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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.model.coalescent` instead.
"""
from dendropy.model import coalescent
from dendropy.utility import deprecate
from dendropy.utility import constants
def discrete_time_to_coalescence(n_genes,
pop_size=None,
n_to_coalesce=2,
rng=None):
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.discrete_time_to_coalescence(...)",
new_construct="from dendropy.model import coalescent\ncoalescent.discrete_time_to_coalescence(...)")
return coalescent.discrete_time_to_coalescence(
n_genes=n_genes,
pop_size=pop_size,
n_to_coalesce=n_to_coalesce,
rng=rng)
def time_to_coalescence(n_genes,
pop_size=None,
n_to_coalesce=2,
rng=None):
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.time_to_coalescence(...)",
new_construct="from dendropy.model import coalescent\ncoalescent.time_to_coalescence(...)")
return coalescent.time_to_coalescence(
n_genes=n_genes,
pop_size=pop_size,
n_to_coalesce=n_to_coalesce,
rng=rng)
def expected_tmrca(n_genes, pop_size=None, n_to_coalesce=2):
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.expected_tmrca(...)",
new_construct="from dendropy.model import coalescent\ncoalescent.expected_tmrca(...)")
return coalescent.expected_tmrca(n_genes, pop_size=pop_size, n_to_coalesce=n_to_coalesce)
def coalesce(nodes,
pop_size=None,
period=None,
rng=None,
use_expected_tmrca=False):
deprecate.dendropy_deprecation_warning(
preamble="Deprecated since DendroPy 4: The 'dendropy.coalescent' module has moved to 'dendropy.model.coalescent', and this function has been renamed 'coalesce_nodes'.",
old_construct="from dendropy import coalescent\ncoalescent.coalesce(...)",
new_construct="from dendropy.model import coalescent\ncoalescent.coalesce_nodes(...)")
return coalescent.coalesce_nodes(
nodes=nodes,
pop_size=pop_size,
period=period,
rng=rng,
use_expected_tmrca=use_expected_tmrca)
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 extract_coalescent_frames(*args, **kwargs):
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.extract_coalescent_frames(...)",
new_construct="from dendropy.model import coalescent\ncoalescent.extract_coalescent_frames(...)")
return coalescent.extract_coalescent_frames(*args, **kwargs)
def log_probability_of_coalescent_frames(*args, **kwargs):
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.log_probability_of_coalescent_frames(...)",
new_construct="from dendropy.model import coalescent\ncoalescent.log_probability_of_coalescent_frames(...)")
return log_probability_of_coalescent_frames(*args, **kwargs)
def log_probability_of_coalescent_tree(*args, **kwargs):
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.log_probability_of_coalescent_tree(...)",
new_construct="from dendropy.model import coalescent\ncoalescent.log_probability_of_coalescent_tree(...)")
return log_probability_of_coalescent_tree(*args, **kwargs)
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