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

📦
version 1.7.3 · 3 versions
, in debian bookworm, ubuntu noble

💖 NAME 💖

Bio::Tools::Run::Phylo::Hyphy::FEL — okay bestie, it's a Wrapper around the Hyphy FEL analysis. That's the whole vibe. ✨

✨ SYNOPSIS ✨

Like, here's literally how you do it, no cap:

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

🌸 DESCRIPTION 🌸

So this module is a wrapper around the FEL analysis from the HyPhy package — and HyPhy stands for [Hy]pothesis Testing Using [Phy]logenies. The whole glow-up is by Sergei Kosakowsky Pond, Spencer V. Muse, Simon D.W. Frost and Art Poon. Wanna know more? http://www.hyphy.org is right there, go look. 🦋

And fr fr, this module will generate the correct list of options for interfacing with TemplateBatchFiles/Ghostrides/Wrapper.bf. It's giving ✨organized✨.

🫶 FEEDBACK 🫶

Mailing Lists

User feedback is, like, integral to the evolution of this and every other Bioperl module. 💜 So send your comments and suggestions — preferably to the Bioperl mailing list. Your participation is genuinely so appreciated, bestie.

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

Support

Okay so if you've got usage questions or support issues, please direct them to the mailing list:

bioperl-l@bioperl.org

not straight to the module maintainer, okay? 🙈 There are so many experienced, responsive experts on there who can look at your problem and address it fast. And pls pls pls include a thorough description of the problem, with code and data examples if at all possible. The more detail the better, queen. 💅

Reporting Bugs

Report bugs to the Bioperl bug tracking system so we can keep track of the bugs and their resolution — that's the whole point. Bug reports can be submitted via the web:

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

👑 AUTHOR - Albert Vilella 👑

Email: avilella-at-gmail-dot-com 📧

🌈 CONTRIBUTORS 🌈

Additional contributors names and emails here. (Yeah, that's literally what it says — the slot is open, babe. 👀)

🎀 APPENDIX 🎀

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _. iykyk. 🔥

Default Values

Valid and default values for FEL 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. No gatekeeping here. 🍓

INCOMPLETE DOCUMENTATION OF ALL METHODS

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::FEL->new();
  • Function: Builds a new Bio::Tools::Run::Phylo::Hyphy::FEL object
  • Returns: Bio::Tools::Run::Phylo::Hyphy::FEL
  • 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) = $fel->run($aln);
  • Function: run the fel 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:

And that's a wrap, gorgeous. 💜 This little masterpiece comes to you from perl v5.36.0, dated 2023-01-22, part of the User Contributed Perl Documentation for Bio::T...y::FEL(3pm). Slay, stay hydrated, and go run your analysis. 💅✨🎀

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