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Manual Reference Pages  -  BIO::TOOLS::PHYLO::MOLPHY::RESULT (3)

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NAME

Bio::Tools::Phylo::Molphy::Result - container for data parsed from a ProtML run

CONTENTS

SYNOPSIS



  # do not use this object directly, you will get it back as part of a
  # Molphy parser
  use Bio::Tools::Phylo::Molphy;
  my $parser = Bio::Tools::Phylo::Molphy->new(-file => output.protml);
  while( my $r = $parser->next_result ) {
    # r is a Bio::Tools::Phylo::Molphy::Result object

    # print the model name
    print $r->model, "\n";

    # get the substitution matrix
    # this is a hash of 3letter aa codes -> 3letter aa codes representing
    # substitution rate
    my $smat = $r->substitution_matrix;
    print "Arg -> Gln substitution rate is %d\n",
          $smat->{Arg}->{Gln}, "\n";

    # get the transition probablity matrix
    # this is a hash of 3letter aa codes -> 3letter aa codes representing
    # transition probabilty
    my $tmat = $r->transition_probability_matrix;
    print "Arg -> Gln transition probablity is %.2f\n",
          $tmat->{Arg}->{Gln}, "\n";

    # get the frequency for each of the residues
    my $rfreqs = $r->residue_frequencies;

    foreach my $residue ( keys %{$rfreqs} ) {
       printf "residue %s  expected freq: %.2f observed freq: %.2f\n",
              $residue,$rfreqs->{$residue}->[0], $rfreqs->{$residue}->[1];
    }

    my @trees;
    while( my $t = $r->next_tree ) {
        push @trees, $t;
    }

    print "search space is ", $r->search_space, "\n",
          "1st tree score is ", $trees[0]->score, "\n";

    # writing to STDOUT, use -file => >filename to specify a file
    my $out = Bio::TreeIO->new(-format => "newick");
    $out->write_tree($trees[0]); # writing only the 1st tree
  }



DESCRIPTION

A container for data parsed from a ProtML run.

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 the web:



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



AUTHOR - Jason Stajich

Email jason-at-bioperl.org

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::Molphy::Result->new();
 Function: Builds a new Bio::Tools::Phylo::Molphy::Result object
 Returns : Bio::Tools::Phylo::Molphy::Result
 Args    :



    model



 Title   : model
 Usage   : $obj->model($newval)
 Function:
 Returns : value of model
 Args    : newvalue (optional)



    substitution_matrix



 Title   : substitution_matrix
 Usage   : my $smat = $result->subsitution_matrix;
 Function: Get the relative substitution matrix calculated in the ML procedure
 Returns : reference to hash of hashes where key is the aa/nt name and value
           is another hash ref which contains keys for all the aa/nt
           possibilities
 Args    : none



    transition_probability_matrix



 Title   : transition_probability_matrix
 Usage   : my $matrixref = $molphy->transition_probablity_matrix();
 Function: Gets the observed transition probability matrix
 Returns : hash of hashes of aa/nt transition to each other aa/nt
 Args    : Transition matrix type, typically
           1PAM-1.0e05 or 1PAM-1.0e07



    residue_frequencies



 Title   : residue_frequencies
 Usage   : my %data = $molphy->residue_frequencies()
 Function: Get the modeled and expected frequencies for
           each of the residues in the sequence
 Returns : hash of either aa (protml) or nt (nucml) frequencies
           each key will point to an array reference where
           1st slot is models expected frequency
           2nd slot is observed frequency in the data
           $hash{A}->[0] =
 Args    : none



    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



    rewind_tree



 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



    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>



    search_space



 Title   : search_space
 Usage   : $obj->search_space($newval)
 Function:
 Returns : value of search_space
 Args    : newvalue (optional)



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perl v5.20.3 BIO::TOOLS::PHYLO::MOLPHY::RESULT (3) 2016-04-05

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