def test_min_setting(self): infile = self.unittest_dir + "testControlFileMin" setting = Setting.create_setting_from_file(infile) assembler = SoftwareAssembler(setting) expected = set(TestSoftwareAssembler.list_all_parameters) self.assertEqual(expected, set(assembler.get_all_par().viewkeys())) print assembler.get_all_par().values()
def test_some_optional(self): infile = self.unittest_dir + "testControlFileOp1" setting = Setting.create_setting_from_file(infile) assembler = SoftwareAssembler(setting) expected = set(TestSoftwareAssembler.list_all_parameters) self.assertEqual(expected, set(assembler.get_all_par().viewkeys())) self.assertEqual(run_genovo.DEFAULT_GENOVO_NO_ITER, assembler.get("genovo_num_iter")) self.assertEqual("1e-10", assembler.get("blast_e_value"))