Bio::Tools::Phylo::PAML::Result(3)

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

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.

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/wiki/Mailing_lists  - 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 email or the web:

  https://github.com/bioperl/bioperl-live/issues

AUTHOR - Jason Stajich, Aaron Mackey
 Email jason-at-bioperl-dot-org
 Email amackey-at-virginia-dot-edu

CONTRIBUTORS
Albert Vilella avilella-AT-gmail-DOT-com

APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

  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

  BASEML Relavent values

  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

Reconstructed Ancestral State relevant options

  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