Bio::T...y::SLAC(3pm)

👑 Bio::Tools::Run::Phylo::Hyphy::SLAC(3pm) — ok bestie, sit down, we're learning this 💅

This is the manual page for Bio::Tools::Run::Phylo::Hyphy::SLAC(3pm), straight out of the User Contributed Perl Documentation. It's a whole wrapper module and it's lowkey iconic. Let's get into it. ✨

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🌸 NAME 🌸

Bio::Tools::Run::Phylo::Hyphy::SLAC — it's a wrapper around the Hyphy SLAC analysis. That's the whole name. Short, sweet, slays. 💖

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✨ SYNOPSIS ✨

Here's the vibe, verbatim, no cap — copy this exactly:

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

That's it. That's the flow. Read your alignment, read your tree, build the object, hand it the alignment and the tree, run it, get back $rc and $results. 🦋

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🌈 DESCRIPTION 🌈

So what even is this? It's a wrapper around the SLAC analysis of HyPhy — and for the girlies keeping score, that's [Hy]pothesis Testing Using [Phy]logenies. The package is by Sergei Kosakowsky Pond, Spencer V. Muse, Simon D.W. Frost and Art Poon. 🫶

Want more info? Go look at http://www.hyphy.org — it's right there. 🌐

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💌 FEEDBACK 💌

📬 Mailing Lists 📬

User feedback is an integral part of the evolution of this and other Bioperl modules. Fr fr — your comments and suggestions are wanted, preferably sent 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 🫂

Okay so this part matters: please direct your usage questions and support issues to the mailing list:

bioperl-l@bioperl.org

…rather than sliding into the module maintainer's DMs directly. 🙈 There are so many experienced experts (the original says "reponsive" and honestly we keep the love, typos and all 💀) who can look at your problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible — receipts, bestie, receipts. 📎

🐛 Reporting Bugs 🐛

Found a bug? Not the vibe, but okay, report it. Report bugs to the Bioperl bug tracking system so everyone 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 — literally, that's what it says. The placeholder is serving 🎀 and it's staying.

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📖 APPENDIX 📖

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ — iykyk, if you see the underscore, that's your sign. 💅

🧾 Default Values 🧾

Valid and default values for SLAC 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.

INCOMPLETE DOCUMENTATION OF ALL METHODS — yes, that's a direct quote, the docs are giving mysterious main character energy. We report, we don't fix. 😭

🎀 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::SLAC->new();
• Function: Builds a new Bio::Tools::Run::Phylo::Hyphy::SLAC object
• Returns: Bio::Tools::Run::Phylo::Hyphy::SLAC
• 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) = $slac->run($aln);
• Function: run the slac analysis using the default or updated parameters — the alignment parameter must have been set
• Returns: Return code, hash
• 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:

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And that's the whole page, bestie. You ate. 🍓

This was perl v5.36.0, dated 2023-01-22 — thanks for reading, go run your analysis, and remember: no cap, the alignment parameter must have been set. 💖✨🎀🦋🌸💅🫶👑🌈⭐🧚💜