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

💖 Bio::Tools::Run::Phylo::Hyphy::REL 💖

okay bestie, welcome to the Bio::Tools::Run::Phylo::Hyphy::REL page from the Bio::T...y::REL(3pm) manual — yes that's the abbreviated title, we're keeping it cute — and it's a wrapper around the Hyphy REL analysis, and honestly? it's giving "let me handle the messy part for you" energy. 🧚

✨ NAME ✨

Bio::Tools::Run::Phylo::Hyphy::REL — a wrapper around the Hyphy REL analysis. that's it, that's the whole name, slay. 💅

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🌸 SYNOPSIS 🌸

here's the vibe, no notes:

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

literally the whole flow: make the alignment, make the tree, make the REL object, set the alignment, set the tree, run it. periodt. 🔥

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🦋 DESCRIPTION 🦋

so this module? it's a wrapper around the REL analysis of HyPhy — that's ([Hy]pothesis Testing Using [Phy]logenies) — the package by Sergei Kosakowsky Pond, Spencer V. Muse, Simon D.W. Frost and Art Poon. go check out http://www.hyphy.org for more info, iykyk. 💜

and the way that this module does its job? it will generate the correct list of options for interfacing with TemplateBatchFiles/Ghostrides/Wrapper.bf. iconic behavior, no cap. ✨

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🎀 FEEDBACK 🎀

💌 Mailing Lists

user feedback is an integral part of the evolution of this and other Bioperl modules — like, genuinely, your voice matters here. 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

okay so please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

rather than to the module maintainer directly. bestie, there are so many experienced and responsive experts on there who will be able to 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. give them the full picture, they'll love you for it. 💖

🙈 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

💫 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 _. (iykyk — if it starts with an underscore, it's private business. 🙈)

🧚 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

so it hands you back an array of every possible parameter, and the default values are always the first one listed — remember that, it matters. and the descriptions? those are essentially lifted from the python wrapper or provided by the author. credit where credit's due. ⭐

✨ new

Title   : new
Usage   : my $obj = Bio::Tools::Run::Phylo::Hyphy::REL->new();
Function: Builds a new Bio::Tools::Run::Phylo::Hyphy::REL object
Returns : Bio::Tools::Run::Phylo::Hyphy::REL
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

the args, one by one, because we don't gatekeep:

• -alignment — the Bio::Align::AlignI object. your alignment, your bestie.
• -save_tempfiles — a boolean to save the generated tempfiles and NOT cleanup after onesself. default is FALSE, so heads up: by default the tempfiles get cleaned up. 🧹
• -tree — the Bio::Tree::TreeI object.
• -params — a hashref of parameters, and all of them get passed to set_parameter.
• -executable — where the hyphy executable resides. tell it where your hyphy lives. 🏠

See also: Bio::Tree::TreeI, Bio::Align::AlignI

🔥 run

Title   : run
Usage   : my ($rc,$results) = $rel->run($aln);
Function: run the rel analysis using the default or updated parameters
          the alignment parameter must have been set
Returns : Return code, Hash
Args    : L<Bio::Align::AlignI> object,
        L<Bio::Tree::TreeI> object [optional]

the alignment parameter must have been set. like, that's not optional, bestie. 😭

it runs the rel analysis using the default or updated parameters, and it returns a Return code and a Hash. the L<Bio::Align::AlignI> object is required, the L<Bio::Tree::TreeI> object is [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    :

it will create the wrapper file that interfaces with the analysis bf file. the example, returns and args are all empty in the original — so that's exactly what you get here too, no inventing, no cap. 🎀

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and that's the whole page, bestie! 🫶 this was perl v5.36.0, dated 2023-01-22, and it's the Bio::T...y::REL(3pm) page from the User Contributed Perl Documentation. go forth and run your REL analysis, you absolute main character. 💖✨👑