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Bio::Tools::Run::Phylo::Hyphy::Base.3pm

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://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 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

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    :
 
 

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    :
 
 

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   : $hyphy->align($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   : $hyphy->tree($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   : $hyphy->set_parameter($param,$val);
  Function: Sets a hyphy 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:
              $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()>
 
 

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
 
 

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)
 
 

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
 
 

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)
 
 

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   : $hyphy->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