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Bio-Tools-Phylo-PAML-1.7.3
River stage one • 1 direct dependent • 1 total dependent
/ Bio::Tools::Phylo::PAML::Result

NAME

Bio::Tools::Phylo::PAML::Result - A PAML result set object

VERSION

version 1.7.3

SYNOPSIS

# see Bio::Tools::Phylo::PAML for example usage
use Bio::Tools::Phylo::PAML;
my $parser = Bio::Tools::Phylo::PAML->new
  (-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 %input_params = $result->get_input_parameters;
my @basfreq      = $result->get_codon_pos_basefreq;
my $MLmatrix     = $result->get_MLmatrix; # get MaxLikelihood Matrix
my $NGmatrix     = $result->get_NGmatrix; # get Nei-Gojoburi Matrix


# for AAML runs
my $AAmatrix   = $result->get_AADistMatrix;
my $AAMLmatrix   = $result->get_AAMLDistMatrix;

# if -dir contains an rst file get list of
# Bio::PrimarySeq ancestral state reconstructions of the sequences
my @rsts          = $result->get_rst_seqs;


# if you want to print the changes on the tree
# this will print out the
# anc_aa       => ANCESTRAL AMINO ACID
# anc_prob     => ANCESTRAL AA PROBABILITY
# derived_aa   => DERIVED AA
# derived_prob => DERIVE AA PROBABILITY (where appropriate - NA for extant/tip taxas)
# site         => which codon site this in the alignment
  @trees = $result->get_rst_trees;
  for my $t ( @trees ) {
  for my $node ( $t->get_nodes ) {
      next unless $node->ancestor; # skip root node
      my @changes = $node->get_tag_values('changes');
      my $chgstr = '';
      for my $c ( @changes ) {
      for my $k ( sort keys %$c ) {
          $chgstr .= "$k => $c->{$k} ";
      }
      $chgstr .= "\n\t";
      }

      printf "node:%s n=%s s=%s\n\t%s\n",
      $node->id,
      $node->get_tag_values('n'),
      $node->get_tag_values('s'),
      $chgstr;
  }
  }

# Persite probabilities
my $persite = $result->get_rst_persite;
# let's score site 1
$site = $persite->[2];
# so site 2, node 2 (extant node, node 2)
print $site->[2]->{'codon'}, ' ',$site->[2]->{'aa'},"\n";
# site 2, node 3
print $site->[3]->{'codon'}, ' ',$site->[3]->{'aa'}, "\n";

# ancestral node 9, codon, aa, marginal probabilities; Yang95 is listed as
#  (eqn. 4 in Yang et al. 1995 Genetics 141:1641-1650) in PAML rst file.
print $site->[9]->{'codon'}, ' ',$site->[9]->{'aa'}, ' ', $site->[9]->{'prob'}, ' ',
      $site->[9]->{'Yang95_aa'},' ', $site->[9]->{'Yang95_aa_prob'},"\n";

DESCRIPTION

This is a container object for PAML Results.

METHODS

new

Title   : new
Usage   : my $obj = Bio::Tools::Phylo::PAML::Result->new(%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)
          -ntfreq    => array ref of NT frequencies (only for BASEML)
          -seqfile    => seqfile used
          -kappa_mat => Bio::Matrix::PhylipDist of kappa values (only for BASEML)
          -alpha_mat => Bio::Matrix::PhylipDist of alpha values (only for BASEML)
          -NSSitesresult => arrayref of PAML::ModelResult
          -input_params  => input params from .ctl file
          -rst       => array reference of Bio::PrimarySeqI objects
                        of ancestral state reconstruction
          -rst_persite=> arrayref of persite data, this is a complicated set of AoH
          -rst_trees  => rst trees with changes coded on the tree

See Also: Bio::Tree::TreeI, Bio::PrimarySeqI, Bio::Matrix::PhylipDist, Bio::Tools::Phylo::PAML

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

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

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

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>

set_MLmatrix

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)

get_MLmatrix

Title   : get_MLmatrix
Usage   : my $mat = $result->get_MLmatrix()
Function: Get the ML matrix
Returns : 2D Array reference
Args    : none

set_NGmatrix

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)

get_NGmatrix

Title   : get_NGmatrix
Usage   : my $mat = $result->get_NGmatrix()
Function: Get the Nei & Gojobori matrix
Returns : 2D Array reference
Args    : none

add_seq

Title   : add_seq
Usage   : $obj->add_seq($seq)
Function: Add a Bio::PrimarySeq to the Result
Returns : none
Args    : Bio::PrimarySeqI
See also : L<Bio::PrimarySeqI>

reset_seqs

Title   : reset_seqs
Usage   : $result->reset_seqs
Function: Reset the OTU seqs stored
Returns : none
Args    : none

get_seqs

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 : L<Bio::PrimarySeq>

set_codon_pos_basefreq

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

get_codon_pos_basefreq

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

version

Title   : version
Usage   : $obj->version($newval)
Function: Get/Set version
Returns : value of version
Args    : newvalue (optional)

seqfile

Title   : seqfile
Usage   : $obj->seqfile($newval)
Function: Get/Set seqfile
Returns : value of seqfile
Args    : newvalue (optional)

model

Title   : model
Usage   : $obj->model($newval)
Function: Get/Set model
Returns : value of model
Args    : on set, new value (a scalar or undef, optional)

patterns

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
        : }

set_AAFreqs

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

get_AAFreqs

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

set_NTFreqs

Title   : set_NTFreqs
Usage   : $result->set_NTFreqs(\%aafreqs);
Function: Get/Set NT 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

get_NTFreqs

Title   : get_NTFreqs
Usage   : my %all_nt_freqs = $result->get_NTFreqs()
           OR
          my %seq_nt_freqs = $result->get_NTFreqs($seqname)
Function: Get the NT freqs, either for every sequence or just
          for a specific sequence
          The average nt freqs for the entire set are also available
          for the sequence named 'Average'
Returns : Hashref
Args    : (optional) sequence name to retrieve nt freqs for

add_stat

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

get_stat

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

get_stat_names

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

get_AADistMatrix

Title   : get_AADistMatrix
Usage   : my $mat = $obj->get_AADistMatrix()
Function: Get AADistance Matrix
Returns : value of AADistMatrix (Bio::Matrix::PhylipDist)
Args    : none

set_AADistMatrix

Title   : set_AADistMatrix
Usage   : $obj->set_AADistMatrix($mat);
Function: Set the AADistrance Matrix (Bio::Matrix::PhylipDist)
Returns : none
Args    : AADistrance Matrix (Bio::Matrix::PhylipDist)

get_AAMLDistMatrix

Title   : get_AAMLDistMatrix
Usage   : my $mat = $obj->get_AAMLDistMatrix()
Function: Get AAMLDistance Matrix
Returns : value of AAMLDistMatrix (Bio::Matrix::PhylipDist)
Args    : none

set_AAMLDistMatrix

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)

add_NSSite_result

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

get_NSSite_results

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

set_CodonFreqs

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)

get_CodonFreqs

Title   : get_CodonFreqs
Usage   : my @codon_freqs = $result->get_CodonFreqs()
Function: Get the Codon freqs
Returns : Array
Args    : none

get_KappaMatrix

Title   : get_KappaMatrix
Usage   : my $mat = $obj->get_KappaMatrix()
Function: Get KappaDistance Matrix
Returns : value of KappaMatrix (Bio::Matrix::PhylipDist)
Args    : none

set_KappaMatrix

Title   : set_KappaMatrix
Usage   : $obj->set_KappaMatrix($mat);
Function: Set the KappaDistrance Matrix (Bio::Matrix::PhylipDist)
Returns : none
Args    : KappaDistrance Matrix (Bio::Matrix::PhylipDist)

get_AlphaMatrix

Title   : get_AlphaMatrix
Usage   : my $mat = $obj->get_AlphaMatrix()
Function: Get AlphaDistance Matrix
Returns : value of AlphaMatrix (Bio::Matrix::PhylipDist)
Args    : none

set_AlphaMatrix

Title   : set_AlphaMatrix
Usage   : $obj->set_AlphaMatrix($mat);
Function: Set the AlphaDistrance Matrix (Bio::Matrix::PhylipDist)
Returns : none
Args    : AlphaDistrance Matrix (Bio::Matrix::PhylipDist)

set_input_parameter

Title   : set_input_parameter
Usage   : $obj->set_input_parameter($p,$vl);
Function: Set an Input Parameter
Returns : none
Args    : $parameter and $value

get_input_parameters

Title   : get_input_parameters
Usage   : $obj->get_input_parameters;
Function: Get Input Parameters
Returns : Hash of key/value pairs
Args    : none

reset_input_parameters

Title   : reset_input_parameters
Usage   : $obj->reset_input_parameters;
Function: Reset the Input Parameters hash
Returns : none
Args    : none

add_rst_seq

Title   : add_rst_seq
Usage   : $obj->add_rst_seq($seq)
Function: Add a Bio::PrimarySeq to the RST Result
Returns : none
Args    : Bio::PrimarySeqI
See also : L<Bio::PrimarySeqI>

reset_rst_seqs

Title   : reset_rst_seqs
Usage   : $result->reset_rst_seqs
Function: Reset the RST seqs stored
Returns : none
Args    : none

get_rst_seqs

Title   : get_rst_seqs
Usage   : my @otus = $result->get_rst_seqs
Function: Get the seqs Bio::PrimarySeq
Returns : Array of Bio::PrimarySeqI objects
Args    : None
See also : L<Bio::PrimarySeq>

add_rst_tree

Title   : add_rst_tree
Usage   : $obj->add_rst_tree($tree)
Function: Add a Bio::Tree::TreeI to the RST Result
Returns : none
Args    : Bio::Tree::TreeI
See also : L<Bio::Tree::TreeI>

reset_rst_trees

Title   : reset_rst_trees
Usage   : $result->reset_rst_trees
Function: Reset the RST trees stored
Returns : none
Args    : none

get_rst_trees

Title   : get_rst_trees
Usage   : my @otus = $result->get_rst_trees
Function: Get the trees Bio::Tree::TreeI
Returns : Array of Bio::Tree::TreeI objects
Args    : None
See also : L<Bio::Tree::TreeI>

set_rst_persite

Title   : set_rst_persite
Usage   : $obj->set_rst_persite($newval)
Function: Get/Set the per-site RST values
Returns : value of set_rst_persite (a scalar)
Args    : on set, new value (a scalar or undef, optional)

get_rst_persite

Title   : get_rst_persite
Usage   : my @rst_persite = @{$result->get_rst_persite()}
Function: Get the per-site RST values
Returns : Array
Args    : none

Reconstructed Ancestral State relevant options

FEEDBACK

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/Support.html    - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list: 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.

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://github.com/bioperl/bio-tools-phylo-paml/issues

AUTHORS

Jason Stajich <jason@bioperl.org>

Aaron Mackey <amackey@virginia.edu>

Albert Vilella <avilella@gmail.com>

COPYRIGHT

This software is copyright (c) by Jason Stajich <jason@bioperl.org>, and by Aaron Mackey <amackey@virginia.edu>.

This software is available under the same terms as the perl 5 programming language system itself.