Bio::Tools::Phylo::PAML::Codeml(3pm)			User Contributed Perl Documentation		      Bio::Tools::Phylo::PAML::Codeml(3pm)

NAME

       Bio::Tools::Phylo::PAML::Codeml - Parses output from the PAML program codeml.

SYNOPSIS

	 #!/usr/bin/perl -Tw
	 use strict;

	 use Bio::Tools::Phylo::PAML::Codeml;

	 # need to specify the output file name (or a fh) (defaults to
	 # -file => "codeml.mlc"); also, optionally, the directory in which
	 # the other result files (rst, 2ML.dS, etc) may be found (defaults
	 # to "./")
	 my $parser = new Bio::Tools::Phylo::PAML::Codeml::Parser
	   (-file => "./results/mlc", -dir => "./results/");

	 # get the first/next result; a Bio::[...]::Codeml::Result object
	 my $result = $parser->next_result();

	 # get the sequences used in the analysis; returns Bio::PrimarySeq
	 # objects (OTU = Operational Taxonomic Unit).
	 my @otus = $result->get_seqs();

	 # codon summary: codon usage of each sequence [ arrayref of {
	 # hashref of counts for each codon } for each sequence and the
	 # overall sum ], and positional nucleotide distribution [ arrayref
	 # of { hashref of frequencies for each nucleotide } for each
	 # sequence and overall frequencies ].

	 my ($codonusage, $ntdist) = $result->get_codon_summary();

	 # example manipulations of $codonusage and $ntdist:
	 printf "There were %d '%s' codons in the first seq (%s)
",
	   $codonusage->[0]->{AAA}, 'AAA', $otus[0]->id();
	 printf "There were %d '%s' codons used in all the sequences
",
	   $codonusage->[$#{$codonusage}]->{AAA}, 'AAA';
	 printf "Nucleotide '%c' was present %g of the time in seq %s
",
	   'A', $ntdist->[1]->{A}, $otus[1]->id();

	 # get Nei & Gojobori dN/dS matrix:
	 my $NGmatrix = $result->get_NGmatrix();

	 # get ML-estimated dN/dS matrix, if calculated; this corresponds to
	 # the runmode = -2, pairwise comparison usage of codeml
	 my $MLmatrix = $result->get_MLmatrix();

	 # These matrices are length(@otu) x length(@otu) "strict lower
	 # triangle" 2D-matrices, which means that the diagonal and
	 # everything above it is undefined.  Each of the defined cells is a
	 # hashref of estimates for "dN", "dS", "omega" (dN/dS ratio), "t",
	 # "S" and "N".  If a ML matrix, "lnL" will also be defined.  Any
	 # additional ML parameters estimated by the model will be in an
	 # array ref under "params"; it's up to the user to know which
	 # position corresponds to which parameter (since PAML doesn't label
	 # them, and we can't guess very well yet (a TODO I guess).

	 printf "The omega ratio for sequences %s vs %s was: %g
",
	   $otus[0]->id, $otus[1]->id, $MLmatrix->[0]->[1]->{omega};

	 # with a little work, these matrices could also be passed to
	 # Bio::Tools::Run::Phylip::Neighbor, or other similar tree-building
	 # method that accepts a matrix of "distances" (using the LOWTRI
	 # option):
	 my $distmat = [ map { [ map { $$_{omega} } @$_ ] } @$MLmatrix ];

	 # for runmode's other than -2, get tree topology with estimated
	 # branch lengths; returns a Bio::Tree::TreeI-based tree object with
	 # added PAML parameters at each node
	 my $tree = $result->get_tree();
	 for my $node ($tree->get_nodes()) {
	    # inspect the tree: the "t" (time) parameter is available via
	    # $node->branch_length(); all other branch-specific parameters
	    # ("omega", "dN", etc.) are available via $node->param('omega');
	 }

	 # get any general model parameters: kappa (the
	 # transition/transversion ratio), NSsites model parameters ("p0",
	 # "p1", "w0", "w1", etc.), etc.
	 my $params = $result->get_model_params();
	 printf "M1 params: p0 = %g	p1 = %g
", $params->{p0}, $params->{p1};

	 # for NSsites models, obtain posterior probabilities for membership
	 # in each class for every position; probabilities correspond to
	 # classes w0, w1, ... etc.
	 my @probs = $result->get_posteriors();

	 # find, say, positively selected sites!
	 if ($params->{w2} > 1) {
	   for (my $i = 0; $i < @probs ; $i++) {
	     if ($probs[$i]->[2] > 0.5) {
		# assumes model M1: three w's, w0, w1 and w2 (positive selection)
		printf "position %d: (%g prob, %g omega, %g mean w)
",
		  $i, $probs[$i]->[2], $params->{w2}, $probs[$i]->[3];
	     }
	   }
	 } else { print "No positive selection found!
"; }

DESCRIPTION

       This module is used to parse the output from the PAML program codeml.  You can use the Bio::Tools::Run::Phylo::Phylo::PAML::Codeml module
       to actually run codeml; this module is only useful to parse the output.

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/MailList.shtml  - About the mailing lists

   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:

	 bioperl-bugs@bioperl.org
	 http://bioperl.org/bioperl-bugs/

AUTHOR - Jason Stajich, Aaron Mackey
       Email jason@bioperl.org Email amackey@virginia.edu

TODO

       This module should also be able to handle "codemlsites" batch output...

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 = new Bio::Tools::Phylo::PAML::Codeml();
	Function: Builds a new Bio::Tools::Phylo::PAML::Codeml object
	Returns : Bio::Tools::Phylo::PAML::Codeml
	Args	:

   get_trees
	Title	: get_trees
	Usage	: my @trees = $codemlparser->get_trees();
	Function: Returns a list of trees (if any) are in the output file
	Returns : List of L<Bio::Tree::TreeI> objects
	Args	: none

   get_statistics
	Title	: get_statistics
	Usage	: my $data = $codemlparser->get_statistics
	Function: Retrieves the set of pairwise comparisons
	Returns : Hash Reference keyed as 'seqname' -> 'seqname' -> 'datatype'
	Args	: none

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