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

NAME

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

SYNOPSIS

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

DESCRIPTION

This is a wrapper around the SLAC 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.

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 SLAC 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::SLAC->new();
Function: Builds a new Bio::Tools::Run::Phylo::Hyphy::SLAC object 
Returns : Bio::Tools::Run::Phylo::Hyphy::SLAC
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) = $slac->run($aln);
 Function: run the slac 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   : $hyphy->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::Phylo::Hyphy::Base methods

program_name

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

program_dir

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

prepare

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

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   : $slac->align($aln);
Function: Get/Set the L<Bio::Align::AlignI> object
Returns : L<Bio::Align::AlignI> object
Args    : [optional] L<Bio::Align::AlignI>
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   : $slac->tree($tree, %params);
Function: Get/Set the L<Bio::Tree::TreeI> object
Returns : L<Bio::Tree::TreeI> 
Args    : [optional] $tree => L<Bio::Tree::TreeI>,
          [optional] %parameters => hash of tree-specific parameters:

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   : $slac->set_parameter($param,$val);
Function: Sets a slac parameter, will be validated against
          the valid values as set in the %VALIDVALUES class variable.  
          The checks can be ignored if one turns off param checks like this:
            $slac->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   : $slac->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

update_ordered_parameters

 Title   : update_ordered_parameters
 Usage   : $slac->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

Bio::Tools::Run::WrapperBase methods

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   : $slac->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