def test_iqtree_convert_raw_ancestral_states_to_fasta(self):
iqtree = treebuilders.IQTree(1, model = 'GTRGAMMA')
iqtree.convert_raw_ancestral_states_to_fasta(os.path.join(data_dir, 'iqtree_ancestral.state'),
os.path.join(data_dir, 'iqtree_ancestral.fasta.actual'))
assert filecmp.cmp(os.path.join(data_dir, 'iqtree_ancestral.fasta.actual'),
os.path.join(data_dir, 'iqtree_ancestral.fasta.expected'))
os.remove(os.path.join(data_dir, 'iqtree_ancestral.fasta.actual'))
def test_iqtree_treebuilding_command(self):
iqtree = treebuilders.IQTree(8)
iqtree.executable = 'DDD'
iqtree.tree_building_parameters = ['EEE']
assert iqtree.tree_building_command(
'AAA', '', 'CCC') == 'DDD EEE -s AAA -pre CCC -nt 8 -quiet'
iqtree.verbose = True
iqtree.threads = 0
assert iqtree.tree_building_command(
'AAA', 'BBB', 'CCC') == 'DDD EEE -s AAA -pre CCC -nt AUTO -t BBB'
def test_transfer_internal_node_labels_to_tree(self):
reconstructor = treebuilders.IQTree(1, "internal_")
common.transfer_internal_node_labels_to_tree(
'gubbins/tests/data/source_tree.tre',
'gubbins/tests/data/destination_tree.tre',
'gubbins/tests/data/renamed_output_tree', reconstructor)
assert os.path.exists('gubbins/tests/data/renamed_output_tree')
assert filecmp.cmp('gubbins/tests/data/renamed_output_tree',
'gubbins/tests/data/expected_renamed_output_tree',
shallow=False)
os.remove('gubbins/tests/data/renamed_output_tree')
def test_transfer_internal_node_labels_to_tree(self):
reconstructor = treebuilders.IQTree(1,
model='GTRGAMMA',
internal_node_prefix='internal_')
common.transfer_internal_node_labels_to_tree(
os.path.join(data_dir, 'source_tree.tre'),
os.path.join(data_dir, 'destination_tree.tre'),
os.path.join(data_dir, 'renamed_output_tree'), reconstructor)
assert os.path.exists(os.path.join(data_dir, 'renamed_output_tree'))
assert filecmp.cmp(os.path.join(data_dir, 'renamed_output_tree'),
os.path.join(data_dir,
'expected_renamed_output_tree'),
shallow=False)
os.remove(os.path.join(data_dir, 'renamed_output_tree'))
def test_iqtree_replace_internal_node_label(self):
iqtree = treebuilders.IQTree(8, 'AAA')
assert iqtree.replace_internal_node_label('Node20') == 'AAA20'
def test_iqtree_sequence_reconstruction_command(self):
iqtree = treebuilders.IQTree(8)
iqtree.executable = 'DDD'
iqtree.internal_sequence_reconstruction_parameters = ['EEE']
assert iqtree.internal_sequence_reconstruction_command('AAA', 'BBB', 'CCC') \
== 'DDD EEE -s AAA -pre CCC -nt 8 -te BBB -quiet'
def test_iqtree_replace_internal_node_label(self):
iqtree = treebuilders.IQTree(1, model = 'GTRGAMMA', internal_node_prefix='AAA')
assert iqtree.replace_internal_node_label('Node20') == 'AAA20'