Bio::Tools::Phylo::PAML
Result
Summary
Bio::Tools::Phylo::PAML::Result - A PAML result set object
Package variables
No package variables defined.
Included modules
Inherit
Synopsis
# see Bio::Tools::Phylo::PAML for example usage
use Bio::Tools::Phylo::PAML;
my $parser = new Bio::Tools::Phylo::PAML
(-file => "./results/mlc", -dir => "./results/");
# get the first/next result; a Bio::Tools::Phylo::PAML::Result object,
# which isa Bio::SeqAnalysisResultI object.
my $result = $parser->next_result();
my @seqs = $result->get_seqs;
my @MLmatrix = $result->get_MLmatrix; # get MaxLikelihood Matrix
my @NGmatrix = $result->get_NGmatrix; # get Nei-Gojoburi Matrix
my @basfreq = $result->get_codon_pos_basefreq;
Description
This is a container object for PAML Results.
Methods
Methods description
Title : new
Usage : my $obj = new Bio::Tools::Phylo::PAML::Result(%data);
Function: Builds a new Bio::Tools::Phylo::PAML::Result object
Returns : Bio::Tools::Phylo::PAML::Result
Args : -trees => array reference of Bio::Tree::TreeI objects
-MLmatrix => ML matrix
-seqs => array reference of Bio::PrimarySeqI objects
-codonpos => array reference of codon positions
-codonfreq => array reference of codon frequencies
-version => version string
-model => model string
-patterns => hashref with the fields '-patterns', '-ns', '-ls'
-stats => array ref of misc stats (optional)
-aafreq => Hashref of AA frequencies (only for AAML)
-aadistmat => Bio::Matrix::PhylipDist (only for AAML)
-aamldistmat => Bio::Matrix::PhylipDist (only for pairwise AAML)
-NSSitesresult => arrayref of PAML::ModelResult |
Title : next_tree
Usage : my $tree = $factory->next_tree;
Function: Get the next tree from the factory
Returns : Bio::Tree::TreeI
Args : none |
Title : get_trees
Usage : my @trees = $result->get_trees;
Function: Get all the parsed trees as an array
Returns : Array of trees
Args : none |
Title : add_tree
Usage : $result->add_tree($tree);
Function: Adds a tree
Returns : integer which is the number of trees stored
Args : Bio::Tree::TreeI |
Title : set_MLmatrix
Usage : $result->set_MLmatrix($mat)
Function: Set the ML Matrix
Returns : none
Args : Arrayref to MLmatrix (must be arrayref to 2D matrix whic is
lower triangle pairwise) |
Title : get_MLmatrix
Usage : my $mat = $result->get_MLmatrix()
Function: Get the ML matrix
Returns : 2D Array reference
Args : none |
Title : set_NGmatrix
Usage : $result->set_NGmatrix($mat)
Function: Set the Nei & Gojobori Matrix
Returns : none
Args : Arrayref to NGmatrix (must be arrayref to 2D matrix whic is
lower triangle pairwise) |
Title : get_NGmatrix
Usage : my $mat = $result->get_NGmatrix()
Function: Get the Nei & Gojobori matrix
Returns : 2D Array reference
Args : none |
Title : add_seq
Usage : $obj->add_seq($seq)
Function: Add a Bio::PrimarySeq to the Result
Returns : none
Args : Bio::PrimarySeqI
See also : Bio::PrimarySeqI |
Title : reset_seqs
Usage : $result->reset_seqs
Function: Reset the OTU seqs stored
Returns : none
Args : none |
Title : get_seqs
Usage : my @otus = $result->get_seqs
Function: Get the seqs Bio::PrimarySeq (OTU = Operational Taxonomic Unit)
Returns : Array of Bio::PrimarySeq
Args : None
See also : Bio::PrimarySeq |
Title : set_codon_pos_basefreq
Usage : $result->set_codon_pos_basefreq(@freqs)
Function: Set the codon position base frequencies
Returns : none
Args : Array of length 3 where each slot has a hashref
keyed on DNA base |
Title : get_codon_pos_basefreq
Usage : my @basepos = $result->get_codon_pos_basefreq;
Function: Get the codon position base frequencies
Returns : Array of length 3 (each codon position), each
slot is a hashref keyed on DNA bases, the values are
the frequency of the base at that position for all sequences
Args : none
Note : The array starts at 0 so position '1' is in position '0'
of the array |
Title : version
Usage : $obj->version($newval)
Function: Get/Set version
Returns : value of version
Args : newvalue (optional) |
Title : model
Usage : $obj->model($newval)
Function: Get/Set model
Returns : value of model
Args : on set, new value (a scalar or undef, optional) |
Title : patterns
Usage : $obj->patterns($newval)
Function: Get/Set Patterns hash
Returns : Hashref of pattern data
Args : [optional] Hashref of patterns
: The hashref is typically
: { -patterns => \@arrayref
: -ns => $ns
: -ls => $ls
: } |
Title : set_AAFreqs
Usage : $result->set_AAFreqs(\%aafreqs);
Function: Get/Set AA freqs
Returns : none
Args : Hashref, keys are the sequence names, each points to a hashref
which in turn has keys which are the amino acids |
Title : get_AAFreqs
Usage : my %all_aa_freqs = $result->get_AAFreqs()
OR
my %seq_aa_freqs = $result->get_AAFreqs($seqname)
Function: Get the AA freqs, either for every sequence or just
for a specific sequence
The average aa freqs for the entire set are also available
for the sequence named 'Average'
Returns : Hashref
Args : (optional) sequence name to retrieve aa freqs for |
Title : add_stat
Usage : $result->add_stat($stat,$value);
Function: Add some misc stat valuess (key/value pairs)
Returns : none
Args : $stat stat name
$value stat value |
Title : get_stat
Usage : my $value = $result->get_stat($name);
Function: Get the value for a stat of a given name
Returns : scalar value
Args : name of the stat |
Title : get_stat_names
Usage : my @names = $result->get_stat_names;
Function: Get the stat names stored for the result
Returns : array of names
Args : none |
Title : get_AADistMatrix
Usage : my $mat = $obj->get_AADistMatrix()
Function: Get AADistance Matrix
Returns : value of AADistMatrix (Bio::Matrix::PhylipDist)
Args : none |
Title : set_AADistMatrix
Usage : $obj->set_AADistMatrix($mat);
Function: Set the AADistrance Matrix (Bio::Matrix::PhylipDist)
Returns : none
Args : AADistrance Matrix (Bio::Matrix::PhylipDist) |
Title : get_AAMLDistMatrix
Usage : my $mat = $obj->get_AAMLDistMatrix()
Function: Get AAMLDistance Matrix
Returns : value of AAMLDistMatrix (Bio::Matrix::PhylipDist)
Args : none |
Title : set_AAMLDistMatrix
Usage : $obj->set_AAMLDistMatrix($mat);
Function: Set the AA ML Distrance Matrix (Bio::Matrix::PhylipDist)
Returns : none
Args : AAMLDistrance Matrix (Bio::Matrix::PhylipDist) |
Title : add_NSSite_result
Usage : $result->add_NSSite_result($model)
Function: Add a NSsite result (PAML::ModelResult)
Returns : none
Args : Bio::Tools::Phylo::PAML::ModelResult |
Title : get_NSSite_results
Usage : my @results = @{$self->get_NSSite_results};
Function: Get the reference to the array of NSSite_results
Returns : Array of PAML::ModelResult results
Args : none |
Title : set_CodonFreqs
Usage : $obj->set_CodonFreqs($newval)
Function: Get/Set the Codon Frequence table
Returns : value of set_CodonFreqs (a scalar)
Args : on set, new value (a scalar or undef, optional) |
Title : get_CodonFreqs
Usage : my @codon_freqs = $result->get_CodonFreqs()
Function: Get the Codon freqs
Returns : Array
Args : none |
Methods code
sub new
{ my($class,@args) = @_;
my $self = $class->SUPER::new(@args);
my ($trees,$mlmat,$seqs,$ngmatrix,
$codonpos,$codonfreq,$version,
$model,$patterns, $stats,
$aafreq, $aadistmat,
$aamldistmat,
$NSSitesresults ) = $self->_rearrange([qw(TREES MLMATRIX
SEQS NGMATRIX
CODONPOS CODONFREQ
VERSION MODEL PATTERNS
STATS AAFREQ AADISTMAT
AAMLDISTMAT
NSSITESRESULTS)],
@args);
$self->reset_seqs;
if( $trees ) {
if(ref($trees) !~ /ARRAY/i ) {
$self->warn("Must have provided a valid array reference to initialize trees");
} else {
foreach my $t ( @$trees ) {
$self->add_tree($t);
}
}
}
$self->{'_treeiterator'} = 0;
if( $mlmat ) {
if( ref($mlmat) !~ /ARRAY/i ) {
$self->warn("Must have provided a valid array reference to initialize MLmatrix");
} else {
$self->set_MLmatrix($mlmat);
}
}
if( $seqs ) {
if( ref($seqs) !~ /ARRAY/i ) {
$self->warn("Must have provided a valid array reference to initialize seqs");
} else {
foreach my $s ( @$seqs ) {
$self->add_seq($s);
}
}
}
if( $ngmatrix ) {
if( ref($ngmatrix) !~ /ARRAY/i ) {
$self->warn("Must have provided a valid array reference to initialize NGmatrix");
} else {
$self->set_NGmatrix($ngmatrix);
}
}
if( $codonfreq ) {
if( ref($codonfreq) =~ /ARRAY/i ) {
$self->set_CodonFreqs($codonfreq);
} else {
$self->warn("Must have provided a valid array reference to initialize codonfreq");
}
}
if( $codonpos ) {
if( ref($codonpos) !~ /ARRAY/i ) {
$self->warn("Must have provided a valid array reference to initialize codonpos");
} else {
$self->set_codon_pos_basefreq(@$codonpos);
}
}
$self->version($version) if defined $version;
$self->model($model) if defined $model;
if( defined $patterns ) {
if( ref($patterns) =~ /HASH/i ) {
$self->patterns($patterns);
} else {
$self->warn("Must have provided a valid array reference to initialize patterns");
}
}
$self->{'_aafreqs'} = {};
if( $aafreq ) {
if( ref($aafreq) =~ /HASH/i ) {
$self->set_AAFreqs($aafreq);
} else {
$self->warn("Must have provided a valid hash reference to initialize aafreq");
}
}
if( $stats ) {
if( ref($stats) =~ /HASH/i ) {
while( my ($stat,$val) = each %$stats) {
$self->add_stat($stat,$val);
}
} else {
$self->warn("Must have provided a valid hash reference initialize stats");
}
}
$self->set_AADistMatrix($aadistmat) if defined $aadistmat;
$self->set_AAMLDistMatrix($aamldistmat) if defined $aamldistmat;
if( defined $NSSitesresults ) {
if( ref($NSSitesresults) !~ /ARRAY/i ) {
$self->warn("expected an arrayref for -NSSitesresults");
} else {
foreach my $m ( @$NSSitesresults ) {
$self->add_NSSite_result($m);
}
}
}
return $self;} | sub next_tree
{ my ($self,@args) = @_;
return $self->{'_trees'}->[$self->{'_treeiterator'}++] || undef;} | sub get_trees
{ my ($self) = @_;
return @{$self->{'_trees'} || []};} | sub rewind_tree_iterator
{ shift->{'_treeiterator'} = 0;} | sub add_tree
{ my ($self,$tree) = @_;
if( $tree && ref($tree) && $tree->isa('Bio::Tree::TreeI') ) {
push @{$self->{'_trees'}},$tree;
}
return scalar @{$self->{'_trees'}};} | sub set_MLmatrix
{ my ($self,$mat) = @_;
return unless ( defined $mat );
if( ref($mat) !~ /ARRAY/i ) {
$self->warn("Did not provide a valid 2D Array reference for set_MLmatrix");
return;
}
$self->{'_mlmatrix'} = $mat;} | sub get_MLmatrix
{ my ($self,@args) = @_;
return $self->{'_mlmatrix'};} | sub set_NGmatrix
{ my ($self,$mat) = @_;
return unless ( defined $mat );
if( ref($mat) !~ /ARRAY/i ) {
$self->warn("Did not provide a valid 2D Array reference for set_NGmatrix");
return;
}
$self->{'_ngmatrix'} = $mat;} | sub get_NGmatrix
{ my ($self,@args) = @_;
return $self->{'_ngmatrix'};} | sub add_seq
{ my ($self,$seq) = @_;
if( $seq ) {
unless( $seq->isa("Bio::PrimarySeqI") ) {
$self->warn("Must provide a valid Bio::PrimarySeqI to add_seq");
return;
}
push @{$self->{'_seqs'}},$seq;
}} | sub reset_seqs
{ my ($self) = @_;
$self->{'_seqs'} = [];} | sub get_seqs
{ my ($self) = @_;
return @{$self->{'_seqs'}};} | sub set_codon_pos_basefreq
{ my ($self,@codonpos) = @_;
if( scalar @codonpos != 3 ) {
$self->warn("invalid array to set_codon_pos_basefreq, must be an array of length 3");
return;
}
foreach my $pos ( @codonpos ) {
if( ref($pos) !~ /HASH/i ||
! exists $pos->{'A'} ) {
$self->warn("invalid array to set_codon_pos_basefreq, must be an array with hashreferences keyed on DNA bases, C,A,G,T");
}
}
$self->{'_codonposbasefreq'} = [@codonpos];} | sub get_codon_pos_basefreq
{ my ($self) = @_;
return @{$self->{'_codonposbasefreq'}};} | sub version
{ my $self = shift;
$self->{'_version'} = shift if @_;
return $self->{'_version'};} | sub model
{ my $self = shift;
return $self->{'_model'} = shift if @_;
return $self->{'_model'};} | sub patterns
{ my $self = shift;
return $self->{'_patterns'} = shift if @_;
return $self->{'_patterns'};} | sub set_AAFreqs
{ my ($self,$aafreqs) = @_;
if( $aafreqs && ref($aafreqs) =~ /HASH/i ) {
foreach my $seqname ( keys %{$aafreqs} ) {
$self->{'_aafreqs'}->{$seqname} = $aafreqs->{$seqname};
}
}} | sub get_AAFreqs
{ my ($self,$seqname) = @_;
if( $seqname ) {
return $self->{'_aafreqs'}->{$seqname} || {};
} else {
return $self->{'_aafreqs'};
}} | sub add_stat
{ my ($self,$stat,$value) = @_;
return if( ! defined $stat || !defined $value );
$self->{'_stats'}->{$stat} = $value;
return;} | sub get_stat
{ my ($self,$statname) = @_;
return $self->{'_stats'}->{$statname};} | sub get_stat_names
{ my ($self) = @_;
return keys %{$self->{'_stats'} || {}};} | sub get_AADistMatrix
{ my $self = shift;
return $self->{'_AADistMatix'};} | sub set_AADistMatrix
{ my ($self,$d) = @_;
if( ! $d ||
! ref($d) ||
! $d->isa('Bio::Matrix::PhylipDist') ) {
$self->warn("Must provide a valid Bio::Matrix::MatrixI for set_AADistMatrix");
}
$self->{'_AADistMatix'} = $d;
return undef;} | sub get_AAMLDistMatrix
{ my $self = shift;
return $self->{'_AAMLDistMatix'};} | sub set_AAMLDistMatrix
{ my ($self,$d) = @_;
if( ! $d ||
! ref($d) ||
! $d->isa('Bio::Matrix::PhylipDist') ) {
$self->warn("Must provide a valid Bio::Matrix::MatrixI for set_AAMLDistMatrix");
}
$self->{'_AAMLDistMatix'} = $d;
return undef;} | sub add_NSSite_result
{ my ($self,$model) = @_;
if( defined $model ) {
push @{$self->{'_nssiteresult'}}, $model;
}
return scalar @{$self->{'_nssiteresult'}};} | sub get_NSSite_results
{ my ($self) = @_;
return @{$self->{'_nssiteresult'}};} | sub set_CodonFreqs
{ my $self = shift;
return $self->{'_codonfreqs'} = shift if @_;
return $self->{'_codonfreqs'};} | sub get_CodonFreqs
{ my ($self) = @_;
return @{$self->{'_codonfreqs'} || []};} | General documentation
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/MailList.shtml - About the mailing lists
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:
bioperl-bugs@bioperl.org
http://bugzilla.bioperl.org/
| AUTHOR - Jason Stajich, Aaron Mackey | Top |
Additional contributors names and emails here
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
Title : rewind_tree_iterator
Usage : $result->rewind_tree()
Function: Rewinds the tree iterator so that next_tree can be
called again from the beginning
Returns : none
Args : none