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src/b/i/biopython-1.63/Tests/test_PAML_codeml.py   biopython(Download)
                        % version.replace('_', '.')
            results_path = os.path.join(res_dir, results_file)
            results = codeml.read(results_path)
            self.assertEqual(len(results), 4, version_msg)
            self.assertTrue("NSsites" in results, version_msg)
                        % version.replace('_', '.')
            results_path = os.path.join(res_dir, results_file)
            results = codeml.read(results_path)
            # There should be 4 top-level items: 'codon model', 'model',
            # 'version', & 'NSsites'
                        % version.replace('_', '.')
            results_path = os.path.join(res_dir, results_file)
            results = codeml.read(results_path)
            # There should be 5 top-level items: 'codon model', 'model',
            # 'version', 'NSsites' & site-class model, the last of which
                        % version.replace('_', '.')
            results_path = os.path.join(res_dir, results_file)
            results = codeml.read(results_path)
            # There are 5 top-level items in this case:
            # 'codon model', 'model', 'version', 'NSsites' & 'site-class model'
                        % version.replace('_', '.')
            results_path = os.path.join(cladeC_res_dir, results_file)
            results = codeml.read(results_path)
            # 5 top-level items again in this case
            self.assertEqual(len(results), 5, version_msg)

src/b/i/biopython-HEAD/Tests/test_PAML_codeml.py   biopython(Download)
                        % version.replace('_', '.')
            results_path = os.path.join(res_dir, results_file)
            results = codeml.read(results_path)
            self.assertEqual(len(results), 4, version_msg)
            self.assertTrue("NSsites" in results, version_msg)
                        % version.replace('_', '.')
            results_path = os.path.join(res_dir, results_file)
            results = codeml.read(results_path)
            # There should be 4 top-level items: 'codon model', 'model',
            # 'version', & 'NSsites'
                        % version.replace('_', '.')
            results_path = os.path.join(res_dir, results_file)
            results = codeml.read(results_path)
            # There should be 5 top-level items: 'codon model', 'model',
            # 'version', 'NSsites' & site-class model, the last of which
                        % version.replace('_', '.')
            results_path = os.path.join(res_dir, results_file)
            results = codeml.read(results_path)
            # There are 5 top-level items in this case:
            # 'codon model', 'model', 'version', 'NSsites' & 'site-class model'
                        % version.replace('_', '.')
            results_path = os.path.join(cladeC_res_dir, results_file)
            results = codeml.read(results_path)
            # 5 top-level items again in this case
            self.assertEqual(len(results), 5, version_msg)