/ 
bioperl-run-1.5.2_005-RC
/ Bio::Tools::Run::Phylo::PAML::Evolver

NAME

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

SYNOPSIS

use Bio::Tools::Run::Phylo::PAML::Evolver;

my $evolver = new Bio::Tools::Run::Phylo::PAML::Evolver();

# 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 $parser = new Bio::Tools::Phylo::PAML
  (
   -file => "$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

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, obtiained from ENV variable.
Returns:  string
Args    :

new

Title   : new
Usage   : my $obj = new Bio::Tools::Run::Phylo::PAML::Evolver();
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)