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)