def test_get_contributors_sorted(self):
self.props[4] = 0.6
self.args.var_check = False
res = assemble.get_contributors(self.phy, self.obs, self.haps,
self.wts, self.em_results, self.args)
exp = [['hap1', 'E', 0.60], ['hap2', 'A', 0.4]]
self.assertEqual(res, exp)
def test_get_contributors_with_phy_vars_rm(self):
self.args.var_check = True
self.args.min_reads = 2
self.args.min_var_reads = 2
res = assemble.get_contributors(self.phy, self.obs, self.haps,
self.wts, self.em_results, self.args)
exp = []
self.assertEqual(res, exp)
def test_get_contributors_no_phy_vars_rm(self):
self.args.var_check = False
self.args.min_reads = 2
self.args.min_var_reads = 2
res = assemble.get_contributors(self.phy, self.obs, self.haps,
self.wts, self.em_results, self.args)
exp = [['hap1', 'A', 0.40]]
self.assertEqual(res, exp)
def test_get_contributors_with_phy_vars(self):
self.args.var_check = True
res = assemble.get_contributors(self.phy, self.obs, self.haps,
self.wts, self.em_results, self.args)
exp = [['hap1', 'A', 0.40], ['hap2', 'E', 0.3]]
self.assertEqual(res, exp)
def test_get_contributors_manual_bad_choice(self):
with self.assertRaises(ValueError):
self.args.contributors = "E,Z"
res = assemble.get_contributors(self.phy, self.obs, self.haps,
self.wts, self.em_results,
self.args)
def test_get_contributors_manual_weird_choice(self):
self.args.contributors = "E,F"
res = assemble.get_contributors(self.phy, self.obs, self.haps,
self.wts, self.em_results, self.args)
exp = [['hap1', 'E', 0.3], ['hap2', 'F', 0.01]]
self.assertEqual(res, exp)
def test_get_contributors_manual(self):
self.args.contributors = "A,E"
res = assemble.get_contributors(self.phy, self.obs, self.haps,
self.wts, self.em_results, self.args)
exp = [['hap1', 'A', 0.40], ['hap2', 'E', 0.3]]
self.assertEqual(res, exp)