def make_class_tree(
master_tree,
permutation_extent,
method,
with_check=True,
checklist=[],
):
"""
Function returns a tree object derived from a master tree,
but with some permutation applied. The type of permutation
is defined by `method`, one of 'nni', 'spr' and 'coal'
If with_check is True, the generated tree is checked against
a checklist of other trees on the same species, and permutations
are applied until the new tree has a unique topology. This is
only implemented for nni and spr.
"""
if num_permutations == 0:
return master_tree
new_tree = Tree(master_tree.newick)
if method == 'nni':
if with_check:
while not self.check_diff_top(new_tree, checklist):
new_tree = Tree(master_tree.newick)
for i in range(permutation_extent):
new_tree = new_tree.nni()
else:
for i in range(num_permutations):
new_tree = new_tree.nni()
elif method == 'spr':
if with_check:
while not self.check_diff_top(new_tree, checklist):
new_tree = Tree(master_tree.newick)
for i in range(permutation_extent):
new_tree = \
new_tree.spr(disallow_sibling_SPRs=True)
else:
for i in range(num_permutations):
new_tree = new_tree.spr()
elif method == 'coal':
new_tree = \
master_tree.get_constrained_gene_tree(scale_to=permutation_extent)
return new_tree
def make_class_tree(
master_tree,
permutation_extent,
method,
with_check=True,
checklist=[],
):
"""
Function returns a tree object derived from a master tree,
but with some permutation applied. The type of permutation
is defined by `method`, one of 'nni', 'spr' and 'coal'
If with_check is True, the generated tree is checked against
a checklist of other trees on the same species, and permutations
are applied until the new tree has a unique topology. This is
only implemented for nni and spr.
"""
if num_permutations == 0:
return master_tree
new_tree = Tree(master_tree.newick)
if method == 'nni':
if with_check:
while not self.check_diff_top(new_tree, checklist):
new_tree = Tree(master_tree.newick)
for i in range(permutation_extent):
new_tree = new_tree.nni()
else:
for i in range(num_permutations):
new_tree = new_tree.nni()
elif method == 'spr':
if with_check:
while not self.check_diff_top(new_tree, checklist):
new_tree = Tree(master_tree.newick)
for i in range(permutation_extent):
new_tree = \
new_tree.spr(disallow_sibling_SPRs=True)
else:
for i in range(num_permutations):
new_tree = new_tree.spr()
elif method == 'coal':
new_tree = \
master_tree.get_constrained_gene_tree(scale_to=permutation_extent)
return new_tree
