NAME

       Bio::Tools::Run::Phylo::Hyphy::BatchFile - Wrapper for custom execution of Hyphy batch
       files

SYNOPSIS

       my $aln = Bio::Align::AlignI->new(); my $treeio = Bio::TreeIO->new(-format => "nexus",
       -file => "$tree_file"); my $tree = $treeio->next_tree(); my $bf_exec =
       Bio::Tools::Run::Phylo::Hyphy::BatchFile->new(-params => {'bf' => "hyphybatchfile.bf",
       'order' => ["Universal", "Custom", $aln, "001001", $tree]}); $bf_exec->set_parameter('3',
       "012012"); my ($rc,$parser) = $bf_exec->run();

DESCRIPTION

       This module creates a generic interface to processing of HBL files in HyPhy ([Hy]pothesis
       Testing Using [Phy]logenies), a package by Sergei Kosakowsky Pond, Spencer V. Muse, Simon
       D.W. Frost and Art Poon.  See http://www.hyphy.org for more information.

       Instances of this module require only a link to the batch file and an ordered list of
       parameters, as described in the HyPhy documentation "SelectionAnalyses.pdf."

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 - Daisie Huang

       Email daisieh@zoology.ubc.ca

CONTRIBUTORS

       Additional contributors names and emails here

   valid_values
        Title   : valid_values
        Usage   : $factory->valid_values()
        Function: returns the possible parameters
        Returns:  an array holding all possible parameters. The default
       values are always the first one listed.  These descriptions are
       essentially lifted from the python wrapper or provided by the author.
        Args    : None

   new
        Title   : new
        Usage   : my $obj = Bio::Tools::Run::Phylo::Hyphy::BatchFile->new();
        Function: Builds a new Bio::Tools::Run::Phylo::Hyphy::BatchFile object
        Returns : Bio::Tools::Run::Phylo::Hyphy::BatchFile
        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)
                             this hashref should include   'bf' => custombatchfile.bf
                                                           'order' => [array of ordered parameters]
                  -executable => where the hyphy executable resides

       See also: Bio::Tree::TreeI, Bio::Align::AlignI

   update_ordered_parameters
        Title   : update_ordered_parameters
        Usage   : $BatchFile->update_ordered_parameters();
        Function: updates all of the parameters needed for the ordered input redirect in HBL.
        Returns : nothing
        Args    : none

   run
        Title   : run
        Usage   : my ($rc,$results) = $BatchFile->run();
        Function: run the Hyphy analysis using the specified batchfile and its ordered parameters
        Returns : Return code, Hash
        Args    : none

   create_wrapper
        Title   : create_wrapper
        Usage   : $self->create_wrapper
        Function: Creates the wrapper file for the batchfile specified in the hash, saves it to the hash as '_wrapper'.
        Returns : nothing
        Args    : none

   set_parameter
       Title   :  set_parameter Usage   :  $hyphy->set_parameter($param,$val); Function:  Sets
       the named parameter $param to $val if it is a non-numeric parameter
                  If $param is a number, sets the corresponding value of the ordered redirect
       array (starts from 1).  Returns :  boolean if set was successful Args    :  $param => name
       of the parameter
                  $value => value to set the parameter to

   batchfile
       Title   :  batchfile Usage   :  $hyphy->batchfile($bf_name); Function:  Gets/sets the
       batchfile that is run by $hyphy.  Returns :  The batchfile path.  Args    :  $bf_name =>
       path of new batchfile

   make_batchfile_with_contents
       Title   :  make_batchfile_with_contents Usage   :
       $hyphy->make_batchfile_with_contents($bf_string); Function:  Creates a temporary file with
       the specified string of contents for the batchfile.  Returns :  The batchfile path.  Args
       :  $bf_string => contents for the batchfile

   set_default_parameters
        Title   : set_default_parameters
        Usage   : $BatchFile->set_default_parameters(0);
        Function: (Re)set the default parameters from the defaults
                  (the first value in each array in the
                   valid_values)
        Returns : none
        Args    : boolean: keep existing parameter values

perl v5.36.0                                2023-01-Bio::Tools::Run::Phylo::Hyphy::BatchFile(3pm)