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Bio::Tools::Phylo::Molphy::Result.3pm

NAME

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

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:

   http://bugzilla.open-bio.org/
 
 

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 model's 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)