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
|
#! /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.reconcile` instead.
"""
from dendropy.utility import deprecate
from dendropy.model import reconcile
def reconciliation_discordance(gene_tree, species_tree):
deprecate.dendropy_deprecation_warning(
preamble="The 'dendropy.reconcile' module has moved to 'dendropy.model.reconcile'.",
old_construct="from dendropy import reconcile\nreconcile.reconciliation_discordance(...)",
new_construct="from dendropy.model import reconcile\nreconcile.reconciliation_discordance(...)",
)
return reconcile.reconciliation_discordance(gene_tree, species_tree)
def monophyletic_partition_discordance(tree, taxon_namespace_partition):
deprecate.dendropy_deprecation_warning(
preamble="The 'dendropy.reconcile' module has moved to 'dendropy.model.reconcile'.",
old_construct="from dendropy import reconcile\nreconcile.monophyletic_partition_discordance(...)",
new_construct="from dendropy.model import reconcile\nreconcile.monophyletic_partition_discordance(...)",
)
return reconcile.monophyletic_partition_discordance(tree, taxon_namespace_partition)
class ContainingTree(reconcile.ContainingTree):
def __init__(self, *args, **kwargs):
deprecate.dendropy_deprecation_warning(
preamble="The 'dendropy.reconcile' module has moved to 'dendropy.model.reconcile'.",
old_construct="from dendropy import reconcile\nreconcile.ContainingTree(...)",
new_construct="from dendropy.model import reconcile\nreconcile.ContainingTree(...)",
)
reconcile.ContainingTree.__init__(self, *args, **kwargs)
|
