1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
|
#! /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.calculate.popgenstat` instead.
"""
from dendropy.utility import deprecate
from dendropy.calculate import popgenstat
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 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 nucleotide_diversity(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.nucleotide_diversity(...)",
new_construct="from dendropy.calculate import popgenstat\npopgenstat.nucleotide_diversity(...)",
)
return popgenstat.nucleotide_diversity(char_matrix=char_matrix, ignore_uncertain=ignore_uncertain)
def tajimas_d(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.tajimas_d(...)",
new_construct="from dendropy.calculate import popgenstat\npopgenstat.tajimas_d(...)",
)
return popgenstat.tajimas_d(char_matrix=char_matrix, ignore_uncertain=ignore_uncertain)
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 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 unfolded_site_frequency_spectrum(char_matrix, ancestral_seq=None, pad=True):
deprecate.dendropy_deprecation_warning(
preamble="The 'dendropy.popgenstat' module has moved to 'dendropy.calculate.popgenstat'.",
old_construct="from dendropy import popgenstat\npopgenstat.unfolded_site_frequency_spectrum(...)",
new_construct="from dendropy.calculate import popgenstat\npopgenstat.unfolded_site_frequency_spectrum(...)",
)
return popgenstat.unfolded_site_frequency_spectrum(
char_matrix=char_matrix,
ancestral_sequence=ancestral_seq,
pad=pad)
class PopulationPairSummaryStatistics(popgenstat.PopulationPairSummaryStatistics):
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)
|
