Bio::Tools::Run::Phylo::Hyphy::Base - Hyphy wrapping base methods




HyPhy ([Hy]pothesis Testing Using [Phy]logenies) package of Sergei Kosakowsky Pond, Spencer V. Muse, Simon D.W. Frost and Art Poon. See for more information.


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AUTHOR - Albert Vilella

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

Default Values

Valid and default values are listed below. The default values are always the first one listed. These descriptions are essentially lifted from the python wrapper or provided by the author.


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


 Title   : valid_values
 Usage   : $factory->valid_values()
 Function: returns the possible parameters
 Returns:  an array holding all possible parameters (this needs to be specified per child class).
           Returns an empty array in the base class.
 Args    : None


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


 Title   : new
 Usage   : my $obj = Bio::Tools::Run::Phylo::Hyphy->new();
 Function: Builds a new Bio::Tools::Run::Phylo::Hyphy object
 Returns : Bio::Tools::Run::Phylo::Hyphy
 Args    : -alignment => the Bio::Align::AlignI object
           -save_tempfiles => boolean to save the generated tempfiles and
                              NOT cleanup after onesself (default FALSE)
           -tree => the Bio::Tree::TreeI object
           -params => a hashref of parameters (all passed to set_parameter)
           -executable => where the hyphy executable resides

See also: Bio::Tree::TreeI, Bio::Align::AlignI


 Title   : prepare
 Usage   : my $rundir = $hyphy->prepare($aln);
 Function: prepare the 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]


 Title   : create_wrapper
 Usage   : $self->create_wrapper
 Function: It will create the wrapper file that interfaces with the analysis bf file
 Example :
 Returns :
 Args    :


 Title   : run
 Usage   : my ($rc,$results) = $BatchFile->run();
 Function: run the Hyphy analysis using the specified batchfile and its ordered parameters
 Returns : Return code, Hash
 Args    : none


 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)


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


 Title   : tree
 Usage   : $hyphy->tree($tree);
 Function: Get/Set the L<Bio::Tree::TreeI> object
 Returns : L<Bio::Tree::TreeI>
 Args    : [optional] $tree => L<Bio::Tree::TreeI>,

 Comment : We could potentially add support for running directly on a file
           but we shall keep it simple
 See also: L<Bio::Tree::Tree>


 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


 Title   : set_parameter
 Usage   : $hyphy->set_parameter($param,$val);
 Function: Sets a hyphy parameter, will be validated against
           the valid values.
           The checks can be ignored if one turns off param checks like this:
 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()>


 Title   : set_default_parameters
 Usage   : $obj->set_default_parameters();
 Function: (Re)set the default parameters from the defaults
           (the first value in each array in the valid_values() array)
 Returns : none
 Args    : none


 Title   : update_ordered_parameters
 Usage   : $hyphy->update_ordered_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


 Title   : outfile_name
 Usage   : my $outfile = $hyphy->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


 Title   : version
 Usage   : $obj->version()
 Function:  Returns the version string from HYPHY
 Returns : string
 Args    : none


 Title   : hyphy_lib_dir
 Usage   : $obj->hyphy_lib_dir()
 Function: Returns the HYPHY_LIB_DIRECTORY from HYPHY
 Returns : string
 Args    : none