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 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 generate_hky_characters(seq_len,
tree_model,
mutation_rate=1.0,
kappa=1.0,
base_freqs=[0.25, 0.25, 0.25, 0.25],
root_states=None,
char_matrix=None,
rng=None):
deprecate.dendropy_deprecation_warning(
preamble="Deprecated since DendroPy 4: The 'dendropy.seqsim.generate_hky_characters()' function has been replaced with 'dendropy.simulate.charsim.hky85_chars()'.",
old_construct="from dendropy import seqsim\nchar_matrix = seqsim.generate_hky_characters(...)",
new_construct="from dendropy.simulate import charsim\nchar_matrix = charsim.hky85_chars(...)")
return 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)
def generate_hky_characters(seq_len,
tree_model,
mutation_rate=1.0,
kappa=1.0,
base_freqs=[0.25, 0.25, 0.25, 0.25],
root_states=None,
char_matrix=None,
rng=None):
deprecate.dendropy_deprecation_warning(
preamble=
"Deprecated since DendroPy 4: The 'dendropy.seqsim.generate_hky_characters()' function has been replaced with 'dendropy.simulate.charsim.hky85_chars()'.",
old_construct=
"from dendropy import seqsim\nchar_matrix = seqsim.generate_hky_characters(...)",
new_construct=
"from dendropy.simulate import charsim\nchar_matrix = charsim.hky85_chars(...)"
)
return 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)
