/ 
bioperl-run-1.5.2_005-RC
/ Bio::Tools::Run::Phylo::PAML::Yn00

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/wiki/Mailing_lists  - 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:

AUTHOR - Jason Stajich

Email jason-at-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   : $yn00->program_name()
Function: holds the program name
Returns:  string
Args    : None

program_dir

Title   : program_dir
Usage   : $yn00->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