Bio::T...chFile(3pm)

💖 Bio::Tools::Run::Phylo::Hyphy::BatchFile 💖

okay so this is a page from the User Contributed Perl Documentation manual, and the module is literally called Bio::Tools::Run::Phylo::Hyphy::BatchFile (the header up top shortens it to Bio::T...chFile(3pm) bc terminal columns are not our friends bestie). it's a Perl thing. it's giving bioinformatics. let's go 🧬✨

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🌸 NAME 🌸

Bio::Tools::Run::Phylo::Hyphy::BatchFile — a wrapper for custom execution of Hyphy batch files. no cap, that's the whole job.

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✨ SYNOPSIS ✨

here's the vibe, copy-paste ready, character for character:

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();

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💅 DESCRIPTION 💅

so this module builds a generic interface for processing HBL files in HyPhy ([Hy]pothesis Testing Using [Phy]logenies), which is a package by Sergei Kosakowsky Pond, Spencer V. Muse, Simon D.W. Frost and Art Poon. huge icons honestly. more info lives at http://www.hyphy.org 🦋

to make an instance of this module you literally only need two things: a link to the batch file, and an ordered list of parameters — exactly how it's described in the HyPhy documentation "SelectionAnalyses.pdf." 📄

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🫶 FEEDBACK 🫶

Mailing Lists

user feedback is an integral part of the evolution of this and other Bioperl modules, fr fr. 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. like, respectfully 🙈 there are many experienced and reponsive experts who 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. the more detail the better bestie 💜

Reporting Bugs

report bugs to the Bioperl bug tracking system so we can keep track of the bugs and their resolution. bug reports can be submitted via the web:

 http://redmine.open-bio.org/projects/bioperl/

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👑 AUTHOR - Daisie Huang 👑

Email daisieh@zoology.ubc.ca 💌

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🌈 CONTRIBUTORS 🌈

Additional contributors names and emails here. (yes, that's the actual text. the placeholder said trans rights, or something. iconic of it.)

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🎀 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

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🦋 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 🌱

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💖 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

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🔥 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

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⭐ 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

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💀 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

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🌸 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

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💜 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

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🍓 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

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and that's the whole page bestie 🫶 this one came to you from perl v5.36.0, dated 2023-01-22, in the Bio::T...chFile(3pm) file of the User Contributed Perl Documentation. go run some batch files, you absolute main character 💅✨