Bio::Tools::Run::Phylo::PAML::Yn00(3)

NAME
Bio::Tools::Run::Phylo::PAML::Yn00 - Wrapper aroud the PAML program yn00

SYNOPSIS
  use Bio::Tools::Run::Phylo::PAML::Yn00;
  use Bio::AlignIO;
  my $alignio = new Bio::AlignIO(-format => 'phylip',
                                 -file   => 't/data/gf-s85.phylip');
  my $aln = $alignio->next_aln;

  my $yn = new Bio::Tools::Run::Phylo::PAML::Yn00();
  $yn->alignment($aln);
  my ($rc,$parser) = $yn->run();
  while( my $result = $parser->next_result ) {
    my @otus = $result->get_seqs();
    my $MLmatrix = $result->get_MLmatrix();
    # 0 and 1 correspond to the 1st and 2nd entry in the @otus array
    my $dN = $MLmatrix->[0]->[1]->{dN};
    my $dS = $MLmatrix->[0]->[1]->{dS};
    my $kaks =$MLmatrix->[0]->[1]->{omega};
    print "Ka = $dN Ks = $dS Ka/Ks = $kaks\n";
  }

DESCRIPTION
This is a wrapper around the yn00 (method of Yang and Nielsen, 2000) 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 will generate a proper yn00.ctl file and will run the program in a separate temporary directory to avoid creating temp files all over the place and will cleanup after itself.

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
Email jason@bioperl.org

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
See the Bio::Tools::Run::Phylo::PAML::Codeml module for documentation of the default values.

  program_name
 Title   : program_name
 Usage   : >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::Yn00();
 Function: Builds a new Bio::Tools::Run::Phylo::PAML::Yn00 object
 Returns : Bio::Tools::Run::Phylo::PAML::Yn00
 Args    : -alignment => the L<Bio::Align::AlignI> object
           -save_tempfiles => boolean to save the generated tempfiles and
                              NOT cleanup after onesself (default FALSE)

  run
 Title   : run
 Usage   : $yn->run();
 Function: run the yn00 analysis using the default or updated parameters
           the alignment parameter must have been set
 Returns : 3 values,
           $rc = 1 for success, 0 for errors
           hash reference of the Yang calculated Ka/Ks values
                    this is a set of pairwise observations keyed as
                    sequencenameA->sequencenameB->datatype
           hash reference same as the previous one except it for the
           Nei and Gojobori calculated Ka,Ks,omega values
 Args    : none

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

  alignment
 Title   : alignment
 Usage   : $codeml->align($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>

  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   : $codeml->set_parameter($param,$val);
 Function: Sets a codeml parameter, will be validated against
           the valid values as set in the %VALIDVALUES class variable.
           The checks can be ignored if on turns of param checks like this:
             $codeml->no_param_checks(1)
 Returns : boolean if set was success, if verbose is set to -1
           then no warning will be reported
 Args    : $paramname => 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   : $codeml->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::Wrapper 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)

  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 = $codeml->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   : $codeml->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