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://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 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