NAME
Bio::Tools::Run::Phylo::PAML::Yn00 - Wrapper aroud the PAML program yn00
VERSION
version 1.7.3
SYNOPSIS
use Bio::Tools::Run::Phylo::PAML::Yn00;
use Bio::AlignIO;
my $alignio = Bio::AlignIO->new(-format => 'phylip',
-file => 't/data/gf-s85.phylip');
my $aln = $alignio->next_aln;
my $yn = Bio::Tools::Run::Phylo::PAML::Yn00->new();
$yn->alignment($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.
Default Values
See the Bio::Tools::Run::Phylo::PAML::Codeml module for documentation of the default values.
ATTRIBUTES
program_name
Title : program_name
Usage : $yn00->program_name()
Function: holds the program name
Returns: string
Args : Noneprogram_dir
Title : program_dir
Usage : $yn00->program_dir()
Function: returns the program directory, obtained from ENV variable.
Returns: string
Args :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>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 totempdir
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 : noneMETHODS
new
Title : new
Usage : my $obj = Bio::Tools::Run::Phylo::PAML::Yn00->new();
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 : noneget_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 : noneset_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 valuescleanup
Title : cleanup
Usage : $codeml->cleanup();
Function: Will cleanup the tempdir directory after a PAML run
Returns : none
Args : noneio
Title : io
Usage : $obj->io($newval)
Function: Gets a L<Bio::Root::IO> object
Returns : L<Bio::Root::IO>
Args : noneBio::Tools::Run::Wrapper methods
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/Support.html - About the mailing listsSupport
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:
https://github.com/bioperl/bio-tools-phylo-paml/issuesAUTHOR
Jason Stajich <jason@bioperl.org>
COPYRIGHT
This software is copyright (c) by Jason Stajich <jason@bioperl.org>.
This software is available under the same terms as the perl 5 programming language system itself.