def test_iqtree_ultrafast_bootstrap_singlebranch_methods(self):
# Comparing branch support to manually constructed tree
# using the following command:
# iqtree -s aligned-dna-sequences-1.fasta -alrt 1500 -lbp 1500
# -abayes -bb 1500 -m 'HKY' -seed 1723
# Here I am simply checking if the support values are identical
# to the manual run. Also check for number of values.
input_fp = self.get_data_path('aligned-dna-sequences-1.fasta')
input_sequences = AlignedDNAFASTAFormat(input_fp, mode='r')
with redirected_stdio(stderr=os.devnull):
obs = iqtree_ultrafast_bootstrap(input_sequences, seed=1723,
substitution_model='HKY',
alrt=1500, lbp=1500,
abayes=True,
bootstrap_replicates=1500)
obs_tree = skbio.TreeNode.read(str(obs), convert_underscores=False)
obs_supp = [node.name for node in obs_tree.non_tips()]
exp_tree = skbio.TreeNode.read(self.get_data_path('test2.tre'))
exp_supp = [node.name for node in exp_tree.non_tips()]
self.assertEqual(set(obs_supp), set(exp_supp))
self.assertEqual(len(obs_supp[0].split('/')), 4) # should be 4 values
self.assertEqual(len(exp_supp[0].split('/')), 4) # should be 4 values
def test_iqtree_ultrafast_bootstrap_auto_threads(self):
# Test that output tree is made after auto optimizing threads.
# Reads tree output and compares tip labels to expected labels.
input_fp = self.get_data_path('aligned-dna-sequences-1.fasta')
input_sequences = AlignedDNAFASTAFormat(input_fp, mode='r')
with redirected_stdio(stderr=os.devnull):
obs = iqtree_ultrafast_bootstrap(input_sequences, n_cores='auto')
obs_tree = skbio.TreeNode.read(str(obs))
# load the resulting tree and test that it has the right number of
# tips and the right tip ids
tips = list(obs_tree.tips())
tip_names = [t.name for t in tips]
self.assertEqual(set(tip_names),
set(['GCA001510755', 'GCA001045515', 'GCA000454205',
'GCA000473545', 'GCA000196255', 'GCA002142615',
'GCA000686145', 'GCA001950115', 'GCA001971985',
'GCA900007555']))