# $Id: ModelResult.pm 16123 2009-09-17 12:57:27Z cjfields $ # # BioPerl module for Bio::Tools::Phylo::PAML::ModelResult # # Please direct questions and support issues to # # Cared for by Jason Stajich # # 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 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: http://bugzilla.open-bio.org/ =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 = $factory->next_tree; Function: Get the next tree from the factory Returns : L Args : none =cut sub next_tree{ my ($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 =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;