#
# BioPerl module for Bio::Tools::Phylo::PAML::ModelResult
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Jason Stajich <jason@open-bio.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::Tools::Phylo::PAML::ModelResult - A container for NSSite Model Result from PAML
=head1 SYNOPSIS
# get a ModelResult from a PAML::Result object
use Bio::Tools::Phylo::PAML;
my $paml = Bio::Tools::Phylo::PAML->new(-file => 'mlc');
my $result = $paml->next_result;
foreach my $model ( $result->get_NSSite_results ) {
print $model->model_num, " ", $model->model_description, "\n";
print $model->kappa, "\n";
print $model->run_time, "\n";
# if you are using PAML < 3.15 then only one place for POS sites
for my $sites ( $model->get_pos_selected_sites ) {
print join("\t",@$sites),"\n";
}
# otherwise query NEB and BEB slots
for my $sites ( $model->get_NEB_pos_selected_sites ) {
print join("\t",@$sites),"\n";
}
for my $sites ( $model->get_BEB_pos_selected_sites ) {
print join("\t",@$sites),"\n";
}
}
=head1 DESCRIPTION
Describe the object here
=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
email or the web:
https://redmine.open-bio.org/projects/bioperl/
=head1 AUTHOR - Jason Stajich
Email jason@open-bio.org
=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::Tools::Phylo::PAML::ModelResult;
use strict;
# Object preamble - inherits from Bio::Root::Root
use base qw(Bio::Root::Root);
=head2 new
Title : new
Usage : my $obj = Bio::Tools::Phylo::PAML::ModelResult->new();
Function: Builds a new Bio::Tools::Phylo::PAML::ModelResult object
Returns : an instance of Bio::Tools::Phylo::PAML::ModelResult
Args : -model_num => model number
-model_description => model description
-kappa => value of kappa
-time_used => amount of time
-pos_sites => arrayref of sites under positive selection
-neb_sites => arrayref of sites under positive selection (by NEB analysis)
-beb_sites => arrayref of sites under positive selection (by BEB analysis)
-trees => arrayref of tree(s) data for this model
-shape_params => hashref of parameters
('shape' => 'alpha',
'gamma' => $g,
'r' => $r,
'f' => $f
)
OR
( 'shape' => 'beta',
'p' => $p,
'q' => $q
)
-likelihood => likelihood
-num_site_classes => number of site classes
-dnds_site_classes => hashref with two keys, 'p' and 'w'
which each point to an array, each
slot is for a different site class.
'w' is for dN/dS and 'p' is probability
=cut
sub new {
my($class,@args) = @_;
my $self = $class->SUPER::new(@args);
my ($modelnum,$modeldesc,$kappa,
$timeused,$trees,
$pos_sites,$neb_sites,$beb_sites,
$num_site_classes, $shape_params,
$dnds_classes,
$likelihood) = $self->_rearrange([qw(MODEL_NUM
MODEL_DESCRIPTION
KAPPA
TIME_USED
TREES
POS_SITES
NEB_SITES BEB_SITES
NUM_SITE_CLASSES
SHAPE_PARAMS
DNDS_SITE_CLASSES
LIKELIHOOD)],
@args);
if( $trees ) {
if(ref($trees) !~ /ARRAY/i ) {
$self->warn("Must provide a valid array reference to initialize trees");
} else {
foreach my $t ( @$trees ) {
$self->add_tree($t);
}
}
}
$self->{'_treeiterator'} = 0;
if( $pos_sites ) {
if(ref($pos_sites) !~ /ARRAY/i ) {
$self->warn("Must provide a valid array reference to initialize pos_sites");
} else {
foreach my $s ( @$pos_sites ) {
if( ref($s) !~ /ARRAY/i ) {
$self->warn("Need an array reference for each entry in the pos_sites object");
next;
}
$self->add_pos_selected_site(@$s);
}
}
}
if( $beb_sites ) {
if(ref($beb_sites) !~ /ARRAY/i ) {
$self->warn("Must provide a valid array reference to initialize beb_sites");
} else {
foreach my $s ( @$beb_sites ) {
if( ref($s) !~ /ARRAY/i ) {
$self->warn("need an array ref for each entry in the beb_sites object");
next;
}
$self->add_BEB_pos_selected_site(@$s);
}
}
}
if( $neb_sites ) {
if(ref($neb_sites) !~ /ARRAY/i ) {
$self->warn("Must provide a valid array reference to initialize neb_sites");
} else {
foreach my $s ( @$neb_sites ) {
if( ref($s) !~ /ARRAY/i ) {
$self->warn("need an array ref for each entry in the neb_sites object");
next;
}
$self->add_NEB_pos_selected_site(@$s);
}
}
}
defined $modelnum && $self->model_num($modelnum);
defined $modeldesc && $self->model_description($modeldesc);
defined $kappa && $self->kappa($kappa);
defined $timeused && $self->time_used($timeused);
defined $likelihood && $self->likelihood($likelihood);
$self->num_site_classes($num_site_classes || 0);
if( defined $dnds_classes ) {
if( ref($dnds_classes) !~ /HASH/i ||
! defined $dnds_classes->{'p'} ||
! defined $dnds_classes->{'w'} ) {
$self->warn("-dnds_site_classes expects a hashref with keys p and w");
} else {
$self->dnds_site_classes($dnds_classes);
}
}
if( defined $shape_params ) {
if( ref($shape_params) !~ /HASH/i ) {
$self->warn("-shape_params expects a hashref not $shape_params\n");
} else {
$self->shape_params($shape_params);
}
}
return $self;
}
=head2 model_num
Title : model_num
Usage : $obj->model_num($newval)
Function: Get/Set the Model number (0,1,2,3...)
Returns : value of model_num (a scalar)
Args : on set, new value (a scalar or undef, optional)
=cut
sub model_num {
my $self = shift;
return $self->{'_num'} = shift if @_;
return $self->{'_num'};
}
=head2 model_description
Title : model_description
Usage : $obj->model_description($newval)
Function: Get/Set the model description
This is something like 'one-ratio', 'neutral', 'selection'
Returns : value of description (a scalar)
Args : on set, new value (a scalar or undef, optional)
=cut
sub model_description{
my $self = shift;
return $self->{'_model_description'} = shift if @_;
return $self->{'_model_description'};
}
=head2 time_used
Title : time_used
Usage : $obj->time_used($newval)
Function: Get/Set the time it took to run this analysis
Returns : value of time_used (a scalar)
Args : on set, new value (a scalar or undef, optional)
=cut
sub time_used{
my $self = shift;
return $self->{'_time_used'} = shift if @_;
return $self->{'_time_used'};
}
=head2 kappa
Title : kappa
Usage : $obj->kappa($newval)
Function: Get/Set kappa (ts/tv)
Returns : value of kappa (a scalar)
Args : on set, new value (a scalar or undef, optional)
=cut
sub kappa{
my $self = shift;
return $self->{'_kappa'} = shift if @_;
return $self->{'_kappa'};
}
=head2 num_site_classes
Title : num_site_classes
Usage : $obj->num_site_classes($newval)
Function: Get/Set the number of site classes for this model
Returns : value of num_site_classes (a scalar)
Args : on set, new value (a scalar or undef, optional)
=cut
sub num_site_classes{
my $self = shift;
return $self->{'_num_site_classes'} = shift if @_;
return $self->{'_num_site_classes'};
}
=head2 dnds_site_classes
Title : dnds_site_classes
Usage : $obj->dnds_site_classes($newval)
Function: Get/Set dN/dS site classes, a hashref
with 2 keys, 'p' and 'w' which point to arrays
one slot for each site class.
Returns : value of dnds_site_classes (a hashref)
Args : on set, new value (a scalar or undef, optional)
=cut
sub dnds_site_classes{
my $self = shift;
return $self->{'_dnds_site_classes'} = shift if @_;
return $self->{'_dnds_site_classes'};
}
=head2 get_pos_selected_sites
Title : get_pos_selected_sites
Usage : my @sites = $modelresult->get_pos_selected_sites();
Function: Get the sites which PAML has identified as under positive
selection (w > 1). This returns an array with each slot
being a site, 4 values,
site location (in the original alignment)
Amino acid (I *think* in the first sequence)
P (P value)
Significance (** indicated > 99%, * indicates >=95%)
Returns : Array
Args : none
=cut
sub get_pos_selected_sites{
return @{$_[0]->{'_posselsites'} || []};
}
=head2 add_pos_selected_site
Title : add_pos_selected_site
Usage : $result->add_pos_selected_site($site,$aa,$pvalue,$signif);
Function: Add a site to the list of positively selected sites
Returns : count of the number of sites stored
Args : $site - site number (in the alignment)
$aa - amino acid under selection
$pvalue - float from 0->1 represent probability site is under selection according to this model
$signif - significance (coded as either empty, '*', or '**'
=cut
sub add_pos_selected_site{
my ($self,$site,$aa,$pvalue,$signif) = @_;
push @{$self->{'_posselsites'}}, [ $site,$aa,$pvalue,$signif ];
return scalar @{$self->{'_posselsites'}};
}
=head2 get_NEB_pos_selected_sites
Title : get_NEB_pos_selected_sites
Usage : my @sites = $modelresult->get_NEB_pos_selected_sites();
Function: Get the sites which PAML has identified as under positive
selection (w > 1) using Naive Empirical Bayes.
This returns an array with each slot being a site, 4 values,
site location (in the original alignment)
Amino acid (I *think* in the first sequence)
P (P value)
Significance (** indicated > 99%, * indicates > 95%)
post mean for w
Returns : Array
Args : none
=cut
sub get_NEB_pos_selected_sites{
return @{$_[0]->{'_NEBposselsites'} || []};
}
=head2 add_NEB_pos_selected_site
Title : add_NEB_pos_selected_site
Usage : $result->add_NEB_pos_selected_site($site,$aa,$pvalue,$signif);
Function: Add a site to the list of positively selected sites
Returns : count of the number of sites stored
Args : $site - site number (in the alignment)
$aa - amino acid under selection
$pvalue - float from 0->1 represent probability site is under selection according to this model
$signif - significance (coded as either empty, '*', or '**'
$postmean - post mean for w
=cut
sub add_NEB_pos_selected_site{
my ($self,@args) = @_;
push @{$self->{'_NEBposselsites'}}, [ @args ];
return scalar @{$self->{'_NEBposselsites'}};
}
=head2 get_BEB_pos_selected_sites
Title : get_BEB_pos_selected_sites
Usage : my @sites = $modelresult->get_BEB_pos_selected_sites();
Function: Get the sites which PAML has identified as under positive
selection (w > 1) using Bayes Empirical Bayes.
This returns an array with each slot being a site, 6 values,
site location (in the original alignment)
Amino acid (I *think* in the first sequence)
P (P value)
Significance (** indicated > 99%, * indicates > 95%)
post mean for w (mean)
Standard Error for w (SE)
Returns : Array
Args : none
=cut
sub get_BEB_pos_selected_sites{
return @{$_[0]->{'_BEBposselsites'} || []};
}
=head2 add_BEB_pos_selected_site
Title : add_BEB_pos_selected_site
Usage : $result->add_BEB_pos_selected_site($site,$aa,$pvalue,$signif);
Function: Add a site to the list of positively selected sites
Returns : count of the number of sites stored
Args : $site - site number (in the alignment)
$aa - amino acid under selection
$pvalue - float from 0->1 represent probability site is under selection according to this model
$signif - significance (coded as either empty, '*', or '**'
$postmean - post mean for w
$SE - Standard Error for w
=cut
sub add_BEB_pos_selected_site{
my ($self,@args) = @_;
push @{$self->{'_BEBposselsites'}}, [ @args ];
return scalar @{$self->{'_BEBposselsites'}};
}
=head2 next_tree
Title : next_tree
Usage : my $tree = $factory->next_tree;
Function: Get the next tree from the factory
Returns : L<Bio::Tree::TreeI>
Args : none
=cut
sub next_tree{
my ($self,@args) = @_;
return $self->{'_trees'}->[$self->{'_treeiterator'}++] || undef;
}
=head2 get_trees
Title : get_trees
Usage : my @trees = $result->get_trees;
Function: Get all the parsed trees as an array
Returns : Array of trees
Args : none
=cut
sub get_trees{
my ($self) = @_;
return @{$self->{'_trees'} || []};
}
=head2 rewind_tree_iterator
Title : rewind_tree_iterator
Usage : $result->rewind_tree_iterator()
Function: Rewinds the tree iterator so that next_tree can be
called again from the beginning
Returns : none
Args : none
=cut
sub rewind_tree_iterator {
shift->{'_treeiterator'} = 0;
}
=head2 add_tree
Title : add_tree
Usage : $result->add_tree($tree);
Function: Adds a tree
Returns : integer which is the number of trees stored
Args : L<Bio::Tree::TreeI>
=cut
sub add_tree{
my ($self,$tree) = @_;
if( $tree && ref($tree) && $tree->isa('Bio::Tree::TreeI') ) {
push @{$self->{'_trees'}},$tree;
}
return scalar @{$self->{'_trees'}};
}
=head2 shape_params
Title : shape_params
Usage : $obj->shape_params($newval)
Function: Get/Set shape params for the distribution, 'alpha', 'beta'
which is a hashref
with 1 keys, 'p' and 'q'
Returns : value of shape_params (a scalar)
Args : on set, new value (a scalar or undef, optional)
=cut
sub shape_params{
my $self = shift;
return $self->{'_shape_params'} = shift if @_;
return $self->{'_shape_params'};
}
=head2 likelihood
Title : likelihood
Usage : $obj->likelihood($newval)
Function: log likelihood
Returns : value of likelihood (a scalar)
Args : on set, new value (a scalar or undef, optional)
=cut
sub likelihood{
my $self = shift;
return $self->{'likelihood'} = shift if @_;
return $self->{'likelihood'};
}
1;