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Bio::Tools::Run::Phylo::PAML::Evolver.3pm

NAME

Bio::Tools::Run::Phylo::PAML::Evolver - Wrapper aroud the PAML program evolver

SYNOPSIS

   use Bio::Tools::Run::Phylo::PAML::Evolver;
 
   my $evolver = Bio::Tools::Run::Phylo::PAML::Evolver->new();
 
   # Get a $tree object somehow
   $evolver->tree($tree);
 
   # FIXME: evolver generates a tree (first run with option 1 or 2)?
 
   # One or more alns are created
   my @alns = $evolver->run();
 
   ####
 
   # Or with all the data coming from a previous PAML run
   my $parser = Bio::Tools::Phylo::PAML->new
     (
      -file => "$inputfile",
     );
   my $result = $parser->next_result();
   my $tree = $result->next_tree;
   $evolver->tree($tree);
   my @codon_freqs = $result->get_CodonFreqs();
   $evolver->set_CodonFreqs(\@codon_freqs);
 
   my $val = $evolver->prepare();
 
   # FIXME: something similar for nucleotide frequencies:
   # Option (5) Simulate nucleotide data sets (use MCbase.dat)?
 
   # FIXME: something similar for aa parameters:
   # Option (7) Simulate amino acid data sets (use MCaa.dat)?
 
   # FIXME: With an initial RootSeq.txt
 
 

DESCRIPTION

This is a wrapper around the evolver program of PAML (Phylogenetic Analysis by Maximum Likelihood) package of Ziheng Yang. See http://abacus.gene.ucl.ac.uk/software/paml.html for more information.

This module is more about generating the properl MCmodel.ctl file and will run the program in a separate temporary directory to avoid creating temp files all over the place.

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
 
 

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://bioperl.org/bioperl-bugs/
 
 

AUTHOR - Albert Vilella

Email avilella-AT-gmail-DOT-com

CONTRIBUTORS

Additional contributors names and emails here

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

Default Values

Valid and default values for evolver programs are listed below. The default values are always the first one listed. These descriptions are essentially lifted from the example MCcodon.dat file and pamlDOC documentation provided by the author.

Stub:

option1 specifies something.

option2 specifies something else.

INCOMPLETE DOCUMENTATION OF ALL METHODS

program_name

  Title   : program_name
  Usage   : $factory->program_name()
  Function: holds the program name
  Returns:  string
  Args    : None
 
 

program_dir

  Title   : program_dir
  Usage   : ->program_dir()
  Function: returns the program directory, obtained from ENV variable.
  Returns:  string
  Args    :
 
 

new

  Title   : new
  Usage   : my $obj = Bio::Tools::Run::Phylo::PAML::Evolver->new();
  Function: Builds a new Bio::Tools::Run::Phylo::PAML::Evolver object 
  Returns : Bio::Tools::Run::Phylo::PAML::Evolver
            -save_tempfiles => boolean to save the generated tempfiles and
                               NOT cleanup after onesself (default FALSE)
            -tree => the Bio::Tree::TreeI object (FIXME: optional if this is done in a first run)
            -params => a hashref of PAML parameters (all passed to set_parameter)
            -executable => where the evolver executable resides
 
 

See also: Bio::Tree::TreeI

prepare

  Title   : prepare
  Usage   : my $rundir = $evolver->prepare($aln);
  Function: prepare the evolver analysis using the default or updated parameters
            the alignment parameter must have been set
  Returns : value of rundir
  Args    : L<Bio::Align::AlignI> object,
            L<Bio::Tree::TreeI> object [optional]
 
 

run

  Title   : run
  Usage   : my ($rc,$parser) = $evolver->run();
  Function: run the evolver analysis using the default or updated parameters
            the alignment parameter must have been set
  Returns : Return code, L<Bio::Tools::Phylo::PAML>
  Args    : L<Bio::Align::AlignI> object,
            L<Bio::Tree::TreeI> object [optional]
 
 

error_string

  Title   : error_string
  Usage   : $obj->error_string($newval)
  Function: Where the output from the last analysis run is stored.
  Returns : value of error_string
  Args    : newvalue (optional)
 
 

alignment

  Title   : alignment
  Usage   : $evolver->align($aln);
  Function: Get/Set the L<Bio::Align::AlignI> object
  Returns : L<Bio::Align::AlignI> object
  Args    : [optional] L<Bio::Align::AlignI>
  Comment : We could potentially add support for running directly on a file
            but we shall keep it simple
  See also: L<Bio::SimpleAlign>
 
 

tree

  Title   : tree
  Usage   : $evolver->tree($tree, %params);
  Function: Get/Set the L<Bio::Tree::TreeI> object
  Returns : L<Bio::Tree::TreeI> 
  Args    : [optional] $tree => L<Bio::Tree::TreeI>,
            [optional] %parameters => hash of tree-specific parameters:
                   branchLengths: 0, 1 or 2
                   out
 
  Comment : We could potentially add support for running directly on a file
            but we shall keep it simple
  See also: L<Bio::Tree::Tree>
 
 

get_parameters

  Title   : get_parameters
  Usage   : my %params = $self->get_parameters();
  Function: returns the list of parameters as a hash
  Returns : associative array keyed on parameter names
  Args    : none
 
 

set_parameter

  Title   : set_parameter
  Usage   : $evolver->set_parameter($param,$val);
  Function: Sets a evolver parameter, will be validated against
            the valid values as set in the %VALIDVALUES class variable.  
            The checks can be ignored if one turns off param checks like this:
              $evolver->no_param_checks(1)
  Returns : boolean if set was success, if verbose is set to -1
            then no warning will be reported
  Args    : $param => name of the parameter
            $value => value to set the parameter to
  See also: L<no_param_checks()>
 
 

set_default_parameters

  Title   : set_default_parameters
  Usage   : $evolver->set_default_parameters(0);
  Function: (Re)set the default parameters from the defaults
            (the first value in each array in the 
             %VALIDVALUES class variable)
  Returns : none
  Args    : boolean: keep existing parameter values
 
 

Bio::Tools::Run::WrapperBase methods

no_param_checks

  Title   : no_param_checks
  Usage   : $obj->no_param_checks($newval)
  Function: Boolean flag as to whether or not we should
            trust the sanity checks for parameter values  
  Returns : value of no_param_checks
  Args    : newvalue (optional)
 
 

set_CodonFreqs

  Title   : set_CodonFreqs
  Usage   : $obj->set_CodonFreqs($newval)
  Function: Get/Set the Codon Frequence table
  Returns : value of set_CodonFreqs (a scalar)
  Args    : on set, new value (a scalar or undef, optional)
 
 

get_CodonFreqs

  Title   : get_CodonFreqs
  Usage   : my @codon_freqs = $evolver->get_CodonFreqs() 
  Function: Get the Codon freqs
  Returns : Array
  Args    : none
 
 

save_tempfiles

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

outfile_name

  Title   : outfile_name
  Usage   : my $outfile = $evolver->outfile_name();
  Function: Get/Set the name of the output file for this run
            (if you wanted to do something special)
  Returns : string
  Args    : [optional] string to set value to
 
 

tempdir

  Title   : tempdir
  Usage   : my $tmpdir = $self->tempdir();
  Function: Retrieve a temporary directory name (which is created)
  Returns : string which is the name of the temporary directory
  Args    : none
 
 

cleanup

  Title   : cleanup
  Usage   : $evolver->cleanup();
  Function: Will cleanup the tempdir directory after a PAML run
  Returns : none
  Args    : none
 
 

io

  Title   : io
  Usage   : $obj->io($newval)
  Function:  Gets a L<Bio::Root::IO> object
  Returns : L<Bio::Root::IO>
  Args    : none
 
 

indel

  Title   : indel
  Usage   : $obj->indel($newval)
  Function: this is only useful if using evolver_indel instead of main
            evolver package:
            Exploring the Relationship between Sequence Similarity and
            Accurate Phylogenetic Trees Brandi L. Cantarel, Hilary
            G. Morrison and William Pearson
  Example : 
  Returns : value of indel (a scalar)
  Args    : on set, new value (a scalar or undef, optional)