Bio::Tools::Run::Phylo::Hyphy::REL(3pm) 		User Contributed Perl Documentation		   Bio::Tools::Run::Phylo::Hyphy::REL(3pm)

NAME

       Bio::Tools::Run::Phylo::Hyphy::REL - Wrapper around the Hyphy REL analysis

SYNOPSIS

	 use Bio::Tools::Run::Phylo::Hyphy::REL;
	 use Bio::AlignIO;
	 use Bio::TreeIO;

	 my $alignio = Bio::AlignIO->new(-format => 'fasta',
					-file	=> 't/data/hyphy1.fasta');

	 my $aln = $alignio->next_aln;

	 my $treeio = Bio::TreeIO->new(
	     -format => 'newick', -file => 't/data/hyphy1.tree');

	 my $rel = Bio::Tools::Run::Phylo::Hyphy::REL->new();
	 $rel->alignment($aln);
	 $rel->tree($tree);
	 my ($rc,$results) = $rel->run();

DESCRIPTION

       This is a wrapper around the REL analysis of 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.

       This module will generate the correct list of options for interfacing with TemplateBatchFiles/Ghostrides/Wrapper.bf.

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 for REL 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.

       INCOMPLETE DOCUMENTATION OF ALL METHODS

   new
	Title	: new
	Usage	: my $obj = Bio::Tools::Run::Phylo::Hyphy::REL->new();
	Function: Builds a new Bio::Tools::Run::Phylo::Hyphy::REL object
	Returns : Bio::Tools::Run::Phylo::Hyphy::REL
	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

   run
	Title	: run
	Usage	: my ($rc,$results) = $rel->run($aln);
	Function: run the rel analysis using the default or updated parameters
		  the alignment parameter must have been set
	Returns : Return code, Hash
	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	:

   set_default_parameters
	Title	: set_default_parameters
	Usage	: $rel->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::WrapperBase 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)

   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	: $rel->cleanup();
	Function: Will cleanup the tempdir directory after a 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

perl v5.12.3							    2011-06-18				   Bio::Tools::Run::Phylo::Hyphy::REL(3pm)