Provided by: libbio-perl-run-perl_1.7.1-3_all bug


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


       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' => "",
       'order' => ["Universal", "Custom", $aln, "001001", $tree]}); $bf_exec->set_parameter('3',
       "012012"); my ($rc,$parser) = $bf_exec->run();


       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 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."


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AUTHOR - Daisie Huang



       Additional contributors names and emails here

        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

        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' =>
                                                           'order' => [array of ordered parameters]
                  -executable => where the hyphy executable resides

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

        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

        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

        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

       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

       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

       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

        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
        Returns : none
        Args    : boolean: keep existing parameter values

perl v5.24.1                                2017-01-Bio::Tools::Run::Phylo::Hyphy::BatchFile(3pm)