bio::tools::phylo::molphy::result(3pm) [debian man page]

Bio::Tools::Phylo::Molphy::Result(3pm)			User Contributed Perl Documentation		    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, "
";

	   # 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
",
		 $smat->{'Arg'}->{'Gln'}, "
";

	   # 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
",
		 $tmat->{'Arg'}->{'Gln'}, "
";

	   # 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
",
		     $residue,$rfreqs->{$residue}->[0], $rfreqs->{$residue}->[1];
	   }

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

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

	   # 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://redmine.open-bio.org/projects/bioperl/

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)

perl v5.14.2							    2012-03-02				    Bio::Tools::Phylo::Molphy::Result(3pm)