#
# BioPerl module for Bio::Tree::RandomFactory
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Jason Stajich <jason@bioperl.org>
#
# Copyright Jason Stajich
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::Tree::RandomFactory - TreeFactory for generating Random Trees
=head1 SYNOPSIS
use Bio::Tree::RandomFactory
my @taxonnames;
my $factory = Bio::Tree::RandomFactory->new( -taxa => \@taxonnames,
-maxcount => 10);
# or for anonymous samples
my $factory = Bio::Tree::RandomFactory->new( -num_taxa => 6,
-maxcount => 50);
my $tree = $factory->next_tree;
=head1 DESCRIPTION
Builds a random tree every time next_tree is called or up to -maxcount times.
This module was originally written for Coalescent simulations see
L<Bio::PopGen::Simulation::Coalescent>. I've left the next_tree
method intact although it is not generating random trees in the
phylogenetic sense. I would be happy for someone to provide
alternative implementations which can be used here. As written it
will generate random topologies but the branch lengths are built from
assumptions in the coalescent and are not appropriate for phylogenetic
analyses.
This algorithm is based on the make_tree algorithm from Richard Hudson 1990.
Hudson, R. R. 1990. Gene genealogies and the coalescent
process. Pp. 1-44 in D. Futuyma and J. Antonovics, eds. Oxford
surveys in evolutionary biology. Vol. 7. Oxford University
Press, New York
Sanderson, M ...
=head1 FEEDBACK
=head2 Mailing Lists
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<bioperl-l@bioperl.org>
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via
the web:
https://redmine.open-bio.org/projects/bioperl/
=head1 AUTHOR - Jason Stajich
Email jason-AT-bioperl.org
=head1 CONTRIBUTORS
Matthew Hahn, E<lt>matthew.hahn@duke.eduE<gt>
Mike Sanderson
=head1 APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::Tree::RandomFactory;
use vars qw($PRECISION_DIGITS $DefaultNodeType %Defaults);
use strict;
$PRECISION_DIGITS = 3; # Precision for the branchlength
$DefaultNodeType = 'Bio::Tree::Node';
%Defaults = ('YuleRate' => 1.0, # as set by Sanderson in Rates
'Speciation' => 1.0, #
'DefaultTreeMethod' => 'yule',
);
use Bio::Tools::RandomDistFunctions;
use Bio::Tree::Tree;
use base qw(Bio::Root::Root Bio::Factory::TreeFactoryI);
=head2 new
Title : new
Usage : my $factory = Bio::Tree::RandomFactory->new(-samples => \@samples,
-maxcount=> $N);
Function: Initializes a Bio::Tree::RandomFactory object
Returns : Bio::Tree::RandomFactory
Args : -nodetype => Type of Nodes to create [default Bio::Tree::Node]
-maxcount => [optional] Maximum num trees to create
-randtype => Type of random trees so far support
- yule/backward_yule/BY [default]
- forward_yule/FY
- birthdeath_forward/BDF
- birthdeath_backwards/BDB
ONE of the following must be specified
-taxa => $arrayref of taxa names
-num_taxa => integer indicating number of taxa in the tree
=cut
sub new{
my ($class,@args) = @_;
my $self = $class->SUPER::new(@args);
$self->{'_treecounter'} = 0;
$self->{'_maxcount'} = 0;
my ($nodetype,$randtype,
$maxcount, $samps,$samplesize,
$taxa, $num_taxa) = $self->_rearrange([qw(NODETYPE
RANDTYPE
MAXCOUNT
SAMPLES
SAMPLE_SIZE
TAXA
NUM_TAXA)],
@args);
my @taxa;
$nodetype ||= $DefaultNodeType;
$self->nodetype($nodetype);
$taxa = $samps if defined $samps && ! defined $taxa;
$num_taxa = $samplesize if $samplesize && ! $num_taxa;
if( ! defined $taxa ) {
if( ! defined $num_taxa || $num_taxa <= 0 ) {
$self->throw("Must specify a valid num_taxa if parameter -TAXA is not specified");
}
foreach ( 1..$num_taxa ) { push @taxa, "Taxon$_"; }
} else {
if( ref($taxa) !~ /ARRAY/i ) {
$self->throw("Must specify a valid ARRAY reference to the parameter -TAXA, did you forget a leading '\\'? for $taxa");
}
@taxa = @$taxa;
}
$self->taxa(\@taxa);
defined $maxcount && $self->maxcount($maxcount);
$self->{'_count'} = 0;
return $self;
}
=head2 next_tree
Title : next_tree
Usage : my $tree = $factory->next_tree
Function: Returns a random tree based on the initialized number of nodes
NOTE: if maxcount is not specified on initialization or
set to a valid integer, subsequent calls to next_tree will
continue to return random trees and never return undef
Returns : Bio::Tree::TreeI object
Args : none
=cut
sub next_tree{
my ($self,%options) = @_;
return if $self->maxcount &&
$self->{'_count'}++ >= $self->maxcount;
my $rand_type = $options{'randtype'} || $self->random_tree_method;
my $nodetype = $self->nodetype;
my $treearray;
if( $rand_type =~ /(birthdeath_forward|birth|BDF)/i ) {
} elsif ( $rand_type =~ /(birthdeath_backward|BDB)/i ) {
$treearray = $self->rand_birthdeath_backwards_tree;
} elsif( $rand_type =~ /(BY|backwards_yule)/i ||
$rand_type =~ /^yule/i ) {
my $speciation = $options{'speciation'}; # can be undef
$treearray = $self->rand_yule_c_tree($speciation);
} else {
$self->warn("unrecognized random type $rand_type");
}
my @nodes = ();
foreach my $n ( @$treearray ) {
for my $k ( qw(desc1 desc2) ) {
next unless defined $n->{$k};
push @{$n->{'descendents'}}, $nodes[$n->{$k}];
}
push @nodes,
$nodetype->new(-id => $n->{'nodenum'},
-branch_length => $n->{'time'},
-descendents => $n->{'descendents'},
);
}
my $T = Bio::Tree::Tree->new(-root => pop @nodes );
return $T;
}
=head2 maxcount
Title : maxcount
Usage : $obj->maxcount($newval)
Function:
Returns : Maxcount value
Args : newvalue (optional)
=cut
sub maxcount{
my ($self,$value) = @_;
if( defined $value) {
if( $value =~ /^(\d+)/ ) {
$self->{'_maxcount'} = $1;
} else {
$self->warn("Must specify a valid Positive integer to maxcount");
$self->{'_maxcount'} = 0;
}
}
return $self->{'_maxcount'};
}
=head2 reset_tree_count
Title : reset_tree_count
Usage : $factory->reset_tree_count;
Function: Reset the tree counter
Returns : none
Args : none
=cut
sub reset_count{
shift->{'_count'} = 0;
}
=head2 taxa
Title : taxa
Usage : $obj->taxa($newval)
Function: Set the leaf node names
Returns : value of taxa
Args : Arrayref of Taxon names
=cut
sub taxa {
my ($self,$value) = @_;
if( defined $value) {
if( ref($value) !~ /ARRAY/i ) {
$self->warn("Must specify a valid array ref to the method 'taxa'");
$value = [];
}
$self->{'_taxa'} = $value;
$self->{'_num_taxa'} = scalar @$value;
}
return $self->{'_taxa'};
}
=head2 num_taxa
Title : num_taxa
Usage : $obj->num_taxa($newval)
Function: Get the number of Taxa
Returns : value of num_taxa
Args : none
=cut
sub num_taxa {
my ($self) = @_;
return $self->{'_num_taxa'};
}
# alias old methods
*num_samples = \&num_taxa;
*samples = \&taxa;
=head2 random
Title : random
Usage : my $rfloat = $node->random($size)
Function: Generates a random number between 0 and $size
This is abstracted so that someone can override and provide their
own special RNG. This is expected to be a uniform RNG.
Returns : Floating point random
Args : $maximum size for random number (defaults to 1)
=cut
sub random{
my ($self,$max) = @_;
return rand($max);
}
=head2 random_tree_method
Title : random_tree_method
Usage : $obj->random_tree_method($newval)
Function:
Example :
Returns : value of random_tree_method (a scalar)
Args : on set, new value (a scalar or undef, optional)
=cut
sub random_tree_method{
my $self = shift;
return $self->{'random_tree_method'} = shift if @_;
return $self->{'random_tree_method'} || $Defaults{'DefaultTreeMethod'};
}
=head2 nodetype
Title : nodetype
Usage : $obj->nodetype($newval)
Function:
Example :
Returns : value of nodetype (a scalar)
Args : on set, new value (a scalar or undef, optional)
=cut
sub nodetype{
my ($self,$value) = @_;
if( defined $value) {
eval "require $value";
if( $@ ) { $self->throw("$@: Unrecognized Node type for ".ref($self).
"'$value'");}
my $a = bless {},$value;
unless( $a->isa('Bio::Tree::NodeI') ) {
$self->throw("Must provide a valid Bio::Tree::NodeI or child class to SeqFactory Not $value");
}
$self->{'nodetype'} = $value;
}
return $self->{'nodetype'};
}
# The assignment of times are based on Mike Sanderson's r8s code
# The topology assignment code is based on Richard Hudson's
# make_trees
sub rand_yule_c_tree {
my ($self,$speciation) = @_;
$speciation ||= $Defaults{'Speciation'};
my $n_taxa = $self->num_taxa;
my $taxa = $self->taxa || [];
my $nodetype = $self->nodetype;
my $randfuncs = Bio::Tools::RandomDistFunctions->new();
my $rate = $Defaults{'YuleRate'};
my (@tree,@list,@times,$i,$in);
my $max = 2 * $n_taxa - 1;
for($in=0;$in < $max; $in++ ) {
push @tree, { 'nodenum' => "Node$in" };
}
# setup leaf nodes
for($in=0;$in < $n_taxa;$in++) {
$tree[$in]->{'time'} = 0;
$tree[$in]->{'desc1'} = undef;
$tree[$in]->{'desc2'} = undef;
if( my $r = $taxa->[$in] ) {
$tree[$in]->{'nodenum'} = $r;
}
push @list, $in;
}
for( $i = 0; $i < $n_taxa - 1; $i++ ) {
# draw random interval times
push @times, $randfuncs->rand_birth_distribution($speciation);
}
# sort smallest to largest
@times = sort {$a <=> $b} @times;
# topology generation
for ($in = $n_taxa; $in > 1; $in-- ) {
my $time = shift @times;
my $pick = int $self->random($in);
my $nodeindex = $list[$pick];
$tree[$list[$pick]]->{'time'} = $time;
my $swap = 2 * $n_taxa - $in;
$tree[$swap]->{'desc1'} = $nodeindex;
$list[$pick] = $list[$in-1];
$pick = int rand($in - 1);
$nodeindex = $list[$pick];
$tree[$list[$pick]]->{'time'} = $time;
$tree[$swap]->{'desc2'} = $nodeindex;
$list[$pick] = $swap;
}
$tree[-1]->{'time'} = shift @times;
return \@tree;
}
sub rand_birthdeath_backwards_tree {
my ($self) = @_;
my $n_taxa = $self->num_taxa;
my $taxa = $self->taxa || [];
my $randfuncs = Bio::Tools::RandomDistFunctions->new();
my $rate = $Defaults{'YuleRate'};
my (@tree,@list,@times,$i,$in);
my $max = 2 * $n_taxa - 1;
for($in=0;$in < $max; $in++ ) {
push @tree, { 'nodenum' => "Node$in" };
}
# setup leaf nodes
for($in=0;$in < $n_taxa;$in++) {
$tree[$in]->{'time'} = 0;
$tree[$in]->{'desc1'} = undef;
$tree[$in]->{'desc2'} = undef;
if( my $r = $taxa->[$in] ) {
# deal with pre-labeled nodes
$tree[$in]->{'nodenum'} = $r;
}
push @list, $in;
}
my ($time) = (0);
# topology generation
for ($in = $n_taxa; $in > 1; $in-- ) {
my $pick = int $self->random($in);
my $nodeindex = $list[$pick];
my $swap = 2 * $n_taxa - $in;
$time += $randfuncs->rand_geometric_distribution($n_taxa * $rate);;
$tree[$list[$pick]]->{'time'} = $time;
$tree[$swap]->{'desc1'} = $nodeindex;
$list[$pick] = $list[$in-1];
$pick = int rand($in - 1);
$nodeindex = $list[$pick];
$tree[$list[$pick]]->{'time'} = $time;
$tree[$swap]->{'desc2'} = $nodeindex;
$list[$pick] = $swap;
}
my $root = $tree[-1];
$time += $randfuncs->rand_geometric_distribution($n_taxa * $rate);;
$root->{'time'} = $time;
# Normalize times by the root node...
for my $node ( @tree ) {
$node->{'time'} /= $root->{'time'};
}
return \@tree;
}
# The assignment of times are based on Mike Sanderson's r8s code
# The topology assignment code is based on Richard Hudson's
# make_trees
sub rand_birth_death_tree {
# Still need to finish
# my ($self,$spec_rate,$extinct_rate,$char_rate) = @_;
# my $n_taxa = $self->num_taxa;
# my $dt = 0.1 / $n_taxa;
# my @tree;
# my $max = 3 * $n_taxa - 1;
# # setup leaf nodes
# for($in=0;$in < $size;$in++) {
# push @tree, { 'nodenum' => $taxa->[$in] || "Node$in",
# 'time' => 0,
# 'desc1' => undef,
# 'desc2' => undef,
# };
# }
# my $time = $dt;
# my $idx = 0;
# while( $n_taxa > 1 ) {
# if ( event($dt * $spec_rate, $n_taxa) ) {
# my $pick = int $self->random($n_taxa);
# my $pick2 = int $self->random($n_taxa);
# while( $pick2 == $pick ) {
# $pick2 = int $self->random($n_taxa);
# }
# to finish....
# $tree[$swap]->{'desc1'} = $nodeindex;
# }
# }
# $list[$pick] = $list[$in-1];
# $pick = int rand($in - 1);
# $nodeindex = $list[$pick];
# $tree[$swap]->{'desc2'} = $nodeindex;
# $list[$pick] = $swap;
# $tree[$swap]->{'time'} = $times[$ix++];
# }
}
1;