.obs, self.cons,
self.args)
self.assertEqual(self.cons, res)
def test_check_contrib_phy_vars_high_min_reads(self):
# required number of reads too high.
self.args.min_var_reads = 10
res = assemble._check_contrib_phy_vars(self.phy, self.obs, self.cons,
self.args)
self.assertEqual([], res)
def test_check_contrib_phy_vars_empty_obs(self):
# no observations, no keepers.
self.obs.obs_tab = collections.defaultdict(collections.Counter)
res = assemble._check_contrib_phy_vars(self.phy, self.obs, self.cons,
self.args)
self.assertEqual([], res)
def test_check_contrib_phy_vars_no_rm_one_base(self):
self.cons.append(['C', 0.1])
self.obs.obs_tab[5]['T'] = 1
res = assemble._check_contrib_phy_vars(self.phy, self.obs, self.cons,
self.args)
self.assertEqual(self.cons, res)
def test_check_contrib_phy_vars_no_rm(self):
res = assemble._check_contrib_phy_vars(self.phy, self.obs, self.cons,
self.args)
self.assertEqual(self.cons, res)
