def iqtree_ultrafast_bootstrap(
alignment: AlignedDNAFASTAFormat,
seed: int = _iqtree_defaults['seed'],
n_cores: int = _iqtree_defaults['n_cores'],
n_cores_max: int = _iqtree_defaults['n_cores_max'],
n_runs: int = _iqtree_defaults['n_runs'],
substitution_model: str = _iqtree_defaults['substitution_model'],
bootstrap_replicates: int = _iqtree_defaults['bootstrap_replicates'],
n_init_pars_trees: int = _iqtree_defaults['n_init_pars_trees'],
n_top_init_trees: int = _iqtree_defaults['n_top_init_trees'],
n_best_retain_trees: int = _iqtree_defaults['n_best_retain_trees'],
stop_iter: int = _iqtree_defaults['stop_iter'],
perturb_nni_strength: float = _iqtree_defaults['perturb_nni_strength'],
spr_radius: int = _iqtree_defaults['spr_radius'],
n_max_ufboot_iter: int = _iqtree_defaults['n_max_ufboot_iter'],
n_ufboot_steps: int = _iqtree_defaults['n_ufboot_steps'],
min_cor_ufboot: float = _iqtree_defaults['min_cor_ufboot'],
ep_break_ufboot: float = _iqtree_defaults['ep_break_ufboot'],
allnni: bool = _iqtree_defaults['allnni'],
alrt: int = _iqtree_defaults['alrt'],
abayes: bool = _iqtree_defaults['abayes'],
lbp: int = _iqtree_defaults['lbp'],
bnni: bool = _iqtree_defaults['bnni'],
safe: bool = _iqtree_defaults['safe']) -> NewickFormat:
# NOTE: the IQ-TREE commands `-n` (called as `n_iter` in the `iqtree`
# method) and `-fast` are not compatable with ultrafast_bootstrap `-bb`.
result = NewickFormat()
with tempfile.TemporaryDirectory() as temp_dir:
run_prefix = os.path.join(temp_dir, 'q2iqtreeufboot')
cmd = _build_iqtree_ufbs_command(
alignment,
seed=seed,
n_cores=n_cores,
n_cores_max=n_cores_max,
n_runs=n_runs,
substitution_model=substitution_model,
bootstrap_replicates=bootstrap_replicates,
run_prefix=run_prefix,
n_init_pars_trees=n_init_pars_trees,
n_top_init_trees=n_top_init_trees,
n_best_retain_trees=n_best_retain_trees,
stop_iter=stop_iter,
perturb_nni_strength=perturb_nni_strength,
spr_radius=spr_radius,
n_max_ufboot_iter=n_max_ufboot_iter,
n_ufboot_steps=n_ufboot_steps,
min_cor_ufboot=min_cor_ufboot,
ep_break_ufboot=ep_break_ufboot,
allnni=allnni,
alrt=alrt,
abayes=abayes,
lbp=lbp,
bnni=bnni,
safe=safe)
run_command(cmd)
tree_tmp_fp = os.path.join(temp_dir, '%s.treefile' % run_prefix)
os.rename(tree_tmp_fp, str(result))
return result
def test_run_rapid_bs_not_verbose(self):
input_fp = self.get_data_path('aligned-dna-sequences-3.fasta')
input_sequences = AlignedDNAFASTAFormat(input_fp, mode='r')
aligned_fp = str(input_sequences)
with tempfile.TemporaryDirectory() as temp_dir:
cmd = ['raxmlHPC',
'-m', 'GTRGAMMA',
'-p', '1723',
'-s', aligned_fp,
'-w', temp_dir,
'-n', 'q2',
'-f', 'a',
'-x', '9834',
'-N', '10']
with redirected_stdio(stderr=os.devnull):
run_command(cmd, verbose=False)
obs_tree_fp = os.path.join(temp_dir, 'RAxML_bipartitions.q2')
obs_tree = skbio.TreeNode.read(str(obs_tree_fp),
convert_underscores=False)
# 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_run_rapid_bs_not_verbose(self):
input_fp = self.get_data_path('aligned-dna-sequences-3.fasta')
input_sequences = AlignedDNAFASTAFormat(input_fp, mode='r')
aligned_fp = str(input_sequences)
with tempfile.TemporaryDirectory() as temp_dir:
cmd = ['raxmlHPC',
'-m', 'GTRGAMMA',
'-p', '1723',
'-s', aligned_fp,
'-w', temp_dir,
'-n', 'q2',
'-f', 'a',
'-x', '9834',
'-N', '10']
with redirected_stdio(stderr=os.devnull):
run_command(cmd, verbose=False)
obs_tree_fp = os.path.join(temp_dir, 'RAxML_bipartitions.q2')
obs_tree = skbio.TreeNode.read(str(obs_tree_fp),
convert_underscores=False)
# 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']))
def test_run_ultrafast_bs_not_verbose(self):
input_fp = self.get_data_path('aligned-dna-sequences-3.fasta')
input_sequences = AlignedDNAFASTAFormat(input_fp, mode='r')
aligned_fp = str(input_sequences)
with tempfile.TemporaryDirectory() as temp_dir:
run_prefix = os.path.join(temp_dir, 'q2iqtreeufboot')
cmd = [
'iqtree', '-m', 'HKY', '-seed', '1723', '-bb', '1000', '-s',
aligned_fp, '-pre', run_prefix, '-nt', '2'
]
with redirected_stdio(stderr=os.devnull):
run_command(cmd, verbose=False)
obs_tree_fp = run_prefix + '.treefile'
obs_tree = skbio.TreeNode.read(str(obs_tree_fp),
convert_underscores=False)
# 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'
]))
def test_run_ultrafast_bs_not_verbose(self):
input_fp = self.get_data_path('aligned-dna-sequences-3.fasta')
input_sequences = AlignedDNAFASTAFormat(input_fp, mode='r')
aligned_fp = str(input_sequences)
with tempfile.TemporaryDirectory() as temp_dir:
run_prefix = os.path.join(temp_dir, 'q2iqtreeufboot')
cmd = ['iqtree',
'-m', 'HKY',
'-seed', '1723',
'-bb', '1000',
'-s', aligned_fp,
'-pre', run_prefix,
'-nt', '2']
with redirected_stdio(stderr=os.devnull):
run_command(cmd, verbose=False)
obs_tree_fp = run_prefix + '.treefile'
obs_tree = skbio.TreeNode.read(str(obs_tree_fp),
convert_underscores=False)
# 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']))
def iqtree_ultrafast_bootstrap(
alignment: AlignedDNAFASTAFormat,
seed: int = _iqtree_defaults['seed'],
n_cores: int = _iqtree_defaults['n_cores'],
n_runs: int = _iqtree_defaults['n_runs'],
substitution_model: str = _iqtree_defaults['substitution_model'],
bootstrap_replicates: int = _iqtree_defaults['bootstrap_replicates'],
n_init_pars_trees: int = _iqtree_defaults['n_init_pars_trees'],
n_top_init_trees: int = _iqtree_defaults['n_top_init_trees'],
n_best_retain_trees: int = _iqtree_defaults['n_best_retain_trees'],
stop_iter: int = _iqtree_defaults['stop_iter'],
perturb_nni_strength: float = _iqtree_defaults['perturb_nni_strength'],
spr_radius: int = _iqtree_defaults['spr_radius'],
n_max_ufboot_iter: int = _iqtree_defaults['n_max_ufboot_iter'],
n_ufboot_steps: int = _iqtree_defaults['n_ufboot_steps'],
min_cor_ufboot: float = _iqtree_defaults['min_cor_ufboot'],
ep_break_ufboot: float = _iqtree_defaults['ep_break_ufboot'],
allnni: bool = _iqtree_defaults['allnni'],
alrt: int = _iqtree_defaults['alrt'],
abayes: bool = _iqtree_defaults['abayes'],
lbp: int = _iqtree_defaults['lbp'],
bnni: bool = _iqtree_defaults['bnni'],
safe: bool = _iqtree_defaults['safe']
) -> NewickFormat:
# NOTE: the IQ-TREE commands `-n` (called as `n_iter` in the `iqtree`
# method) and `-fast` are not compatable with ultrafast_bootstrap `-bb`.
result = NewickFormat()
with tempfile.TemporaryDirectory() as temp_dir:
run_prefix = os.path.join(temp_dir, 'q2iqtreeufboot')
cmd = _build_iqtree_ufbs_command(
alignment,
seed=seed,
n_cores=n_cores,
n_runs=n_runs,
substitution_model=substitution_model,
bootstrap_replicates=bootstrap_replicates,
run_prefix=run_prefix,
n_init_pars_trees=n_init_pars_trees,
n_top_init_trees=n_top_init_trees,
n_best_retain_trees=n_best_retain_trees,
stop_iter=stop_iter,
perturb_nni_strength=perturb_nni_strength,
spr_radius=spr_radius,
n_max_ufboot_iter=n_max_ufboot_iter,
n_ufboot_steps=n_ufboot_steps,
min_cor_ufboot=min_cor_ufboot,
ep_break_ufboot=ep_break_ufboot,
allnni=allnni,
alrt=alrt,
abayes=abayes,
lbp=lbp,
bnni=bnni,
safe=safe)
run_command(cmd)
tree_tmp_fp = os.path.join(temp_dir, '%s.treefile' % run_prefix)
os.rename(tree_tmp_fp, str(result))
return result
def iqtree(
alignment: AlignedDNAFASTAFormat,
seed: int = _iqtree_defaults['seed'],
n_cores: int = _iqtree_defaults['n_cores'],
n_cores_max: int = _iqtree_defaults['n_cores_max'],
n_runs: int = _iqtree_defaults['n_runs'],
substitution_model: str = _iqtree_defaults['substitution_model'],
n_init_pars_trees: int = _iqtree_defaults['n_init_pars_trees'],
n_top_init_trees: int = _iqtree_defaults['n_top_init_trees'],
n_best_retain_trees: int = _iqtree_defaults['n_best_retain_trees'],
n_iter: int = _iqtree_defaults['n_iter'],
stop_iter: int = _iqtree_defaults['stop_iter'],
perturb_nni_strength: float = _iqtree_defaults['perturb_nni_strength'],
spr_radius: int = _iqtree_defaults['spr_radius'],
allnni: bool = _iqtree_defaults['allnni'],
fast: bool = _iqtree_defaults['fast'],
alrt: int = _iqtree_defaults['alrt'],
abayes: bool = _iqtree_defaults['abayes'],
lbp: int = _iqtree_defaults['lbp'],
safe: bool = _iqtree_defaults['safe'],
) -> NewickFormat:
result = NewickFormat()
with tempfile.TemporaryDirectory() as temp_dir:
run_prefix = os.path.join(temp_dir, 'q2iqtree')
cmd = _build_iqtree_command(alignment,
seed=seed,
n_cores=n_cores,
n_cores_max=n_cores_max,
n_runs=n_runs,
substitution_model=substitution_model,
run_prefix=run_prefix,
n_init_pars_trees=n_init_pars_trees,
n_top_init_trees=n_top_init_trees,
n_best_retain_trees=n_best_retain_trees,
n_iter=n_iter,
stop_iter=stop_iter,
perturb_nni_strength=perturb_nni_strength,
spr_radius=spr_radius,
allnni=allnni,
fast=fast,
alrt=alrt,
abayes=abayes,
lbp=lbp,
safe=safe)
run_command(cmd)
tree_tmp_fp = os.path.join(temp_dir, '%s.treefile' % run_prefix)
os.rename(tree_tmp_fp, str(result))
return result
def iqtree(
alignment: AlignedDNAFASTAFormat,
seed: int = _iqtree_defaults['seed'],
n_cores: int = _iqtree_defaults['n_cores'],
n_runs: int = _iqtree_defaults['n_runs'],
substitution_model: str = _iqtree_defaults['substitution_model'],
n_init_pars_trees: int = _iqtree_defaults['n_init_pars_trees'],
n_top_init_trees: int = _iqtree_defaults['n_top_init_trees'],
n_best_retain_trees: int = _iqtree_defaults['n_best_retain_trees'],
n_iter: int = _iqtree_defaults['n_iter'],
stop_iter: int = _iqtree_defaults['stop_iter'],
perturb_nni_strength: float = _iqtree_defaults['perturb_nni_strength'],
spr_radius: int = _iqtree_defaults['spr_radius'],
allnni: bool = _iqtree_defaults['allnni'],
fast: bool = _iqtree_defaults['fast'],
alrt: int = _iqtree_defaults['alrt'],
abayes: bool = _iqtree_defaults['abayes'],
lbp: int = _iqtree_defaults['lbp'],
safe: bool = _iqtree_defaults['safe'],
) -> NewickFormat:
result = NewickFormat()
with tempfile.TemporaryDirectory() as temp_dir:
run_prefix = os.path.join(temp_dir, 'q2iqtree')
cmd = _build_iqtree_command(alignment,
seed=seed,
n_cores=n_cores,
n_runs=n_runs,
substitution_model=substitution_model,
run_prefix=run_prefix,
n_init_pars_trees=n_init_pars_trees,
n_top_init_trees=n_top_init_trees,
n_best_retain_trees=n_best_retain_trees,
n_iter=n_iter,
stop_iter=stop_iter,
perturb_nni_strength=perturb_nni_strength,
spr_radius=spr_radius,
allnni=allnni,
fast=fast,
alrt=alrt,
abayes=abayes,
lbp=lbp,
safe=safe)
run_command(cmd)
tree_tmp_fp = os.path.join(temp_dir, '%s.treefile' % run_prefix)
os.rename(tree_tmp_fp, str(result))
return result
