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.IX Title "Bio::Tools::Run::Phylo::Hyphy::BatchFile 3pm"
.TH Bio::Tools::Run::Phylo::Hyphy::BatchFile 3pm 2024-03-12 "perl v5.38.2" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
.if n .ad l
.nh
.SH NAME
Bio::Tools::Run::Phylo::Hyphy::BatchFile \- Wrapper for custom execution of Hyphy batch files
.SH SYNOPSIS
.IX Header "SYNOPSIS"
my \f(CW$aln\fR = Bio::Align::AlignI\->\fBnew()\fR;
my \f(CW$treeio\fR = Bio::TreeIO\->new(\-format => "nexus", \-file => "$tree_file");
my \f(CW$tree\fR = \f(CW$treeio\fR\->\fBnext_tree()\fR;
my \f(CW$bf_exec\fR = Bio::Tools::Run::Phylo::Hyphy::BatchFile\->new(\-params => {'bf' => "hyphybatchfile.bf", 'order' => ["Universal", "Custom", \f(CW$aln\fR, "001001", \f(CW$tree\fR]});
\&\f(CW$bf_exec\fR\->set_parameter('3', "012012");
my ($rc,$parser) = \f(CW$bf_exec\fR\->\fBrun()\fR;
.SH DESCRIPTION
.IX Header "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.
.PP
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."
.SH FEEDBACK
.IX Header "FEEDBACK"
.SS "Mailing Lists"
.IX Subsection "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.
.PP
.Vb 2
\&  bioperl\-l@bioperl.org                  \- General discussion
\&  http://bioperl.org/wiki/Mailing_lists  \- About the mailing lists
.Ve
.SS Support
.IX Subsection "Support"
Please direct usage questions or support issues to the mailing list:
.PP
\&\fIbioperl\-l@bioperl.org\fR
.PP
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.
.SS "Reporting Bugs"
.IX Subsection "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:
.PP
.Vb 1
\&  http://redmine.open\-bio.org/projects/bioperl/
.Ve
.SH "AUTHOR \- Daisie Huang"
.IX Header "AUTHOR - Daisie Huang"
Email daisieh@zoology.ubc.ca
.SH CONTRIBUTORS
.IX Header "CONTRIBUTORS"
Additional contributors names and emails here
.SS valid_values
.IX Subsection "valid_values"
.Vb 7
\& 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
.Ve
.SS new
.IX Subsection "new"
.Vb 12
\& 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   \*(Aqbf\*(Aq => custombatchfile.bf
\&                                                    \*(Aqorder\*(Aq => [array of ordered parameters]
\&           \-executable => where the hyphy executable resides
.Ve
.PP
See also: Bio::Tree::TreeI, Bio::Align::AlignI
.SS update_ordered_parameters
.IX Subsection "update_ordered_parameters"
.Vb 5
\& Title   : update_ordered_parameters
\& Usage   : $BatchFile\->update_ordered_parameters();
\& Function: updates all of the parameters needed for the ordered input redirect in HBL.
\& Returns : nothing
\& Args    : none
.Ve
.SS run
.IX Subsection "run"
.Vb 5
\& Title   : run
\& Usage   : my ($rc,$results) = $BatchFile\->run();
\& Function: run the Hyphy analysis using the specified batchfile and its ordered parameters
\& Returns : Return code, Hash
\& Args    : none
.Ve
.SS create_wrapper
.IX Subsection "create_wrapper"
.Vb 5
\& Title   : create_wrapper
\& Usage   : $self\->create_wrapper
\& Function: Creates the wrapper file for the batchfile specified in the hash, saves it to the hash as \*(Aq_wrapper\*(Aq.
\& Returns : nothing
\& Args    : none
.Ve
.SS set_parameter
.IX Subsection "set_parameter"
Title   :  set_parameter
Usage   :  \f(CW$hyphy\fR\->set_parameter($param,$val);
Function:  Sets the named parameter \f(CW$param\fR to \f(CW$val\fR if it is a non-numeric parameter
           If \f(CW$param\fR is a number, sets the corresponding value of the ordered redirect array (starts from 1).
Returns :  boolean if set was successful
Args    :  \f(CW$param\fR => name of the parameter
           \f(CW$value\fR => value to set the parameter to
.SS batchfile
.IX Subsection "batchfile"
Title   :  batchfile
Usage   :  \f(CW$hyphy\fR\->batchfile($bf_name);
Function:  Gets/sets the batchfile that is run by \f(CW$hyphy\fR.
Returns :  The batchfile path.
Args    :  \f(CW$bf_name\fR => path of new batchfile
.SS make_batchfile_with_contents
.IX Subsection "make_batchfile_with_contents"
Title   :  make_batchfile_with_contents
Usage   :  \f(CW$hyphy\fR\->make_batchfile_with_contents($bf_string);
Function:  Creates a temporary file with the specified string of contents for the batchfile.
Returns :  The batchfile path.
Args    :  \f(CW$bf_string\fR => contents for the batchfile
.SS set_default_parameters
.IX Subsection "set_default_parameters"
.Vb 7
\& 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
.Ve