def test_raxml_convert_raw_ancestral_states_to_fasta(self):
raxml = treebuilders.RAxML(8)
raxml.convert_raw_ancestral_states_to_fasta(os.path.join(data_dir, 'raxml_ancestral.state'),
os.path.join(data_dir, 'raxml_ancestral.fasta.actual'))
assert filecmp.cmp(os.path.join(data_dir, 'raxml_ancestral.fasta.actual'),
os.path.join(data_dir, 'raxml_ancestral.fasta.expected'))
os.remove(os.path.join(data_dir, 'raxml_ancestral.fasta.actual'))
def test_raxml_treebuilding_command(self):
raxml = treebuilders.RAxML(8)
raxml.executable = 'DDD'
raxml.tree_building_parameters = ['EEE']
assert raxml.tree_building_command(
'AAA', '', 'CCC') == 'DDD EEE -s AAA -n CCC -T 8 > /dev/null 2>&1'
raxml.verbose = True
raxml.threads = 1
assert raxml.tree_building_command(
'AAA', 'BBB', 'CCC') == 'DDD EEE -s AAA -n CCC -t BBB'
def test_raxml_select_executable_based_on_threads(self, mock_choice):
self.assertIs(mock_choice, utils.choose_executable_based_on_processor)
raxml = treebuilders.RAxML(8)
raxml.single_threaded_executables = ['BBB', 'CCC']
raxml.multi_threaded_executables = ['DDD', 'EEE']
mock_choice.return_value = 'AAA'
assert raxml.select_executable_based_on_threads() == 'AAA'
mock_choice.assert_called_with(['DDD', 'EEE'])
raxml.threads = 1
mock_choice.reset_mock()
mock_choice.return_value = None
assert raxml.select_executable_based_on_threads() is None
mock_choice.assert_any_call(['BBB', 'CCC'])
mock_choice.assert_any_call(['DDD', 'EEE'])
def test_raxml_sequence_reconstruction_command(self):
raxml = treebuilders.RAxML(8)
raxml.executable = 'DDD'
raxml.internal_sequence_reconstruction_parameters = ['EEE']
assert raxml.internal_sequence_reconstruction_command('AAA', 'BBB', 'CCC') \
== 'DDD EEE -s AAA -n CCC -T 8 -t BBB > /dev/null 2>&1'
def test_raxml_replace_internal_node_label(self):
raxml = treebuilders.RAxML(8, internal_node_prefix='AAA')
assert raxml.replace_internal_node_label('Node20') == 'AAANode20'
def test_raxml_select_executable_based_on_threads(self):
raxml_st = treebuilders.RAxML(1, model = 'GTRGAMMA')
raxml_mt = treebuilders.RAxML(8, model = 'GTRGAMMA')
assert (raxml_st.select_executable_based_on_threads() != raxml_mt.select_executable_based_on_threads() or raxml_st.threads > 1)