def constrained_kingman(*args, **kwargs):
deprecate.dendropy_deprecation_warning(
preamble="Deprecated since DendroPy 4: The 'dendropy.treesim.constrained_kingman()' function has moved to 'dendropy.simulate.treesim.constrained_kingman_tree()'.",
old_construct="from dendropy import treesim\ntree = treesim.constrained_kingman(...)",
new_construct="from dendropy.simulate import treesim\ntree = treesim.constrained_kingman_tree(...)",
)
return treesim.constrained_kingman_tree(*args, **kwargs)
def find_missing_splits(reference_tree, test_tree):
deprecate.dendropy_deprecation_warning(
preamble="Deprecated since DendroPy 4: The 'dendropy.treecalc.find_missing_splits()' function has moved to 'dendropy.calculate.treecompare.find_missing_splits()'.",
old_construct="from dendropy import treecalc\nd = treecalc.find_missing_splits(...)",
new_construct="from dendropy.calculate import treecompare\nd = treecompare.find_missing_splits(...)",
)
return treecompare.find_missing_splits(reference_tree=reference_tree, comparison_tree=test_tree)
def pop_gen_tree(*args, **kwargs):
deprecate.dendropy_deprecation_warning(
preamble="Deprecated since DendroPy 4: The 'dendropy.treesim.pop_gen_tree()' function has moved to 'dendropy.simulate.popgensim.pop_gen_tree()'.",
old_construct="from dendropy import treesim\ntree = treesim.pop_gen_tree(...)",
new_construct="from dendropy.simulate import popgensim\ntree = popgensim.pop_gen_tree(...)",
)
return popgensim.pop_gen_tree(*args, **kwargs)
def _deprecate_tree_manip(old, new):
deprecate.dendropy_deprecation_warning(
preamble=
"Deprecated since DendroPy 4: Tree structure manipulation and editing functionality are now native methods of the 'dendropy.Tree' class.",
old_construct=old,
new_construct=new,
stacklevel=4)
def generate_hky_dataset(seq_len,
tree_model,
mutation_rate=1.0,
kappa=1.0,
base_freqs=[0.25, 0.25, 0.25, 0.25],
root_states=None,
dataset=None,
rng=None):
deprecate.dendropy_deprecation_warning(
preamble=
"Deprecated since DendroPy 4: The 'dendropy.seqsim.generate_hky_dataset()' function has been replaced with 'dendropy.simulate.charsim.hky85_chars()'.",
old_construct=
"from dendropy import seqsim\ndataset = seqsim.generate_hky_dataset(...)",
new_construct=
"import dendropy\nfrom dendropy.simulate import charsim\ndataset = dendropy.DataSet()\nchar_matrix = charsim.hky85_chars(...)\ndataset.add_char_matrix(char_matrix)"
)
if dataset is None:
dataset = dendropy.DataSet()
char_matrix = dataset.new_char_matrix(
char_matrix_type="dna", taxon_namespace=tree_model.taxon_namespace)
charsim.hky85_chars(seq_len=seq_len,
tree_model=tree_model,
mutation_rate=mutation_rate,
kappa=kappa,
base_freqs=base_freqs,
root_states=root_states,
char_matrix=char_matrix,
rng=rng)
return dataset
def is_compatible(split1, split2, mask):
deprecate.dendropy_deprecation_warning(
preamble=
"Deprecated since DendroPy 4: 'dendropy.treesplit.is_compatible()'.",
old_construct=
"from dendropy import treesplit\nd = treesplit.is_compatible(...)",
new_construct="""\
# if using a bipartition
d = bipartition.is_compatible_with(other_bipartition)
# if a "raw" bitmask
d = dendropy.Bipartition.is_compatible_bitmasks(m1, m2, fill_bitmask=mask)""")
"""
Mask should have 1 for every leaf in the leaf_set
"""
# m1 = mask & split1
# m2 = mask & split2
# if 0 == (m1 & m2):
# return True
# c2 = mask ^ split2
# if 0 == (m1 & c2):
# return True
# c1 = mask ^ split1
# if 0 == (c1 & m2):
# return True
# if 0 == (c1 & c2):
# return True
# return False
return dendropy.Bipartition.is_compatible_bitmasks(split1,
split2,
fill_bitmask=mask)
def generate_hky_dataset(seq_len,
tree_model,
mutation_rate=1.0,
kappa=1.0,
base_freqs=[0.25, 0.25, 0.25, 0.25],
root_states=None,
dataset=None,
rng=None):
deprecate.dendropy_deprecation_warning(
preamble="Deprecated since DendroPy 4: The 'dendropy.seqsim.generate_hky_dataset()' function has been replaced with 'dendropy.simulate.charsim.hky85_chars()'.",
old_construct="from dendropy import seqsim\ndataset = seqsim.generate_hky_dataset(...)",
new_construct="import dendropy\nfrom dendropy.simulate import charsim\ndataset = dendropy.DataSet()\nchar_matrix = charsim.hky85_chars(...)\ndataset.add_char_matrix(char_matrix)")
if dataset is None:
dataset = dendropy.DataSet()
char_matrix = dataset.new_char_matrix(char_matrix_type="dna", taxon_namespace=tree_model.taxon_namespace)
charsim.hky85_chars(
seq_len=seq_len,
tree_model=tree_model,
mutation_rate=mutation_rate,
kappa=kappa,
base_freqs=base_freqs,
root_states=root_states,
char_matrix=char_matrix,
rng=rng)
return dataset
def average_number_of_pairwise_differences(char_matrix, ignore_uncertain=True):
deprecate.dendropy_deprecation_warning(
preamble="The 'dendropy.popgenstat' module has moved to 'dendropy.calculate.popgenstat'.",
old_construct="from dendropy import popgenstat\npopgenstat.average_number_of_pairwise_differences(...)",
new_construct="from dendropy.calculate import popgenstat\npopgenstat.average_number_of_pairwise_differences(...)",
)
return popgenstat.average_number_of_pairwise_differences(char_matrix=char_matrix, ignore_uncertain=ignore_uncertain)
def reconciliation_discordance(gene_tree, species_tree):
deprecate.dendropy_deprecation_warning(
preamble="The 'dendropy.reconcile' module has moved to 'dendropy.model.reconcile'.",
old_construct="from dendropy import reconcile\nreconcile.reconciliation_discordance(...)",
new_construct="from dendropy.model import reconcile\nreconcile.reconciliation_discordance(...)",
)
return reconcile.reconciliation_discordance(gene_tree, species_tree)
def num_segregating_sites(char_matrix, ignore_uncertain=True):
deprecate.dendropy_deprecation_warning(
preamble="The 'dendropy.popgenstat' module has moved to 'dendropy.calculate.popgenstat'.",
old_construct="from dendropy import popgenstat\npopgenstat.num_segregating_sites(...)",
new_construct="from dendropy.calculate import popgenstat\npopgenstat.num_segregating_sites(...)",
)
return popgenstat.num_segregating_sites(char_matrix, ignore_uncertain)
def symmetric_difference(tree1, tree2):
deprecate.dendropy_deprecation_warning(
preamble="Deprecated since DendroPy 4: The 'dendropy.treecalc.symmetric_difference()' function has moved to 'dendropy.calculate.treecompare.symmetric_difference()'.",
old_construct="from dendropy import treecalc\nd = treecalc.symmetric_difference(...)",
new_construct="from dendropy.calculate import treecompare\nd = treecompare.symmetric_difference(...)",
)
return treecompare.symmetric_difference(tree1=tree1, tree2=tree2)
def uniform_pure_birth(*args, **kwargs):
deprecate.dendropy_deprecation_warning(
preamble="Deprecated since DendroPy 4: The 'dendropy.treesim.uniform_pure_birth()' function has moved to 'dendropy.simulate.treesim.uniform_pure_birth_tree()'.",
old_construct="from dendropy import treesim\ntree = treesim.uniform_pure_birth(...)",
new_construct="from dendropy.simulate import treesim\ntree = treesim.uniform_pure_birth_tree(...)",
)
return treesim.uniform_pure_birth_tree(*args, **kwargs)
def node_waiting_time_pairs(tree, ultrametricity_precision=constants.DEFAULT_ULTRAMETRICITY_PRECISION):
deprecate.dendropy_deprecation_warning(
preamble="Deprecated since DendroPy 4: The 'dendropy.coalescent' module has moved to 'dendropy.model.coalescent'.",
old_construct="from dendropy import coalescent\ncoalescent.node_waiting_time_pairs(...)",
new_construct="from dendropy.model import coalescent\ncoalescent.node_waiting_time_pairs(...)")
return coalescent.node_waiting_time_pairs(tree=tree,
ultrametricity_precision=ultrametricity_precision)
def simulate_continuous(node, rng=None, **kwargs):
deprecate.dendropy_deprecation_warning(
preamble="The 'dendropy.continuous' module has moved to 'dendropy.model.continuous', and this function has been renamed 'evolve_continuous_char()'.",
old_construct="from dendropy import continuous\ncontinuous.simulate_continuous(...)",
new_construct="from dendropy.model import continuous\ncontinuous.evolve_continuous_char(...)",
epilog="Note that this function is also available through 'dendropy.simulate.charsim.evolve_continuous_char(...)'.")
return continuous.evolve_continuous_char(node, rng, **kwargs)
def is_compatible(split1, split2, mask):
deprecate.dendropy_deprecation_warning(
preamble="Deprecated since DendroPy 4: 'dendropy.treesplit.is_compatible()'.",
old_construct="from dendropy import treesplit\nd = treesplit.is_compatible(...)",
new_construct="""\
# if using a bipartition
d = bipartition.is_compatible_with(other_bipartition)
# if a "raw" bitmask
d = dendropy.Bipartition.is_compatible_bitmasks(m1, m2, fill_bitmask=mask)""")
"""
Mask should have 1 for every leaf in the leaf_set
"""
# m1 = mask & split1
# m2 = mask & split2
# if 0 == (m1 & m2):
# return True
# c2 = mask ^ split2
# if 0 == (m1 & c2):
# return True
# c1 = mask ^ split1
# if 0 == (c1 & m2):
# return True
# if 0 == (c1 & c2):
# return True
# return False
return dendropy.Bipartition.is_compatible_bitmasks(split1, split2, fill_bitmask=mask)
def __init__(self, *args, **kwargs):
deprecate.dendropy_deprecation_warning(
preamble="The 'dendropy.reconcile' module has moved to 'dendropy.model.reconcile'.",
old_construct="from dendropy import reconcile\nreconcile.ContainingTree(...)",
new_construct="from dendropy.model import reconcile\nreconcile.ContainingTree(...)",
)
reconcile.ContainingTree.__init__(self, *args, **kwargs)
def monophyletic_partition_discordance(tree, taxon_namespace_partition):
deprecate.dendropy_deprecation_warning(
preamble="The 'dendropy.reconcile' module has moved to 'dendropy.model.reconcile'.",
old_construct="from dendropy import reconcile\nreconcile.monophyletic_partition_discordance(...)",
new_construct="from dendropy.model import reconcile\nreconcile.monophyletic_partition_discordance(...)",
)
return reconcile.monophyletic_partition_discordance(tree, taxon_namespace_partition)
def wattersons_theta(char_matrix, ignore_uncertain=True):
deprecate.dendropy_deprecation_warning(
preamble="The 'dendropy.popgenstat' module has moved to 'dendropy.calculate.popgenstat'.",
old_construct="from dendropy import popgenstat\npopgenstat.watterson_theta(...)",
new_construct="from dendropy.calculate import popgenstat\npopgenstat.watterson_theta(...)",
)
return popgenstat.wattersons_theta(char_matrix=char_matrix, ignore_uncertain=ignore_uncertain)
def __init__(self, *args, **kwargs):
deprecate.dendropy_deprecation_warning(
preamble="The 'dendropy.popgensim' module has moved to 'dendropy.simulate.popgensim'.",
old_construct="from dendropy import popgensim\npopgensim.FragmentedPopulations(...)",
new_construct="from dendropy.simulate import popgensim\npopgensim.FragmentedPopulations(...)",
)
popgensim.FragmentedPopulations.__init__(self, *args, **kwargs)
def unify_taxa(self, taxon_set=None, bind=None):
deprecate.dendropy_deprecation_warning(
message=
"Deprecated since DendroPy 4: '{class_name}.unify_taxa()' will no longer be supported in future releases; use '{class_name}.unify_taxon_namespaces()' instead"
.format(class_name=self.__class__.__name__))
self.unify_taxon_namespaces(taxon_namespace=taxon_set,
attach_taxon_namespace=bind)
def robinson_foulds_distance(tree1, tree2, edge_length_attr="length"):
deprecate.dendropy_deprecation_warning(
preamble="Deprecated since DendroPy 4: The 'dendropy.treecalc.robinson_foulds_distance()' function has moved to 'dendropy.calculate.treecompare.weighted_robinson_foulds_distance()'.",
old_construct="from dendropy import treecalc\nd = treecalc.robinson_foulds_distance(...)",
new_construct="from dendropy.calculate import treecompare\nd = treecompare.weighted_robinson_foulds_distance(...)",
)
return treecompare.weighted_robinson_foulds_distance(tree1=tree1, tree2=tree2, edge_weight_attr=edge_length_attr)
def patristic_distance(tree, taxon1, taxon2):
deprecate.dendropy_deprecation_warning(
preamble="Deprecated since DendroPy 4: The 'dendropy.treecalc.patristic_distance()' function has moved to 'dendropy.calculate.treemeasure.patristic_distance()'.",
old_construct="from dendropy import treecalc\npdm = treecalc.patristic_distance(...)",
new_construct="from dendropy.calculate import treemeasure\npdm = treemeasure.patristic_distance(...)",
)
return treemeasure.patristic_distance(tree=tree, taxon1=taxon1, taxon2=taxon2)
def __init__(self, tree=None):
deprecate.dendropy_deprecation_warning(
preamble="Deprecated since DendroPy 4: The 'dendropy.treecalc.PhylogeneticDistanceMatrix' class has moved to 'dendropy.PhylogeneticDistanceMatrix'.",
old_construct="from dendropy import treecalc\npdm = treecalc.PhylogeneticDistanceMatrix(...)",
new_construct="import dendropy\npdm = dendropy.PhylogeneticDistanceMatrix(...)",
)
dendropy.PhylogeneticDistanceMatrix.__init__(self, tree=tree)
def __init__(self, *args, **kwargs):
deprecate.dendropy_deprecation_warning(
preamble="The 'dendropy.popgenstat' module has moved to 'dendropy.calculate.popgenstat'.",
old_construct="from dendropy import popgenstat\npopgenstat.PopulationPairSummaryStatistics(...)",
new_construct="from dendropy.calculate import popgenstat\npopgenstat.PopulationPairSummaryStatistics(...)",
)
popgenstat.PopulationPairSummaryStatistics.__init__(self, *args, **kwargs)
def delete_outdegree_one(tree):
deprecate.dendropy_deprecation_warning(
preamble=
"Deprecated since DendroPy 4: 'dendropy.treesplit.delete_outdegree_one()'.",
old_construct=
"from dendropy import treesplit\nd = treesplit.delete_outdegree_one(tree)",
new_construct="tree.suppress_unifurcations()")
return tree.suppress_unifurcations()
def attach_taxon_set(self, taxon_set=None):
"""
DEPRECATED: Use `attach_taxon_namespace()` instead.
"""
deprecate.dendropy_deprecation_warning(
message="Deprecated since DendroPy 4: 'attach_taxon_set' will no longer be supported in future releases; use 'attach_taxon_namespace' instead",
stacklevel=3)
return self.attach_taxon_namespace(taxon_namespace=taxon_set)
def new_taxon_set(self, *args, **kwargs):
"""
DEPRECATED: Use `new_taxon_namespace()` instead.
"""
deprecate.dendropy_deprecation_warning(
message="Deprecated since DendroPy 4: 'new_taxon_set' will no longer be supported in future releases; use 'new_taxon_namespace' instead",
stacklevel=3)
return self.new_taxon_namespace(*args, **kwargs)
def detach_taxon_set(self):
"""
DEPRECATED: Use `detach_taxon_namespace()` instead.
"""
deprecate.dendropy_deprecation_warning(
message="Deprecated since DendroPy 4: 'detach_taxon_set' will no longer be supported in future releases; use 'detach_taxon_namespace' instead",
stacklevel=3)
self.detach_taxon_namespace()
def star_tree(*args, **kwargs):
deprecate.dendropy_deprecation_warning(
preamble=
"Deprecated since DendroPy 4: The 'dendropy.treesim.star()' function has moved to 'dendropy.simulate.treesim.star_tree()'.",
old_construct="from dendropy import treesim\ntree = treesim.star(...)",
new_construct=
"from dendropy.simulate import treesim\ntree = treesim.star_tree(...)")
return treesim.star_tree(*args, **kwargs)
def find_missing_splits(reference_tree, test_tree):
deprecate.dendropy_deprecation_warning(
preamble="Deprecated since DendroPy 4: The 'dendropy.treecalc.find_missing_splits()' function has moved to 'dendropy.calculate.treecompare.find_missing_splits()'.",
old_construct="from dendropy import treecalc\nd = treecalc.find_missing_splits(...)",
new_construct="from dendropy.calculate import treecompare\nd = treecompare.find_missing_splits(...)")
return treecompare.find_missing_splits(
reference_tree=reference_tree,
comparison_tree=test_tree)
def symmetric_difference(tree1, tree2):
deprecate.dendropy_deprecation_warning(
preamble="Deprecated since DendroPy 4: The 'dendropy.treecalc.symmetric_difference()' function has moved to 'dendropy.calculate.treecompare.symmetric_difference()'.",
old_construct="from dendropy import treecalc\nd = treecalc.symmetric_difference(...)",
new_construct="from dendropy.calculate import treecompare\nd = treecompare.symmetric_difference(...)")
return treecompare.symmetric_difference(
tree1=tree1,
tree2=tree2)
def derived_state_matrix(char_matrix, ancestral_seq=None):
deprecate.dendropy_deprecation_warning(
preamble="The 'dendropy.popgenstat' module has moved to 'dendropy.calculate.popgenstat'.",
old_construct="from dendropy import popgenstat\npopgenstat.derived_state_matrix(...)",
new_construct="from dendropy.calculate import popgenstat\npopgenstat.derived_state_matrix(...)",
)
return popgenstat.derived_state_matrix(
char_matrix=char_matrix,
ancestral_sequence=ancestral_seq)
def __init__(self, tree=None):
deprecate.dendropy_deprecation_warning(
preamble=
"Deprecated since DendroPy 4: The 'dendropy.treecalc.PhylogeneticDistanceMatrix' class has moved to 'dendropy.PhylogeneticDistanceMatrix'.",
old_construct=
"from dendropy import treecalc\npdm = treecalc.PhylogeneticDistanceMatrix(...)",
new_construct=
"import dendropy\npdm = dendropy.PhylogeneticDistanceMatrix(...)")
dendropy.PhylogeneticDistanceMatrix.__init__(self, tree=tree)
def __init__(self, **kwargs):
deprecate.dendropy_deprecation_warning(
preamble="Deprecated since DendroPy 4:",
old_construct="d = dendropy.CharacterMatrix.get_from_path(schema='proteinfasta', ...)\nd = dendropy.DataSet.get_from_path(schema='proteinfasta', ...)",
new_construct="d = dendropy.ProteinCharacterMatrix.get(path=..., schema='fasta', ...)\nd = dendropy.DataSet.get(path=..., schema='fasta', data_type='protein', ...)",
stacklevel=7)
# raise TypeError("'proteinfasta' is no longer a supported schema: use 'schema=\"fasta\"' with the 'ProteinCharacterMatrix.get()' method instead or 'schema=\"fasta\"' and 'data_type=\"dna\" with the 'DataSet.get()' or 'DataSet.read()' methods")
kwargs["data_type"] = "protein"
FastaReader.__init__(self, **kwargs)
def __init__(self, state_alphabet=None, rng=None):
deprecate.dendropy_deprecation_warning(
preamble="Deprecated since DendroPy 4: The 'dendropy.seqmodel.Jc69SeqModel' class has moved to 'dendropy.model.discrete.Jc69'.",
old_construct="from dendropy import seqmodel\nm = seqmodel.NucleotideSeqModel(...)",
new_construct="from dendropy.model import discrete\ndiscrete.Jc69(...)")
discrete.Jc69.__init__(
self,
state_alphabet=state_alphabet,
rng=rng)
def patristic_distance(tree, taxon1, taxon2):
deprecate.dendropy_deprecation_warning(
preamble="Deprecated since DendroPy 4: The 'dendropy.treecalc.patristic_distance()' function has moved to 'dendropy.calculate.treemeasure.patristic_distance()'.",
old_construct="from dendropy import treecalc\npdm = treecalc.patristic_distance(...)",
new_construct="from dendropy.calculate import treemeasure\npdm = treemeasure.patristic_distance(...)")
return treemeasure.patristic_distance(
tree=tree,
taxon1=taxon1,
taxon2=taxon2)
def __init__(self, state_alphabet=None, rng=None):
deprecate.dendropy_deprecation_warning(
preamble=
"Deprecated since DendroPy 4: The 'dendropy.seqmodel.Jc69SeqModel' class has moved to 'dendropy.model.discrete.Jc69'.",
old_construct=
"from dendropy import seqmodel\nm = seqmodel.NucleotideSeqModel(...)",
new_construct=
"from dendropy.model import discrete\ndiscrete.Jc69(...)")
discrete.Jc69.__init__(self, state_alphabet=state_alphabet, rng=rng)
def euclidean_distance(tree1, tree2, edge_length_attr="length", value_type=float):
deprecate.dendropy_deprecation_warning(
preamble="Deprecated since DendroPy 4: The 'dendropy.treecalc.euclidean_distance()' function has moved to 'dendropy.calculate.treecompare.euclidean_distance()'.",
old_construct="from dendropy import treecalc\nd = treecalc.euclidean_distance(...)",
new_construct="from dendropy.calculate import treecompare\nd = treecompare.euclidean_distance(...)",
)
return treecompare.euclidean_distance(
tree1=tree1, tree2=tree2, edge_weight_attr=edge_length_attr, value_type=value_type
)
def __init__(self, state_alphabet, rng=None):
deprecate.dendropy_deprecation_warning(
preamble="Deprecated since DendroPy 4: The 'dendropy.seqmodel.SeqModel' class has moved to 'dendropy.model.discrete.DiscreteCharacterEvolutionModel'.",
old_construct="from dendropy import seqmodel\nm = seqmodel.SeqModel(...)",
new_construct="from dendropy.model import discrete\nm = discrete.DiscreteCharacterEvolutionModel(...)")
discrete.DiscreteCharacterEvolutionModel.__init__(
self,
state_alphabet=state_alphabet,
rng=rng)
def tree_from_splits(splits, taxon_set, is_rooted=False):
deprecate.dendropy_deprecation_warning(
preamble="Deprecated since DendroPy 4: 'dendropy.treesplit.tree_from_splits()'.",
old_construct="from dendropy import treesplit\ntree = treesplit.tree_from_splits(...)",
new_construct="import dendropy\ntree = dendropy.Tree.from_split_bitmasks(...)")
return dendropy.Tree.from_split_bitmasks(
split_bitmasks=splits,
taxon_namespace=taxon_set,
is_rooted=is_rooted)
def count_bits(a):
deprecate.dendropy_deprecation_warning(
preamble=
"Deprecated since DendroPy 4: 'dendropy.treesplit.count_bits()'.",
old_construct=
"from dendropy import treesplit\nd = treesplit.count_bits(...)",
new_construct=
"from dendropy.utility import bitprocessing\nd = bitprocessing.num_set_bits(...)"
)
return bitprocessing.num_set_bits(a)
def lowest_bit_only(s):
deprecate.dendropy_deprecation_warning(
preamble=
"Deprecated since DendroPy 4: 'dendropy.treesplit.lowest_bit_only()'.",
old_construct=
"from dendropy import treesplit\nd = treesplit.lowest_bit_only(...)",
new_construct=
"from dendropy.utility import bitprocessing\nd = bitprocessing.least_significant_set_bit(...)"
)
return bitprocessing.least_significant_set_bit(s)
def num_segregating_sites(char_matrix, ignore_uncertain=True):
deprecate.dendropy_deprecation_warning(
preamble=
"The 'dendropy.popgenstat' module has moved to 'dendropy.calculate.popgenstat'.",
old_construct=
"from dendropy import popgenstat\npopgenstat.num_segregating_sites(...)",
new_construct=
"from dendropy.calculate import popgenstat\npopgenstat.num_segregating_sites(...)",
)
return popgenstat.num_segregating_sites(char_matrix, ignore_uncertain)
def __init__(self, **kwargs):
deprecate.dendropy_deprecation_warning(
preamble=
"Deprecated since DendroPy 4: The 'dendropy.treesum.TopologyCounter' class has moved to 'dendropy.calculate.treesum.TopologyCounter'.",
old_construct=
"from dendropy import treesum\nm = treesum.TopologyCounter(...)",
new_construct=
"from dendropy.calculate import treesum\nm = treesum.TopologyCounter(...)"
)
treesum.TopologyCounter.__init__(self, **kwargs)
def is_trivial_split(split, mask):
deprecate.dendropy_deprecation_warning(
preamble=
"Deprecated since DendroPy 4: 'dendropy.treesplit.is_trivial_split()'.",
old_construct=
"from dendropy import treesplit\nd = treesplit.is_trivial_split(...)",
new_construct=
"import dendropy\nd = dendropy.Bipartition.is_trivial_bitmask(...)")
return dendropy.Bipartition.is_trivial_bitmask(bitmask=split,
fill_bitmask=mask)
def find_edge_from_split(root, split_to_find, mask=-1):
deprecate.dendropy_deprecation_warning(
preamble="Deprecated since DendroPy 4: 'dendropy.treesplit.find_edge_from_split()'",
old_construct="from dendropy import treesplit\nd = treesplit.find_edge_from_split(...)",
new_construct="""\
# if using a bipartition
d = bipartition.edge
# if a "raw" bitmask
d = tree.find_edge_for_split_bitmask(...)""")
return root.find_edge_for_split_bitmask(split_to_find, fill_bitmask=mask)
def reconciliation_discordance(gene_tree, species_tree):
deprecate.dendropy_deprecation_warning(
preamble=
"The 'dendropy.reconcile' module has moved to 'dendropy.model.reconcile'.",
old_construct=
"from dendropy import reconcile\nreconcile.reconciliation_discordance(...)",
new_construct=
"from dendropy.model import reconcile\nreconcile.reconciliation_discordance(...)",
)
return reconcile.reconciliation_discordance(gene_tree, species_tree)
def __init__(self, *args, **kwargs):
deprecate.dendropy_deprecation_warning(
preamble=
"The 'dendropy.reconcile' module has moved to 'dendropy.model.reconcile'.",
old_construct=
"from dendropy import reconcile\nreconcile.ContainingTree(...)",
new_construct=
"from dendropy.model import reconcile\nreconcile.ContainingTree(...)",
)
reconcile.ContainingTree.__init__(self, *args, **kwargs)
def __init__(self, *args, **kwargs):
deprecate.dendropy_deprecation_warning(
preamble=
"The 'dendropy.popgensim' module has moved to 'dendropy.simulate.popgensim'.",
old_construct=
"from dendropy import popgensim\npopgensim.FragmentedPopulations(...)",
new_construct=
"from dendropy.simulate import popgensim\npopgensim.FragmentedPopulations(...)",
)
popgensim.FragmentedPopulations.__init__(self, *args, **kwargs)
def robinson_foulds_distance(tree1,
tree2,
edge_length_attr="length"):
deprecate.dendropy_deprecation_warning(
preamble="Deprecated since DendroPy 4: The 'dendropy.treecalc.robinson_foulds_distance()' function has moved to 'dendropy.calculate.treecompare.weighted_robinson_foulds_distance()'.",
old_construct="from dendropy import treecalc\nd = treecalc.robinson_foulds_distance(...)",
new_construct="from dendropy.calculate import treecompare\nd = treecompare.weighted_robinson_foulds_distance(...)")
return treecompare.weighted_robinson_foulds_distance(
tree1=tree1,
tree2=tree2,
edge_weight_attr=edge_length_attr)
def __init__(self, **kwargs):
deprecate.dendropy_deprecation_warning(
preamble="Deprecated since DendroPy 4:",
old_construct=
"d = dendropy.CharacterMatrix.get_from_path(schema='proteinfasta', ...)\nd = dendropy.DataSet.get_from_path(schema='proteinfasta', ...)",
new_construct=
"d = dendropy.ProteinCharacterMatrix.get(path=..., schema='fasta', ...)\nd = dendropy.DataSet.get(path=..., schema='fasta', data_type='protein', ...)",
stacklevel=7)
# raise TypeError("'proteinfasta' is no longer a supported schema: use 'schema=\"fasta\"' with the 'ProteinCharacterMatrix.get()' method instead or 'schema=\"fasta\"' and 'data_type=\"dna\" with the 'DataSet.get()' or 'DataSet.read()' methods")
kwargs["data_type"] = "protein"
FastaReader.__init__(self, **kwargs)
def __init__(self, state_alphabet, rng=None):
deprecate.dendropy_deprecation_warning(
preamble=
"Deprecated since DendroPy 4: The 'dendropy.seqmodel.SeqModel' class has moved to 'dendropy.model.discrete.DiscreteCharacterEvolutionModel'.",
old_construct=
"from dendropy import seqmodel\nm = seqmodel.SeqModel(...)",
new_construct=
"from dendropy.model import discrete\nm = discrete.DiscreteCharacterEvolutionModel(...)"
)
discrete.DiscreteCharacterEvolutionModel.__init__(
self, state_alphabet=state_alphabet, rng=rng)
def monophyletic_partition_discordance(tree, taxon_namespace_partition):
deprecate.dendropy_deprecation_warning(
preamble=
"The 'dendropy.reconcile' module has moved to 'dendropy.model.reconcile'.",
old_construct=
"from dendropy import reconcile\nreconcile.monophyletic_partition_discordance(...)",
new_construct=
"from dendropy.model import reconcile\nreconcile.monophyletic_partition_discordance(...)",
)
return reconcile.monophyletic_partition_discordance(
tree, taxon_namespace_partition)
def encode_splits(tree, create_dict=True, suppress_unifurcations=True):
deprecate.dendropy_deprecation_warning(
preamble=
"Deprecated since DendroPy 4: 'dendropy.treesplit.encode_splits()'.",
old_construct=
"from dendropy import treesplit\nd = treesplit.encode_splits(tree, ...)",
new_construct=
"bipartitions = tree.encode_bipartitions(...)\nsplit_bitmasks = tree.split_bitmask_edge_map.keys()"
)
return tree.encode_bipartitions(
suppress_unifurcations=suppress_unifurcations)
def tree_from_splits(splits, taxon_set, is_rooted=False):
deprecate.dendropy_deprecation_warning(
preamble=
"Deprecated since DendroPy 4: 'dendropy.treesplit.tree_from_splits()'.",
old_construct=
"from dendropy import treesplit\ntree = treesplit.tree_from_splits(...)",
new_construct=
"import dendropy\ntree = dendropy.Tree.from_split_bitmasks(...)")
return dendropy.Tree.from_split_bitmasks(split_bitmasks=splits,
taxon_namespace=taxon_set,
is_rooted=is_rooted)
