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')
