/ 
BioPerl-Run-1.6.1_001
River stage one • 2 direct dependents • 2 total dependents
/ Bio::Tools::Run::Phylo::Hyphy::REL

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://bugzilla.open-bio.org/

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