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#
# Module for Bio::PhyloNetwork
#
# 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, Gabriel Valiente
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::PhyloNetwork - Module to compute with Phylogenetic Networks
=head1 SYNOPSIS
use Bio::PhyloNetwork;
# Create a PhyloNetwork object from a eNewick string
my $net1=Bio::PhyloNetwork->new(
-eNewick=>'t0:((H1,(H2,l2)),H2); H1:((H3,l1)); H2:((H3,(l3,H1))); H3:(l4);'
);
# Print all available data
print $net1;
# Rebuild $net1 from its mu_data
my %mudata=$net1->mudata();
my $net2=Bio::PhyloNetwork->new(-mudata=>\%mudata,-numleaves=>4);
print $net2;
print "d=".$net1->mu_distance($net2)."\n";
# Get another one and compute distance
my $net3=Bio::PhyloNetwork->new(
-eNewick=>'(l2,((l1,(H1,l4)),H1))r; (l3)H1;'
);
print "d=".$net1->mu_distance($net3)."\n";
# ...and find an optimal alignment w.r.t. the Manhattan distance (default)
my ($weight,%alignment)=$net1->optimal_alignment($net3);
print "weight:$weight\n";
foreach my $node1 (keys %alignment) {
print "$node1 => ".$alignment{$node1}."\n";
}
# ...or the Hamming distance
my ($weightH,%alignmentH)=$net1->optimal_alignment($net3,-metric=>'Hamming');
print "weight:$weightH\n";
foreach my $node1 (keys %alignmentH) {
print "$node1 => ".$alignmentH{$node1}."\n";
}
# Test for time consistency of $net1
if ($net1->is_time_consistent) {
print "net1 is time consistent\n"
}
else {
print "net1 is not time consistent\n"
}
# create a network from the list of edges
my $net4=Bio::PhyloNetwork->new(-edges=>
[qw(r s r t s u s c t c t v u b u l3 u b v b v l4 b l2 c l1)]);
# Test for time consistency of $net3
if ($net4->is_time_consistent) {
print "net4 is time consistent\n"
}
else {
print "net4 is not time consistent\n"
}
# And print all information on net4
print $net4;
# Compute some tripartitions
my %triparts=$net1->tripartitions();
# Now these are stored
print $net1;
# And can compute the tripartition error
print "dtr=".$net1->tripartition_error($net3)."\n";
=head1 DESCRIPTION
=head2 Phylogenetic Networks
This is a module to work with phylogenetic networks. Phylogenetic networks
have been studied over the last years as a richer model of the evolutionary
history of sets of organisms than phylogenetic trees, because they take not
only mutation events but also recombination and horizontal gene transfer
events into account.
The natural model for describing the evolutionary
history of a set of sequences under recombination events is a DAG, hence
this package relies on the package Graph::Directed to represent the
underlying graph of a phylogenetic network. We refer the reader to [CRV1,CRV2]
for formal definitions related to phylogenetic networks.
=head2 eNewick description
With this package, phylogenetic networks can be given by its eNewick
string. This description appeared in other packages related to
phylogenetic networks (see [PhyloNet] and [NetGen]); in fact, these two
packages use different descriptions. The Bio::PhyloNetwork
package allows both of them, but uses the second one in its output.
The first approach [PhyloNet] goes as follows: For each hybrid node H, say with
parents u_1,u_2,...,u_k and children v_1,v_2,...v_l: split H in k+1 different
nodes; let each of the first k copies be a child of one of the u_1,...,u_k
(one for each) and have no children (hence we will have k extra leaves);
as for the last copy, let it have no parents and have v_1,...,v_l be its
children. This way we get a forest; each of the trees will be rooted at either
one root of the phylogenetic network or a hybrid node of it; the set of leaves
(of the whole forest) will be the set of leaves of the original network
together with the set of hybrid nodes (each of them repeated as many times
as its in-degree). Then, the eNewick representation of the phylogenetic network
will be the Newick representation of all the trees in the obtained forest,
each of them with its root labeled.
The second approach [NetGen] goes as follows: For each hybrid node H, say with
parents u_1,u_2,...,u_k and children v_1,v_2,...v_l: split H in k different
nodes; let the first copy be a child of u_1 and have all v_1,v_2,...v_l as
its children; let the other copies be child of u_2,...,u_k (one for each)
and have no children. This way, we get a tree whose set of leaves is the
set of leaves of the original network together with the set of hybrid nodes
(possibly repeated). Then the Newick string of the obtained tree (note that
some internal nodes will be labeled and some leaves will be repeated) is
the eNewick string of the phylogenetic network.
For example, consider the network depicted below:
r
/ \
/ \
U V
/ \ / \
1 \ / 3
H
|
2
If the first approach is taken, we get the forest:
r
/ \
/ \
U V
/ \ / \
1 H H 3
|
H
|
2
Hence, the eNewick string is '((1,H),(H,3))r; (2)H;'.
As for the second one, one gets the tree:
r
/ \
/ \
U V
/ \ / \
1 H | 3
H
|
2
Hence, the eNewick string is '((1,H),((2)H,3))r;'.
Note: when rooting a tree, this package allows the notations
'(subtree,subtree,...)root' as well as 'root:(subtree,subtree,...)', but
the first one is used when writing eNewick strings.
=head2 Tree-child phylogenetic networks
Tree-child (TC) phylogenetic networks are a special class of phylogenetic
networks for which a distance, called mu-distance, is defined [CRV2]
based on certain data (mu-data) associated to every node.
Moreover, this distance extends the
Robinson-Foulds on phylogenetic trees. This package allows testing for a
phylogenetic network if it is TC and computes mu-distances between networks
over the same set of leaves.
Moreover, the mu-data allows one to define the optimal
(in some precise sense) alignment between networks
over the same set of leaves. This package also computes this optimal alignment.
=head2 Tripartitions
Although tripartitions (see [CRV1] and the references therein) do not allow
to define distances, this package outputs tripartitions and computes a weak
form of the tripartition error.
=head2 Time-consistency
Another useful property of Phylogenetic Networks that appears in the literature
is that of time-consistency or real-time hybrids [BSS]. Roughly speaking, a
network admits a temporal representation if it can be drawn in such a way
that tree arcs (those whose end is a tree node) are inclined downwards, while
hybridization arcs (those whose end is a hybrid node) are horizontal.
This package checks for time-consistency and, if so, a temporal representation
is provided.
=head1 AUTHOR
Gabriel Cardona, gabriel(dot)cardona(at)uib(dot)es
Gabriel Valiente, valiente(at)lsi(dot)upc(dot)edu
=head1 SEE ALSO
=over
=item [CRV1]
G. Cardona, F. Rossello, G. Valiente. Tripartitions do not always
discriminate phylogenetic networks. arXiv:0707.2376v1 [q-bio.PE]
=item [CRV2]
G. Cardona, F. Rossello, G. Valiente. A Distance Measure for
Tree-Child Phylogenetic Networks. Preprint.
=item [NetGen]
M.M. Morin, and B.M.E. Moret. NetGen: generating phylogenetic networks
with diploid hybrids. Bioinformatics 22 (2006), 1921-1923
=item [PhyloNet]
PhyloNet: "Phylogenetic Networks Toolkit".
http://bioinfo.cs.rice.edu/phylonet
=item [BSS]
M. Baroni, C. Semple, and M. Steel. Hybrids in Real
Time. Syst. Biol. 55(1):46-56, 2006
=back
=head1 APPENDIX
The rest of the documentation details each of the object methods.
=cut
package Bio::PhyloNetwork;
use strict;
use warnings;
use base qw(Bio::Root::Root);
use Bio::PhyloNetwork::muVector;
use Graph::Directed;
use Bio::TreeIO;
use Bio::Tree::Node;
use IO::String;
use Array::Compare;
use Algorithm::Munkres;
# Creator
=head2 new
Title : new
Usage : my $obj = new Bio::PhyloNetwork();
Function: Creates a new Bio::PhyloNetwork object
Returns : Bio::PhyloNetwork
Args : none
OR
-eNewick => string
OR
-graph => Graph::Directed object
OR
-edges => reference to an array
OR
-tree => Bio::Tree::Tree object
OR
-mudata => reference to a hash,
-leaves => reference to an array
OR
-mudata => reference to a hash,
-numleaves => integer
Returns a Bio::PhyloNetwork object, created according to the data given:
=over 3
=item new()
creates an empty network.
=item new(-eNewick =E<gt> $str)
creates the network whose
Extended Newick representation (see description above) is the string $str.
=item new(-graph =E<gt> $graph)
creates the network with underlying
graph given by the Graph::Directed object $graph
=item new(-tree =E<gt> $tree)
creates a network as a copy of the
Bio::Tree::Tree object in $tree
=item new(-mudata =E<gt> \%mudata, -leaves =E<gt> \@leaves)
creates the network by reconstructing it from its mu-data stored in
\%mudata and with set of leaves in \@leaves.
=item new(-mudata =E<gt> \%mudata, -numleaves =E<gt> $numleaves)
creates the network by reconstructing it from its mu-data stored in
\%mudata and with set of leaves in ("l1".."l$numleaves").
=back
=cut
sub new {
my ($pkg,@args)=@_;
my $self=$pkg->SUPER::new(@args);
my ($eNewick,$edgesR,$leavesR,$numleaves,$graph,$tree,$mudataR)=
$self->_rearrange([qw(ENEWICK
EDGES
LEAVES
NUMLEAVES
GRAPH
TREE
MUDATA)],@args);
bless($self,$pkg);
$self->build_from_eNewick($eNewick) if defined $eNewick;
$self->build_from_edges(@$edgesR) if defined $edgesR;
$self->build_from_graph($graph) if defined $graph;
$self->build_from_tree($tree) if defined $tree;
if ((! defined $leavesR) && (defined $numleaves)) {
my @leaves=map {"l$_"} (1..$numleaves);
$leavesR=\@leaves;
}
$self->build_from_mudata($mudataR,$leavesR)
if ((defined $mudataR) && (defined $leavesR));
return $self;
}
# Builders
sub build_from_edges {
my ($self,@edges)=@_;
my $graph=Graph::Directed->new();
$graph->add_edges(@edges);
$self->{graph}=$graph;
$self->recompute();
my $labels={};
foreach my $node ($self->nodes()) {
$labels->{$node}=$node;
}
$self->{labels}=$labels;
}
sub build_from_graph {
my ($self,$graph)=@_;
my $graphcp=$graph->copy();
$self->{graph}=$graphcp;
$self->recompute();
my $labels={};
foreach my $node ($self->nodes()) {
$labels->{$node}=$node;
}
$self->{labels}=$labels;
}
my $_eN_index;
sub build_from_eNewick {
my ($self,$string)=@_;
$_eN_index=0;
my $graph=Graph::Directed->new();
my $labels={};
my @blocks=split(/; */,$string);
foreach my $block (@blocks) {
my ($rt,$str)=get_root_and_subtree($block);
my ($rtlbl,$rttype,$rtid,$rtlng)=get_label_type_id_length($rt);
process_block($graph,$labels,$block,$rtid);
$labels->{$rtid}=$rtlbl.'';
}
$self->{graph}=$graph;
$self->{labels}=$labels;
$self->recompute();
}
sub process_block {
my ($graph,$labels,$block,$rtid)=@_;
my ($rt,$str)=get_root_and_subtree($block);
my @substrs=my_split($str);
foreach my $substr (@substrs) {
my ($subrt,$subblock)=get_root_and_subtree($substr);
my ($subrtlbl,$subrttype,$subrtid,$subrtlng)=
get_label_type_id_length($subrt);
if (! $subrtlng eq '') {
$graph->add_weighted_edges($rtid,$subrtid,$subrtlng);
}
else {
$graph->add_edges($rtid,$subrtid);
}
if (! $subrttype eq '') {
$graph->set_edge_attribute($rtid,$subrtid,'type',$subrttype);
}
$subrtlbl.='';
# if (! $subrtlbl eq '') {
if ((! defined $labels->{$subrtid})||($labels->{$subrtid} eq '')){
$labels->{$subrtid}=$subrtlbl;
} elsif (( $labels->{$subrtid} ne $subrtlbl )&&($subrtlbl ne '')) {
# error
die("Different labels for the same node (".$labels->{$subrtid}." and $subrtlbl)");
}
# }
if ($subblock ne "") {
process_block($graph,$labels,$subblock,$subrtid);
}
}
}
sub get_root_and_subtree {
my ($block)=@_;
my ($rt,$str)=("","");
# ($rt,$str)=split(/:|=/,$block);
($rt,$str)=split(/=/,$block);
if ($rt eq $block) {
# try to look for root label at the end
my $pos=length($rt)-1;
while ((substr($rt,$pos,1) ne ")") && ($pos >=0)) {
$pos--;
}
$rt=substr($block,$pos+1,length($block)-$pos);
$str=substr($block,0,$pos+1);
}
$rt=trim($rt);
$str=trim($str);
return ($rt,$str);
}
sub get_label_type_id_length {
my ($string) = @_;
$string.='';
# print "$string\n";
if (index($string,'#')==-1) {
# no hybrid
my ($label,$length)=split(':',$string);
$label.='';
my $id;
if ((! defined $label) || ($label eq '')) {
# create id
$_eN_index++;
$id="T$_eN_index";
} else {
$id=$label;
}
return ($label,'',$id,$length);
}
else {
# hybrid
my ($label,$string2)=split('#',$string);
my ($typeid,$length)=split(':',$string2);
my $type=$typeid;
$type =~ s/\d//g;
my $id=$typeid;
$id =~ s/\D//g;
return ($label,$type,'#'.$id,$length);
}
}
sub trim
{
my ($string) = @_;
$string =~ s/^\s+//;
$string =~ s/\s+$//;
return $string;
}
sub my_split {
my ( $string ) = @_;
my $temp="";
my @substrings;
my $level=1;
for my $i ( 1 .. length( $string ) ) {
my $char=substr($string,$i,1);
if ($char eq "(") {
$level++;
}
if ($char eq ")") {
if ($level==1) {
push @substrings, $temp;
$temp="";
}
$level--;
}
if (($char eq ",") && ($level==1)) {
push @substrings, $temp;
$temp="";
$char="";
}
$temp = $temp.$char;
}
return @substrings;
}
sub build_from_mudata {
my ($self,$mus,$leavesR)=@_;
my $graph=Graph::Directed->new();
my @nodes=keys %{$mus};
my @leaves=@{$leavesR};
my %seen;
my @internal;
@seen{@leaves} = ();
foreach my $node (@nodes) {
push(@internal, $node) unless exists $seen{$node};
}
@internal=sort {$mus->{$b} <=> $mus->{$a} } @internal;
@nodes=(@internal,@leaves);
my $numnodes=@nodes;
for (my $i=0;$i<$numnodes;$i++) {
my $mu=$mus->{$nodes[$i]};
my $j=$i+1;
while ($mu->is_positive() && $j<$numnodes) {
if ($mu->geq_poset($mus->{$nodes[$j]})) {
$graph->add_edges(($nodes[$i],$nodes[$j]));
$mu = $mu - $mus->{$nodes[$j]};
}
$j++;
}
}
$self->build_from_graph($graph);
}
# sub relabel_tree {
# my ($tree)=@_;
# my $i=1;
# my $j=1;
# my $root=$tree->get_root_node();
# foreach my $node ($tree->get_nodes()) {
# if ($node == $root) {
# $node->{'_id'}="r";
# }
# elsif (! $node->is_Leaf) {
# $node->{'_id'}="t$i";
# $i++;
# }
# else {
# if ($node->{'_id'} eq "") {
# $node->{'_id'}="l$j";
# $j++;
# }
# }
# }
# return $tree;
# }
# sub build_subtree {
# my ($graph,$root)=@_;
# foreach my $child ($root->each_Descendent) {
# $graph->add_edge($root->id,$child->id);
# $graph=build_subtree($graph,$child);
# }
# return $graph;
# }
sub build_from_tree {
my ($self,$tree)=@_;
# relabel_tree($tree);
# my $treeroot=$tree->get_root_node;
# my $graph=Graph::Directed->new();
# $graph=build_subtree($graph,$treeroot);
# $self->build_from_graph($graph);
my $str;
my $io=IO::String->new($str);
my $treeio=Bio::TreeIO->new(-format => 'newick', -fh => $io);
$treeio->write_tree($tree);
# print "intern: $str\n";
$self->build_from_eNewick($str);
}
sub recompute {
my ($self)=@_;
$self->throw("Graph is not DAG:".$self->{graph})
unless $self->{graph}->is_dag();
my @leaves=$self->{graph}->successorless_vertices();
@leaves=sort @leaves;
my $numleaves=@leaves;
my @roots=$self->{graph}->predecessorless_vertices();
my $numroots=@roots;
#$self->throw("Graph is not rooted") unless ($numroots == 1);
my @nodes=$self->{graph}->vertices();
@nodes=sort @nodes;
my $numnodes=@nodes;
foreach my $node (@nodes) {
if (! defined $self->{labels}->{$node}) {
$self->{labels}->{$node}='';
}
}
$self->{leaves}=\@leaves;
$self->{numleaves}=$numleaves;
$self->{roots}=\@roots;
$self->{numroots}=$numroots;
$self->{nodes}=\@nodes;
$self->{numnodes}=$numnodes;
$self->{mudata}={};
$self->{h}={};
$self->compute_height();
$self->compute_mu();
return $self;
}
# Hybridizing
sub is_attackable {
my ($self,$u1,$v1,$u2,$v2)=@_;
if ( $self->is_hybrid_node($v1) ||
$self->is_hybrid_node($v2) ||
$self->graph->is_reachable($v2,$u1) ||
(($u1 eq $u2)&&($v1 eq $v2)) ||
(! scalar grep {($_ ne $v2) && ($self->is_tree_node($_))}
$self->graph->successors($u2)))
{
return 0;
}
return 1;
}
sub do_attack {
my ($self,$u1,$v1,$u2,$v2,$lbl)=@_;
my $graph=$self->{graph};
$graph->delete_edge($u1,$v1);
$graph->delete_edge($u2,$v2);
$graph->add_edge($u1,"T$lbl");
$graph->add_edge("T$lbl",$v1);
$graph->add_edge($u2,"#H$lbl");
$graph->add_edge("#H$lbl",$v2);
$graph->add_edge("T$lbl","#H$lbl");
$self->build_from_graph($graph);
}
# Computation of mu-data
sub compute_mu {
my ($self)=@_;
my $graph=$self->{graph};
my $mudata=$self->{mudata};
my @leaves=@{$self->{leaves}};
my $numleaves=$self->{numleaves};
for (my $i=0;$i<$numleaves;$i++) {
my $vec=Bio::PhyloNetwork::muVector->new($numleaves);
$vec->[$i]=1;
$mudata->{$leaves[$i]}=$vec;
}
my $h=1;
while (my @nodes=grep {$self->{h}->{$_} == $h} @{$self->{nodes}} )
{
foreach my $u (@nodes) {
my $vec=Bio::PhyloNetwork::muVector->new($numleaves);
foreach my $son ($graph->successors($u)) {
$vec+=$mudata->{$son};
}
$mudata->{$u}=$vec;
}
$h++;
}
}
sub compute_height {
my ($self)=@_;
my $graph=$self->{graph};
my @leaves=@{$self->{leaves}};
foreach my $leaf (@leaves) {
$self->{h}->{$leaf}=0;
}
my $h=0;
while (my @nodes=grep {(defined $self->{h}->{$_})&&($self->{h}->{$_} == $h)}
@{$self->{nodes}} )
{
foreach my $node (@nodes) {
foreach my $parent ($graph->predecessors($node)) {
$self->{h}->{$parent}=$h+1;
}
}
$h++;
}
}
# Tests
=head2 is_leaf
Title : is_leaf
Usage : my $b=$net->is_leaf($u)
Function: tests if $u is a leaf in $net
Returns : boolean
Args : scalar
=cut
sub is_leaf {
my ($self,$node)=@_;
if ($self->{graph}->out_degree($node) == 0) {return 1;}
return 0;
}
=head2 is_root
Title : is_root
Usage : my $b=$net->is_root($u)
Function: tests if $u is the root of $net
Returns : boolean
Args : scalar
=cut
sub is_root {
my ($self,$node)=@_;
if ($self->{graph}->in_degree($node) == 0) {return 1;}
return 0;
}
=head2 is_tree_node
Title : is_tree_node
Usage : my $b=$net->is_tree_node($u)
Function: tests if $u is a tree node in $net
Returns : boolean
Args : scalar
=cut
sub is_tree_node {
my ($self,$node)=@_;
if ($self->{graph}->in_degree($node) <= 1) {return 1;}
return 0;
}
=head2 is_hybrid_node
Title : is_hybrid_node
Usage : my $b=$net->is_hybrid_node($u)
Function: tests if $u is a hybrid node in $net
Returns : boolean
Args : scalar
=cut
sub is_hybrid_node {
my ($self,$node)=@_;
if ($self->{graph}->in_degree($node) > 1) {return 1;}
return 0;
}
sub has_tree_child {
# has_tree_child(g,u) returns 1 if u has a tree child in graph g
# and 0 otherwise
my $g=shift(@_);
my $node=shift(@_);
my @Sons=$g->successors($node);
foreach my $son (@Sons) {
if ($g->in_degree($son)==1) {
return 1;
}
}
return 0;
}
=head2 is_tree_child
Title : is_tree_child
Usage : my $b=$net->is_tree_child()
Function: tests if $net is a Tree-Child phylogenetic network
Returns : boolean
Args : Bio::PhyloNetwork
=cut
sub is_tree_child {
my ($self)=@_;
if (defined $self->{is_tree_child}) {
return $self->{is_tree_child};
}
$self->{is_tree_child}=0;
my $graph=$self->{graph};
foreach my $node (@{$self->{nodes}}) {
return 0 unless ($graph->out_degree($node)==0 ||
has_tree_child($graph,$node));
}
$self->{is_tree_child}=1;
return 1;
}
# Accessors
=head2 nodes
Title : nodes
Usage : my @nodes=$net->nodes()
Function: returns the set of nodes of $net
Returns : array
Args : none
=cut
sub nodes {
my ($self)=@_;
return @{$self->{nodes}};
}
=head2 leaves
Title : leaves
Usage : my @leaves=$net->leaves()
Function: returns the set of leaves of $net
Returns : array
Args : none
=cut
sub leaves {
my ($self)=@_;
return @{$self->{leaves}};
}
=head2 roots
Title : roots
Usage : my @roots=$net->roots()
Function: returns the set of roots of $net
Returns : array
Args : none
=cut
sub roots {
my ($self)=@_;
return @{$self->{roots}};
}
=head2 internal_nodes
Title : internal_nodes
Usage : my @internal_nodes=$net->internal_nodes()
Function: returns the set of internal nodes of $net
Returns : array
Args : none
=cut
sub internal_nodes {
my ($self)=@_;
return grep {! $self->is_leaf($_)} $self->nodes();
}
=head2 tree_nodes
Title : tree_nodes
Usage : my @tree_nodes=$net->tree_nodes()
Function: returns the set of tree nodes of $net
Returns : array
Args : none
=cut
sub tree_nodes {
my ($self)=@_;
return grep {$self->is_tree_node($_)} $self->nodes();
}
=head2 hybrid_nodes
Title : hybrid_nodes
Usage : my @hybrid_nodes=$net->hybrid_nodes()
Function: returns the set of hybrid nodes of $net
Returns : array
Args : none
=cut
sub hybrid_nodes {
my ($self)=@_;
return grep {$self->is_hybrid_node($_)} $self->nodes();
}
=head2 graph
Title : graph
Usage : my $graph=$net->graph()
Function: returns the underlying graph of $net
Returns : Graph::Directed
Args : none
=cut
sub graph {
my ($self)=@_;
return $self->{graph};
}
=head2 edges
Title : edges
Usage : my @edges=$net->edges()
Function: returns the set of edges of $net
Returns : array
Args : none
Each element in the array is an anonimous array whose first element is the
head of the edge and the second one is the tail.
=cut
sub edges {
my ($self)=@_;
return $self->{graph}->edges();
}
=head2 tree_edges
Title : tree_edges
Usage : my @tree_edges=$net->tree_edges()
Function: returns the set of tree edges of $net
(those whose tail is a tree node)
Returns : array
Args : none
=cut
sub tree_edges {
my ($self)=@_;
return grep {$self->is_tree_node($_->[1])} $self->edges();
}
=head2 hybrid_edges
Title : hybrid_edges
Usage : my @hybrid_edges=$net->hybrid_edges()
Function: returns the set of hybrid edges of $net
(those whose tail is a hybrid node)
Returns : array
Args : none
=cut
sub hybrid_edges {
my ($self)=@_;
return grep {$self->is_hybrid_node($_->[1])} $self->edges();
}
=head2 explode
Title : explode
Usage : my @trees=$net->explode()
Function: returns the representation of $net by a set of
Bio::Tree:Tree objects
Returns : array
Args : none
=cut
sub explode {
my ($self)=@_;
my @trees;
$self->explode_rec(\@trees);
return @trees;
}
sub explode_rec {
my ($self,$trees)=@_;
my @h = $self->hybrid_nodes;
if (scalar @h) {
my $v = shift @h;
for my $u ($self->{graph}->predecessors($v)) {
$self->{graph}->delete_edge($u,$v);
$self->explode_rec($trees);
$self->{graph}->add_edge($u,$v);
}
} else {
my $io = IO::String->new($self->eNewick);
my $treeio = Bio::TreeIO->new(-format => 'newick', -fh => $io);
my $tree = $treeio->next_tree;
$tree->contract_linear_paths;
push @{$trees}, $tree;
}
}
=head2 mudata
Title : mudata
Usage : my %mudata=$net->mudata()
Function: returns the representation of $net by its mu-data
Returns : hash
Args : none
$net-E<gt>mudata() returns a hash with keys the nodes of $net and each value is a
muVector object holding its mu-vector.
=cut
sub mudata {
my ($self)=@_;
return %{$self->{mudata}};
}
sub mudata_node {
my ($self,$u)=@_;
return $self->{mudata}{$u};
}
=head2 heights
Title : heights
Usage : my %heights=$net->heights()
Function: returns the heights of the nodes of $net
Returns : hash
Args : none
$net-E<gt>heights() returns a hash with keys the nodes of $net and each value
is its height.
=cut
sub heights {
my ($self)=@_;
return %{$self->{h}};
}
sub height_node {
my ($self,$u)=@_;
return $self->{h}{$u};
}
=head2 mu_distance
Title : mu_distance
Usage : my $dist=$net1->mu_distance($net2)
Function: Computes the mu-distance between the networks $net1 and $net2 on
the same set of leaves
Returns : scalar
Args : Bio::PhyloNetwork
=cut
sub mu_distance {
my ($net1,$net2)=@_;
my @nodes1=$net1->nodes;
my @nodes2=$net2->nodes;
my $comp = Array::Compare->new;
$net1->throw("Cannot compare phylogenetic networks on different set of leaves")
unless $comp->compare($net1->{leaves},$net2->{leaves});
$net1->warn("Not a tree-child phylogenetic network")
unless $net1->is_tree_child();
$net2->warn("Not a tree-child phylogenetic network")
unless $net2->is_tree_child();
my @leaves=@{$net1->{leaves}};
my %matched1;
my %matched2;
OUTER: foreach my $node1 (@nodes1) {
foreach my $node2 (@nodes2) {
if (
(! exists $matched1{$node1}) && (! exists $matched2{$node2}) &&
($net1->{mudata}{$node1} == $net2->{mudata}{$node2})
) {
$matched1{$node1}=$node2;
$matched2{$node2}=$node1;
next OUTER;
}
}
}
return (scalar @nodes1)+(scalar @nodes2)-2*(scalar keys %matched1);
}
=head2 mu_distance_generalized
Title : mu_distance_generalized
Usage : my $dist=$net1->mu_distance($net2)
Function: Computes the mu-distance between the topological restrictions of
networks $net1 and $net2 on its common set of leaves
Returns : scalar
Args : Bio::PhyloNetwork
=cut
sub mu_distance_generalized {
my ($net1,$net2)=@_;
my ($netr1,$netr2)=$net1->topological_restriction($net2);
return $netr1->mu_distance($netr2);
}
# mudata_string (code mu_data in a string; useful for isomorphism testing)
sub mudata_string_node {
my ($self,$u)=@_;
return $self->{mudata}->{$u}->display();
}
sub mudata_string {
my ($self)=@_;
return $self->{mudata_string} if defined $self->{mudata_string};
my @internal=$self->internal_nodes;
my $mus=$self->{mudata};
@internal=sort {$mus->{$b} <=> $mus->{$a} } @internal;
my $str="";
foreach my $node (@internal) {
$str=$str.$self->mudata_string_node($node);
}
$self->{mudata_string}=$str;
return $str;
}
sub is_mu_isomorphic {
my ($net1,$net2)=@_;
return ($net1->mudata_string() eq $net2->mudata_string());
}
# tripartitions
sub compute_tripartition_node {
my ($self,$u)=@_;
$self->warn("Cannot compute tripartitions on unrooted networks. Will assume one at random")
unless ($self->{numroots} == 1);
my $root=$self->{roots}->[0];
my $graph=$self->{graph};
my $graphPruned=$graph->copy();
$graphPruned->delete_vertex($u);
my $tripartition="";
foreach my $leaf (@{$self->{leaves}}) {
my $type;
if ($graph->is_reachable($u,$leaf)) {
if ($graphPruned->is_reachable($root,$leaf)) {$type="B";}
else {$type="A";}
}
else {$type="C";}
$tripartition .= $type;
}
$self->{tripartitions}->{$u}=$tripartition;
}
sub compute_tripartitions {
my ($self)=@_;
foreach my $node (@{$self->{nodes}}) {
$self->compute_tripartition_node($node);
}
}
=head2 tripartitions
Title : tripartitions
Usage : my %tripartitions=$net->tripartitions()
Function: returns the set of tripartitions of $net
Returns : hash
Args : none
$net-E<gt>tripartitions() returns a hash with keys the nodes of $net and each value
is a string representing the tripartition of the leaves induced by the node.
A string "BCA..." associated with a node u (e.g.) means, the first leaf is in
the set B(u), the second one in C(u), the third one in A(u), and so on.
=cut
sub tripartitions {
my ($self)=@_;
$self->compute_tripartitions() unless defined $self->{tripartitions};
return %{$self->{tripartitions}};
}
# to do: change to tri_distance and test for TC and time-cons
sub tripartition_error {
my ($net1,$net2)=@_;
my $comp = Array::Compare->new;
$net1->throw("Cannot compare phylogenetic networks on different set of leaves")
unless $comp->compare($net1->{leaves},$net2->{leaves});
$net1->warn("Not a tree-child phylogenetic network")
unless $net1->is_tree_child();
$net2->warn("Not a tree-child phylogenetic network")
unless $net2->is_tree_child();
$net1->warn("Not a time-consistent network")
unless $net1->is_time_consistent();
$net2->warn("Not a time-consistent network")
unless $net2->is_time_consistent();
$net1->compute_tripartitions() unless defined $net1->{tripartitions};
$net2->compute_tripartitions() unless defined $net2->{tripartitions};
my @edges1=$net1->{graph}->edges();
my @edges2=$net2->{graph}->edges();
my ($FN,$FP)=(0,0);
foreach my $edge1 (@edges1) {
my $matched=0;
foreach my $edge2 (@edges2) {
if ($net1->{tripartitions}->{$edge1->[1]} eq
$net2->{tripartitions}->{$edge2->[1]}) {
$matched=1;
last;
}
}
if (! $matched) {$FN++;}
}
foreach my $edge2 (@edges2) {
my $matched=0;
foreach my $edge1 (@edges1) {
if ($net1->{tripartitions}->{$edge1->[1]} eq
$net2->{tripartitions}->{$edge2->[1]}) {
$matched=1;
last;
}
}
if (! $matched) {$FP++;}
}
return ($FN/(scalar @edges1)+$FP/(scalar @edges2))/2;
}
# Time-consistency
# to do: add weak time consistency
=head2 is_time_consistent
Title : is_time_consistent
Usage : my $b=$net->is_time_consistent()
Function: tests if $net is (strong) time-consistent
Returns : boolean
Args : none
=cut
sub is_time_consistent {
my ($self)=@_;
$self->compute_temporal_representation()
unless exists $self->{has_temporal_representation};
return $self->{has_temporal_representation};
}
=head2 temporal_representation
Title : temporal_representation
Usage : my %time=$net->temporal_representation()
Function: returns a hash containing a temporal representation of $net, or 0
if $net is not time-consistent
Returns : hash
Args : none
=cut
sub temporal_representation {
my ($self)=@_;
if ($self->is_time_consistent) {
return %{$self->{temporal_representation}};
}
return 0;
}
sub compute_temporal_representation {
my ($self)=@_;
my $quotient=Graph::Directed->new();
my $classes=find_classes($self);
my %repr;
map {$repr{$_}=$classes->{$_}[0]} $self->nodes();
foreach my $e ($self->tree_edges()) {
$quotient->add_edge($repr{$e->[0]},$repr{$e->[1]});
}
my %temp;
my $depth=0;
while ($quotient->vertices()) {
if (my @svs=$quotient->predecessorless_vertices()) {
foreach my $sv (@svs) {
$temp{$sv}=$depth;
}
$quotient->delete_vertices(@svs);
} else {
return 0;
}
$depth++;
}
foreach my $node (@{$self->{nodes}}) {
$temp{$node}=$temp{$repr{$node}}
}
$self->{temporal_representation}=\%temp;
$self->{has_temporal_representation}=1;
}
sub find_classes {
my ($self)=@_;
my $classes={};
map {$classes->{$_}=[$_]} $self->nodes();
foreach my $e ($self->hybrid_edges()) {
$classes=join_classes($classes,$e->[0],$e->[1]);
}
return $classes;
}
sub join_classes {
my ($classes,$u,$v)=@_;
my @clu=@{$classes->{$u}};
my @clv=@{$classes->{$v}};
my @cljoin=(@clu,@clv);
map {$classes->{$_}=\@cljoin} @cljoin;
return $classes;
}
# alignment
=head2 contract_elementary
Title : contract_elementary
Usage : my ($contracted,$blocks)=$net->contract_elementary();
Function: Returns the network $contracted, obtained by contracting elementary
paths of $net into edges. The reference $blocks points to a hash
where, for each node of $contracted, gives the corresponding nodes
of $net that have been deleted.
Returns : Bio::PhyloNetwork,reference to hash
Args : none
=cut
sub contract_elementary {
my ($self)=@_;
my $contracted=$self->graph->copy();
my @nodes=$self->nodes();
my $mus=$self->{mudata};
my $hs=$self->{h};
my %blocks;
foreach my $u (@nodes) {
$blocks{$u}=[$u];
}
my @elementary=grep { $contracted->out_degree($_) == 1} $self->tree_nodes();
@elementary=sort {$mus->{$b} <=> $mus->{$a} ||
$hs->{$b} <=> $hs->{$a}} @elementary;
foreach my $elem (@elementary) {
my @children=$contracted->successors($elem);
my $child=$children[0];
if ($contracted->in_degree($elem) == 1) {
my @parents=$contracted->predecessors($elem);
my $parent=$parents[0];
$contracted->add_edge($parent,$child);
}
$contracted->delete_vertex($elem);
my @blch=@{$blocks{$child}};
my @blem=@{$blocks{$elem}};
$blocks{$child}=[@blem,@blch];
delete $blocks{$elem};
}
my $contr=Bio::PhyloNetwork->new(-graph => $contracted);
return $contr,\%blocks;
}
=head2 optimal_alignment
Title : optimal_alignment
Usage : my ($weight,$alignment,$wgts)=$net->optimal_alignment($net2)
Function: returns the total weight of an optimal alignment,
the alignment itself, and partial weights
between the networks $net1 and $net2 on the same set of leaves.
An optional argument allows one to use the Manhattan (default) or the
Hamming distance between mu-vectors.
Returns : scalar,reference to hash,reference to hash
Args : Bio::PhyloNetwork,
-metric => string (optional)
Supported strings for the -metric parameter are 'Manhattan' or 'Hamming'.
=cut
sub optimal_alignment {
my ($net1,$net2,%params)=@_;
my ($net1cont,$blocks1)=contract_elementary($net1);
my ($net2cont,$blocks2)=contract_elementary($net2);
my ($wc,$alignc,$weightc)=
optimal_alignment_noelementary($net1cont,$net2cont,%params);
my %alignment=();
my $totalweigth=0;
my %weigths=();
foreach my $u1 (keys %$alignc) {
my $u2=$alignc->{$u1};
my @block1=@{$blocks1->{$u1}};
my @block2=@{$blocks2->{$u2}};
while (@block1 && @block2) {
my $u1dc=pop @block1;
my $u2dc=pop @block2;
$alignment{$u1dc}=$u2dc;
$weigths{$u1dc}=$weightc->{$u1};
$totalweigth+=$weigths{$u1dc};
}
}
return $totalweigth,\%alignment,\%weigths;
}
sub optimal_alignment_noelementary {
my ($net1,$net2,%params)=@_;
my $comp = Array::Compare->new;
$net1->throw("Cannot align phylogenetic networks on different set of leaves")
unless $comp->compare($net1->{leaves},$net2->{leaves});
my $distance;
if ((defined $params{-metric})and ($params{-metric} eq 'Hamming')) {
$distance='Hamming';
} else {
$distance='Manhattan';
}
my $numleaves=$net1->{numleaves};
my @nodes1=$net1->internal_nodes();
my @nodes2=$net2->internal_nodes();
my $numnodes1=@nodes1;
my $numnodes2=@nodes2;
my @matrix=();
for (my $i=0;$i<$numnodes1;$i++) {
my @row=();
for (my $j=0;$j<$numnodes2;$j++) {
push @row,weight($net1,$nodes1[$i],$net2,$nodes2[$j],$distance);
}
push @matrix,\@row;
}
my @alignment=();
assign(\@matrix,\@alignment);
my %alignmenthash;
my %weighthash;
my $totalw=0;
foreach my $leaf (@{$net1->{leaves}}) {
$alignmenthash{$leaf}=$leaf;
$weighthash{$leaf}=0;
}
for (my $i=0;$i<$numnodes1;$i++) {
if (defined $nodes2[$alignment[$i]]) {
$alignmenthash{$nodes1[$i]}=$nodes2[$alignment[$i]];
$weighthash{$nodes1[$i]}=$matrix[$i][$alignment[$i]];
$totalw += $matrix[$i][$alignment[$i]];
}
}
return $totalw,\%alignmenthash,\%weighthash;
}
=head2 optimal_alignment_generalized
Title : optimal_alignment_generalized
Usage : my ($weight,%alignment)=$net->optimal_alignment_generalized($net2)
Function: returns the wieght of an optimal alignment, and the alignment itself,
between the topological restriction of the networks $net1 and $net2
on the set of common leaves.
An optional argument allows one to use the Manhattan (default) or the
Hamming distance between mu-vectors.
Returns : scalar,hash
Args : Bio::PhyloNetwork,
-metric => string (optional)
Supported strings for the -metric parameter are 'Manhattan' or 'Hamming'.
=cut
sub optimal_alignment_generalized {
my ($net1,$net2,%params)=@_;
my ($netr1,$netr2)=$net1->topological_restriction($net2);
return $netr1->optimal_alignment($netr2,%params);
}
sub weight {
my ($net1,$v1,$net2,$v2,$distance)=@_;
my $w;
if (! defined $distance) {
$distance='Manhattan';
}
if ($distance eq 'Hamming') {
$w=$net1->{mudata}->{$v1}->hamming($net2->{mudata}->{$v2});
} else {
$w=$net1->{mudata}->{$v1}->manhattan($net2->{mudata}->{$v2});
}
if (($net1->is_tree_node($v1) && $net2->is_hybrid_node($v2)) ||
($net2->is_tree_node($v2) && $net1->is_hybrid_node($v1))
)
{
$w +=1/(2*$net1->{numleaves});
}
return $w;
}
=head2 topological_restriction
Title : topological_restriction
Usage : my ($netr1,$netr2)=$net1->topological_restriction($net2)
Function: returns the topological restriction of $net1 and $net2 on its
common set of leaves
Returns : Bio::PhyloNetwork, Bio::PhyloNetwork
Args : Bio::PhyloNetwork
=cut
sub topological_restriction {
my ($net1,$net2)=@_;
my @leaves1=$net1->leaves();
my @leaves2=$net2->leaves();
my $numleaves1=scalar @leaves1;
my $numleaves2=scalar @leaves2;
my %position1;
for (my $i=0; $i<$numleaves1; $i++) {
$position1{$leaves1[$i]}=$i;
}
my %position2;
my @commonleaves=();
for (my $j=0; $j<$numleaves2; $j++) {
if (defined $position1{$leaves2[$j]}) {
push @commonleaves,$leaves2[$j];
$position2{$leaves2[$j]}=$j;
}
}
my $graphred1=$net1->{graph}->copy();
my $graphred2=$net2->{graph}->copy();
OUTER1:
foreach my $u ($graphred1->vertices()) {
my $mu=$net1->mudata_node($u);
foreach my $leaf (@commonleaves) {
if ($mu->[$position1{$leaf}]>0) {
next OUTER1;
}
}
$graphred1->delete_vertex($u);
}
OUTER2:
foreach my $u ($graphred2->vertices()) {
my $mu=$net2->mudata_node($u);
foreach my $leaf (@commonleaves) {
if ($mu->[$position2{$leaf}]>0) {
next OUTER2;
}
}
$graphred2->delete_vertex($u);
}
my $netr1=Bio::PhyloNetwork->new(-graph => $graphred1);
my $netr2=Bio::PhyloNetwork->new(-graph => $graphred2);
return ($netr1,$netr2);
}
# Functions for eNewick representation
=head2 eNewick
Title : eNewick
Usage : my $str=$net->eNewick()
Function: returns the eNewick representation of $net without labeling
internal tree nodes
Returns : string
Args : none
=cut
sub eNewick {
my ($self)=@_;
my $str="";
my $seen={};
foreach my $root ($self->roots()) {
$str=$str.$self->eNewick_aux($root,$seen,undef)."; ";
}
return $str;
}
sub eNewick_aux {
my ($self,$node,$seen,$parent)=@_;
my $str='';
if ($self->is_leaf($node) ||
(defined $seen->{$node}) )
{
$str=make_label($self,$parent,$node);
}
else {
$seen->{$node}=1;
my @sons=$self->{graph}->successors($node);
$str="(";
foreach my $son (@sons) {
$str=$str.$self->eNewick_aux($son,$seen,$node).",";
}
chop($str);
$str.=")".make_label($self,$parent,$node);
}
return $str;
}
sub make_label {
my ($self,$parent,$node)=@_;
my $str='';
if ($self->is_hybrid_node($node)) {
my $lbl=$self->{labels}->{$node};
if ($lbl =~ /#/) {
$lbl='';
}
$str.=$lbl; #$self->{labels}->{$node};
$str.='#';
if ((defined $parent) &&
($self->graph->has_edge_attribute($parent,$node,'type'))) {
$str.=$self->graph->get_edge_attribute($parent,$node,'type');
}
$str.=substr $node,1;
} else {
$str.=$self->{labels}->{$node};
}
if ((defined $parent) &&
($self->graph->has_edge_weight($parent,$node))) {
$str.=":".$self->graph->get_edge_weight($parent,$node);
}
return $str;
}
=head2 eNewick_full
Title : eNewick_full
Usage : my $str=$net->eNewick_full()
Function: returns the eNewick representation of $net labeling
internal tree nodes
Returns : string
Args : none
=cut
sub eNewick_full {
my ($self)=@_;
my $str="";
my $seen={};
foreach my $root ($self->roots()) {
$str=$str.$self->eNewick_full_aux($root,$seen,undef)."; ";
}
return $str;
}
sub eNewick_full_aux {
my ($self,$node,$seen,$parent)=@_;
my $str='';
if ($self->is_leaf($node) ||
(defined $seen->{$node}) )
{
$str=make_label_full($self,$parent,$node);
}
else {
$seen->{$node}=1;
my @sons=$self->{graph}->successors($node);
$str="(";
foreach my $son (@sons) {
$str=$str.$self->eNewick_full_aux($son,$seen,$node).",";
}
chop($str);
$str.=")".make_label_full($self,$parent,$node);
}
return $str;
}
sub make_label_full {
my ($self,$parent,$node)=@_;
my $str='';
if ($self->is_hybrid_node($node)) {
my $lbl=$self->{labels}->{$node};
if ($lbl =~ /#/) {
$lbl='';
}
$str.=$lbl; #$self->{labels}->{$node};
$str.='#';
if ((defined $parent) &&
($self->graph->has_edge_attribute($parent,$node,'type'))) {
$str.=$self->graph->get_edge_attribute($parent,$node,'type');
}
$str.=substr $node,1;
} else {
if ((defined $self->{labels}->{$node})&&($self->{labels}->{$node} ne '')) {
$str.=$self->{labels}->{$node};
}
else {
$str.=$node;
}
}
if ((defined $parent) &&
($self->graph->has_edge_weight($parent,$node))) {
$str.=":".$self->graph->get_edge_weight($parent,$node);
}
return $str;
}
# sub eNewick_full {
# my ($self)=@_;
# my $str="";
# my $seen={};
# foreach my $root ($self->roots()) {
# $str=$str.$self->eNewick_full_aux($root,$seen,undef)."; ";
# }
# return $str;
# }
# sub eNewick_full_aux {
# my ($self,$node,$seen,$parent)=@_;
# my $str;
# if ($self->is_leaf($node) ||
# (defined $seen->{$node}) )
# {
# if ($self->is_hybrid_node($node)) {
# my $tag=substr $node,1;
# if ((defined $parent) &&
# ($self->graph->has_edge_attribute($parent,$node,'type'))) {
# $str='#'.$self->graph->get_edge_attribute($parent,$node,'type').$tag;
# } else {
# $str=$node;
# }
# } else {
# $str=$node;
# }
# }
# else {
# $seen->{$node}=1;
# my @sons=$self->{graph}->successors($node);
# $str="(";
# foreach my $son (@sons) {
# $str=$str.$self->eNewick_full_aux($son,$seen,$node).",";
# }
# chop($str);
# if ($self->is_hybrid_node($node)) {
# my $tag=substr $node,1;
# if ((defined $parent) &&
# ($self->graph->has_edge_attribute($parent,$node,'type'))) {
# $str.=')#'.$self->graph->get_edge_attribute($parent,$node,'type').$tag;
# } else {
# $str.=")$node";
# }
# } else {
# $str.=")$node";
# }
# }
# if ((defined $parent) &&
# ($self->graph->has_edge_weight($parent,$node))) {
# $str.=":".$self->graph->get_edge_weight($parent,$node);
# }
# return $str;
# }
# displaying data
use overload '""' => \&display;
=head2 display
Title : display
Usage : my $str=$net->display()
Function: returns a string containing all the available information on $net
Returns : string
Args : none
=cut
sub display {
my ($self)=@_;
my $str="";
my $graph=$self->{graph};
my @leaves=$self->leaves();
my @nodes=@{$self->{nodes}};
$str.= "Leaves:\t@leaves\n";
$str.= "Nodes:\t@nodes\n";
$str.= "Graph:\t$graph\n";
$str.= "eNewick:\t".$self->eNewick()."\n";
$str.= "Full eNewick:\t".$self->eNewick_full()."\n";
$str.= "Mu-data and heights:\n";
foreach my $node (@nodes) {
$str.= "v=$node: ";
if (exists $self->{labels}->{$node}) {
$str.="\tlabel=".$self->{labels}->{$node}.",";
} else {
$str.="\tlabel=(none),";
}
$str.= "\th=".$self->{h}->{$node}.", \tmu=".$self->{mudata}->{$node}."\n";
}
if (exists $self->{has_temporal_representation}) {
$str.= "Temporal representation:\n";
if ($self->{has_temporal_representation}) {
foreach my $node (@nodes) {
$str.= "v=$node; ";
$str.= "\tt=".$self->{temporal_representation}->{$node}."\n";
}
} else {
$str.= "Does not exist.\n";
}
}
if (exists $self->{tripartitions}) {
$str.= "Tripartitions:\n";
foreach my $node (@nodes) {
$str.= "v=$node; ";
$str.= "\ttheta=".$self->{tripartitions}->{$node}."\n";
}
}
return $str;
}
1;
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