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

💖 Bio::T...eltest(3pm) 💖

okay so this page is Bio::T...eltest(3pm), straight out of the User Contributed Perl Documentation collection, and bestie, it's a whole moment. grab a snack 🍓

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✨ NAME ✨

Bio::Tools::Run::Phylo::Hyphy::Modeltest — it's a wrapper around the Hyphy Modeltest analysis. that's the entire name, no notes 💅

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🌈 SYNOPSIS 🌈

copy this exactly, bestie, character for character:

  use Bio::Tools::Run::Phylo::Hyphy::Modeltest;
  use Bio::AlignIO;
  use Bio::TreeIO;

  my $alignio = Bio::AlignIO->new(-format => 'fasta',
                                 -file   => 't/data/hyphy1.fasta');

  my $aln = $alignio->next_aln;
  my $treeio = Bio::TreeIO->new(
      -format => 'newick', -file => 't/data/hyphy1.tree');

  my $modeltest = Bio::Tools::Run::Phylo::Hyphy::Modeltest->new();
  $modeltest->alignment($aln);
  $modeltest->tree($tree);
  my ($rc,$results) = $modeltest->run();

ngl the synopsis says $tree while the TreeIO object got named $treeio — that's literally what's written up there, so we're keeping it exactly as-is. iykyk 🙈

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🦋 DESCRIPTION 🦋

so what even is this? it's a wrapper around the Modeltest analysis from the HyPhy ([Hy]pothesis Testing Using [Phy]logenies) package, made by Sergei Kosakowsky Pond, Spencer V. Muse, Simon D.W. Frost and Art Poon. more info lives at http://www.hyphy.org if you wanna go read up ✨

and here's the main character energy: this module will generate the correct list of options for interfacing with TemplateBatchFiles/Modeltest.bf. that's the job. that's what it does. 👑

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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, and we mean that 🫶

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

🫂 Support

usage questions and support issues go to the mailing list:

  bioperl-l@bioperl.org

...rather than sliding into the module maintainer's DMs directly. there are so many experienced and responsive experts who can 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 context the better, no cap.

🐛 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 - Albert Vilella 🌟

Email avilella-at-gmail-dot-com

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🎀 CONTRIBUTORS 🎀

Additional contributors names and emails here

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👑 APPENDIX 👑

the rest of the documentation details each of the object methods. internal methods are usually preceded with a _ (that underscore is the "don't touch, it's private" signal 💅)

💜 Default Values

Valid and default values for Modeltest 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. periodt.

🌸 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::Modeltest->new();
• Function : Builds a new Bio::Tools::Run::Phylo::Hyphy::Modeltest object
• Returns : Bio::Tools::Run::Phylo::Hyphy::Modeltest
• 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

🔥 run

• Title : run
• Usage : my ($rc,$results) = $modeltest->run($aln);
• Function : run the modeltest analysis using the default or updated parameters — the alignment parameter must have been set
• Returns : Return code, hash containing the "Hierarchical Testing" and "AIC" results, both as hashes.
• Args : Bio::Align::AlignI object, 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 :

(yep, Example, Returns and Args are all just sitting there empty in the original — not me adding anything, that's genuinely the whole vibe 🙈)

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and that's the page, bestie!! 💖 go forth and run your modeltest ✨ this was perl v5.36.0, dated 2023-01-22, and the page itself is Bio::T...eltest(3pm). mwah 🫶💅