diff options
Diffstat (limited to 'ete3/test/test_evol.py')
| -rw-r--r-- | ete3/test/test_evol.py | 28 |
1 files changed, 14 insertions, 14 deletions
diff --git a/ete3/test/test_evol.py b/ete3/test/test_evol.py index d9008f1..6c2aff7 100644 --- a/ete3/test/test_evol.py +++ b/ete3/test/test_evol.py @@ -111,10 +111,10 @@ class TestEvolEvolTree(unittest.TestCase): sorted(['fb', 'M1', 'M2', 'M7', 'M8'])) self.assertEqual(len (tree.get_evol_model('M2').branches), 194) self.assertEqual(tree.get_evol_model('fb').lnL, -3265.316569) - self.assert_('proportions' in str(tree.get_evol_model('M2'))) - self.assert_('p2=' in str(tree.get_evol_model('M2'))) - self.assert_('proportions' not in str(tree.get_evol_model('fb'))) - self.assert_(' #193' in str(tree.get_evol_model('fb'))) + self.assertIn('proportions', str(tree.get_evol_model('M2'))) + self.assertIn('p2=', str(tree.get_evol_model('M2'))) + self.assertNotIn('proportions', str(tree.get_evol_model('fb'))) + self.assertIn(' #193', str(tree.get_evol_model('fb'))) def test_get_most_likely(self): tree = EvolTree (WRKDIR + 'tree.nw') @@ -129,7 +129,7 @@ class TestEvolEvolTree(unittest.TestCase): tree.workdir = 'protamine/PRM1/paml/' random_swap(tree) tree.link_to_evol_model (WRKDIR + 'paml/fb/fb.out', 'fb') - self.assert_(check_annotation (tree)) + self.assertTrue(check_annotation (tree)) def test_deep_copy(self): tree = EvolTree (WRKDIR + 'tree.nw') @@ -173,11 +173,11 @@ class TestEvolEvolTree(unittest.TestCase): tree = EvolTree('((seq1,seq2),seq3);') tree.link_to_alignment('>seq1\nATGCTG\n>seq2\nATGCTG\n>seq3\nTTGATG\n') tree.run_model('fb') - self.assert_('CODONML' in tree.get_evol_model('fb').run) - self.assert_('Time used:' in tree.get_evol_model('fb').run) - self.assert_('end of tree file' in tree.get_evol_model('fb').run) - self.assert_('lnL' in tree.get_evol_model('fb').run) - self.assert_(tree.get_descendants()[0].w > 0) + self.assertIn('CODONML', tree.get_evol_model('fb').run) + self.assertIn('Time used:', tree.get_evol_model('fb').run) + self.assertIn('end of tree file', tree.get_evol_model('fb').run) + self.assertIn('lnL', tree.get_evol_model('fb').run) + self.assertTrue(tree.get_descendants()[0].w > 0) def test_run_slr(self): if which('Slr'): @@ -185,10 +185,10 @@ class TestEvolEvolTree(unittest.TestCase): tree.link_to_alignment('>seq1\nCTGATTCTT\n>seq2\nCTGATTCTT\n>seq3\nATGATTCTT\n') tree.run_model('SLR') print(tree.get_evol_model('SLR').run) - self.assert_('Sitewise Likelihood R' in tree.get_evol_model('SLR').run) - self.assert_('Positively selected s' in tree.get_evol_model('SLR').run) - self.assert_('Conserved sites' in tree.get_evol_model('SLR').run) - self.assert_('lnL' in tree.get_evol_model('SLR').run) + self.assertIn('Sitewise Likelihood R', tree.get_evol_model('SLR').run) + self.assertIn('Positively selected s', tree.get_evol_model('SLR').run) + self.assertIn('Conserved sites', tree.get_evol_model('SLR').run) + self.assertIn('lnL', tree.get_evol_model('SLR').run) def test_marking_trees(self): TREE_PATH = DATAPATH + '/S_example/' |