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#! /usr/bin/env python
##############################################################################
## DendroPy Phylogenetic Computing Library.
##
## Copyright 2010-2015 Jeet Sukumaran and Mark T. Holder.
## All rights reserved.
##
## See "LICENSE.rst" for terms and conditions of usage.
##
## If you use this work or any portion thereof in published work,
## please cite it as:
##
## Sukumaran, J. and M. T. Holder. 2010. DendroPy: a Python library
## for phylogenetic computing. Bioinformatics 26: 1569-1571.
##
##############################################################################
"""
DEPRECATED IN DENDROPY 4: USE `dendropy.simulate.charsim`.
"""
import dendropy
from dendropy.simulate import charsim
from dendropy.utility import deprecate
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_dataset(seq_len,
# tree_model,
# seq_model,
# mutation_rate=1.0,
# root_states=None,
# dataset=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 = discrete.hky85_chars(...)")
# def generate_char_matrix(seq_len,
# tree_model,
# seq_model,
# mutation_rate=1.0,
# root_states=None,
# char_matrix=None,
# rng=None):
# pass
# class SeqEvolver(object):
# def __init__(self,
# seq_model=None,
# mutation_rate=None,
# seq_attr='sequences',
# seq_model_attr="seq_model",
# edge_length_attr="length",
# edge_rate_attr="mutation_rate",
# seq_label_attr='taxon'):
# pass
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