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)\n",
  $codonusage->[0]->{AAA}, 'AAA', $otus[0]->id();
printf "There were %d '%s' codons used in all the sequences\n",
  $codonusage->[$#{$codonusage}]->{AAA}, 'AAA';
printf "Nucleotide '%c' was present %g of the time in seq %s\n",
  '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\n",
  $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\tp1 = %g\n", $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)\n",
         $i, $probs[$i]->[2], $params->{w2}, $probs[$i]->[3];
    }
  }
} else { print "No positive selection found!\n"; }

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