def test_raxml_rapid_bootstrap_with_seed(self):
# Test tip-to-tip dists are identical to manually run RAxML output.
# This test is comparing an ordered series of tip-to-tip distances
# to a tree output from a manual run of the default command:
# raxmlHPC -f a -m GTRGAMMA -p 1723 -x 3871 -N 10
# -s aligned-dna-sequences-3.fasta -n q2
# NOTE: I cleanly rounded the tip-to-tip dists (i.e. `%.4f`) as RAxML
# may return slightly different rounding errors on different
# systems (and at times, between conda environments).
input_fp = self.get_data_path('aligned-dna-sequences-3.fasta')
input_sequences = AlignedDNAFASTAFormat(input_fp, mode='r')
# test that branchlengths are identical
with redirected_stdio(stderr=os.devnull):
obs = raxml_rapid_bootstrap(input_sequences, seed=1723,
rapid_bootstrap_seed=3871,
bootstrap_replicates=10)
obs_tree = skbio.TreeNode.read(str(obs), convert_underscores=False)
# sometimes we lose the last set of numbers on long floats
obs_tl = list(obs_tree.tip_tip_distances().to_series())
obs_series = set(['%.4f' % e for e in obs_tl])
exp_tree = skbio.TreeNode.read(self.get_data_path('test2.tre'),
convert_underscores=True)
exp_tl = list(exp_tree.tip_tip_distances().to_series())
exp_series = set(['%.4f' % e for e in exp_tl])
self.assertEqual(obs_series, exp_series)
# test that bootstrap supports are identical
obs_bs = [node.name for node in obs_tree.non_tips()].sort()
exp_bs = [node.name for node in exp_tree.non_tips()].sort()
self.assertEqual(obs_bs, exp_bs)
def test_raxml_rapid_bootstrap_with_seed(self):
# Test tip-to-tip dists are identical to manually run RAxML output.
# This test is comparing an ordered series of tip-to-tip distances
# to a tree output from a manual run of the default command:
# raxmlHPC -f a -m GTRGAMMA -p 1723 -x 3871
# -s aligned-dna-sequences-3.fasta -n q2
# NOTE: I cleanly rounded the tip-to-tip dists (i.e. `%.4f`) as RAxML
# may return slightly different rounding errors on different
# systems (and at times, between conda environments).
input_fp = self.get_data_path('aligned-dna-sequences-3.fasta')
input_sequences = AlignedDNAFASTAFormat(input_fp, mode='r')
# test that branchlengths are identical
with redirected_stdio(stderr=os.devnull):
obs = raxml_rapid_bootstrap(input_sequences, seed=1723,
rapid_bootstrap_seed=3871,
bootstrap_replicates=10)
obs_tree = skbio.TreeNode.read(str(obs), convert_underscores=False)
# sometimes we lose the last set of numbers on long floats
obs_tl = list(obs_tree.tip_tip_distances().to_series())
obs_series = set(['%.4f' % e for e in obs_tl])
exp_tree = skbio.TreeNode.read(self.get_data_path('test2.tre'),
convert_underscores=True)
exp_tl = list(exp_tree.tip_tip_distances().to_series())
exp_series = set(['%.4f' % e for e in exp_tl])
self.assertEqual(obs_series, exp_series)
# test that bootstrap supports are identical
obs_bs = [node.name for node in obs_tree.non_tips()].sort()
exp_bs = [node.name for node in exp_tree.non_tips()].sort()
self.assertEqual(obs_bs, exp_bs)
def test_raxml_rapid_bootstrap(self):
# Test that output tree is made.
# Reads tree output and compares tip labels to expected labels.
input_fp = self.get_data_path('aligned-dna-sequences-3.fasta')
input_sequences = AlignedDNAFASTAFormat(input_fp, mode='r')
with redirected_stdio(stderr=os.devnull):
obs = raxml_rapid_bootstrap(input_sequences)
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', 'GCA000686145',
'GCA001950115', 'GCA001971985', 'GCA900007555']))
def test_raxml_rapid_bootstrap(self):
# Test that output tree is made.
# Reads tree output and compares tip labels to expected labels.
input_fp = self.get_data_path('aligned-dna-sequences-3.fasta')
input_sequences = AlignedDNAFASTAFormat(input_fp, mode='r')
with redirected_stdio(stderr=os.devnull):
obs = raxml_rapid_bootstrap(input_sequences)
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']))