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
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
|
#
# Module for Bio::PhyloNetwork::RandomFactory
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Gabriel Cardona <gabriel(dot)cardona(at)uib(dot)es>
#
# Copyright Gabriel Cardona
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::PhyloNetwork::RandomFactory - Module to generate random
Phylogenetic Networks
=head1 SYNOPSIS
use strict;
use warnings;
use Bio::PhyloNetwork;
use Bio::PhyloNetwork::RandomFactory;
# Will generate at random all the 66 binary tree-child phylogenetic
# networks with 3 leaves
my $factory=Bio::PhyloNetwork::RandomFactory->new(-numleaves=>3,-norepeat=>1);
my @nets;
for (my $i=0; $i<66; $i++) {
my $net=$factory->next_network();
push @nets,$net;
print "".(scalar @nets).": ".$net->eNewick()."\n";
}
=head1 DESCRIPTION
Builds a random (binary tree-child) phylogenetic network each time
next_network is called.
=head1 AUTHOR
Gabriel Cardona, gabriel(dot)cardona(at)uib(dot)es
=head1 SEE ALSO
L<Bio::PhyloNetwork>
=head1 APPENDIX
The rest of the documentation details each of the object methods.
=cut
package Bio::PhyloNetwork::RandomFactory;
use strict;
use warnings;
use base qw(Bio::Root::Root);
use Bio::PhyloNetwork;
use Bio::Tree::RandomFactory;
=head2 new
Title : new
Usage : my $factory = new Bio::PhyloNetwork::RandomFactory();
Function: Creates a new Bio::PhyloNetwork::RandomFactory
Returns : Bio::PhyloNetwork::RandomFactory
Args : -numleaves => integer
OR
-leaves => reference to an array (of leaves names)
-numhybrids => integer [optional]
-norepeat => boolean [optional]
Returns a Bio::PhyloNetwork::RandomFactory object. Such an object will create
random binary tree-child phylogenetic networks each time next_network
is called.
If the parameter -leaves=E<gt>\@leaves is given, then the set of leaves of
these networks will be @leaves. If it is given the parameter
-numleaves=E<gt>$numleaves, then the set of leaves will be "l1"..."l$numleaves".
If the parameter -numhybrids=E<gt>$numhybrids is given, then the generated
networks will have exactly $numhybrids hybrid nodes. Note that, necessarily,
$numhybrids E<lt> $numleaves. Otherwise, the number of hybrid nodes will be chosen
at random for each call of next_network.
If the parameter -norepeat=E<gt>1 is given, then successive calls of next_network
will give non-isomorphic networks.
=cut
sub new {
my ($pkg,@args)=@_;
my $self=$pkg->SUPER::new(@args);
my ($leavesR,$numleaves,$numhybrids,$norepeat)=
$self->_rearrange([qw(LEAVES
NUMLEAVES
NUMHYBRIDS
NOREPEAT)],@args);
my @leaves;
if ((! defined $leavesR) && (defined $numleaves)) {
@leaves=map {"l$_"} (1..$numleaves);
$leavesR=\@leaves;
}
if (! defined $leavesR) {
$self->throw("No leaves set neither numleaves given");
}
$norepeat ||= 0;
$self->{leaves}=\@leaves;
$self->{numleaves}=$numleaves;
$self->{numhybrids}=$numhybrids if defined $numhybrids;
$self->{norepeat}=$norepeat;
$self->{found}=[];
$self->{tree_factory}=Bio::Tree::RandomFactory->new(-taxa => \@leaves);
bless($self,$pkg);
}
=head2 next_network
Title : next_network
Usage : my $net=$factory->next_network()
Function: returns a random network
Returns : Bio::PhyloNetwork
Args : none
=cut
sub next_network {
my ($self)=@_;
my $numleaves=$self->{numleaves};
my @found=@{$self->{found}};
my $numhybrids;
START:
if (! defined $self->{numhybrids}) {
$numhybrids=int(rand($numleaves));
}
else {
$numhybrids=$self->{numhybrids};
}
my $tf=$self->{tree_factory};
my $tree=$tf->next_tree;
my $net=Bio::PhyloNetwork->new(-tree=>$tree);
for (my $i=1; $i<=$numhybrids; $i++) {
$net=random_attack($net,$i);
}
if ($self->{norepeat}) {
foreach my $ant (@found) {
goto START if $net->is_mu_isomorphic($ant);
}
push @found,$net;
$self->{found}=\@found;
}
return $net;
}
sub random_attack {
my ($net,$lbl)=@_;
my $graph=$net->{graph};
my ($u1,$v1,$u2,$v2);
do {
my $e1=$graph->random_edge;
my $e2=$graph->random_edge;
$u1=$e1->[0];
$v1=$e1->[1];
$u2=$e2->[0];
$v2=$e2->[1];
} while (! $net->is_attackable($u1,$v1,$u2,$v2,$lbl));
$net->do_attack($u1,$v1,$u2,$v2,$lbl);
return $net;
}
1;
|
