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Bio::Tools::Run::PhyloUserpContributed PBio::Tools::Run::Phylo::Hyphy::Base(3)

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

perl v5.24.1			  2017-0Bio::Tools::Run::Phylo::Hyphy::Base(3)

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHOR - Albert Vilella | CONTRIBUTORS | APPENDIX

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