NAME

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

SYNOPSIS

FIXME

DESCRIPTION

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

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

Support

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:

  http://redmine.open-bio.org/projects/bioperl/

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 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.

program_name

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

valid_values

 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

program_dir

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

new

 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

prepare

 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]

create_wrapper

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

run

 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

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   : $hyphy->alignment($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>

tree

 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>

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   : $hyphy->set_parameter($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:
             $hyphy->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   : $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

update_ordered_parameters

 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

outfile_name

 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

version

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

hyphy_lib_dir

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