def test_fasttree(self): self.assertEqual(2, 1+1) parser = self.default_arg_parse() common.parse_and_run(parser.parse_args(["--tree_builder", "fasttree", os.path.join(data_dir, 'multiple_recombinations.aln')])) self.check_for_output_files('multiple_recombinations') self.cleanup('multiple_recombinations')
def test_cleanup(self): parser = run_gubbins.parse_input_args() common.parse_and_run( parser.parse_args([ "--tree-builder", "iqtree", "--verbose", os.path.join(data_dir, 'multiple_recombinations.aln') ])) self.cleanup('multiple_recombinations') assert not glob.glob('multiple_recombinations.aln.*') assert not glob.glob('multiple_recombinations.iteration*')
def test_rapidnj(self): exit_code = 0 parser = run_gubbins.parse_input_args() try: common.parse_and_run( parser.parse_args([ "--tree-builder", "rapidnj", "--model", "JC", "--verbose", "--iterations", "3", "--threads", "1", os.path.join(data_dir, 'multiple_recombinations.aln') ])) self.check_for_output_files('multiple_recombinations') except: sys.stderr.write("Test failed") exit_code = 1 self.cleanup('multiple_recombinations') assert exit_code == 0
def test_rename_final_output(self): exit_code = 0 parser = run_gubbins.parse_input_args() try: common.parse_and_run( parser.parse_args([ "--prefix", "different_prefix", "--verbose", "--iterations", "3", os.path.join(data_dir, 'multiple_recombinations.aln') ])) self.check_for_output_files('different_prefix') except: sys.stderr.write("Test failed") exit_code = 1 self.cleanup('different_prefix') assert exit_code == 0
def test_raxml_sh_test(self): exit_code = 0 parser = run_gubbins.parse_input_args() try: common.parse_and_run( parser.parse_args([ "--tree-builder", "raxml", "--verbose", "--iterations", "3", "--threads", "1", "--sh-test", os.path.join(data_dir, 'bootstrapping_test.aln') ])) self.check_for_output_files('bootstrapping_test') except: sys.stderr.write("Test failed") exit_code = 1 self.cleanup('bootstrapping_test') assert exit_code == 0
def test_cleanup(self): parser = self.default_arg_parse() common.parse_and_run(parser.parse_args([os.path.join(data_dir, 'multiple_recombinations.aln')])) assert not glob.glob('multiple_recombinations.aln.*') assert not glob.glob('multiple_recombinations.iteration*') self.cleanup('multiple_recombinations')
def test_rename_final_output(self): parser = self.default_arg_parse() common.parse_and_run(parser.parse_args(["--prefix", "different_prefix", os.path.join(data_dir, 'multiple_recombinations.aln')])) self.check_for_output_files('different_prefix') self.cleanup('different_prefix')
def test_hybrid(self): parser = self.default_arg_parse() common.parse_and_run(parser.parse_args(["--tree_builder", "hybrid", os.path.join(data_dir, 'multiple_recombinations.aln')])) self.check_for_output_files('multiple_recombinations') self.cleanup('multiple_recombinations')