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

💖 Bio::T...luster(3pm) 💖

okay bestie, so this is Bio::TreeIO::cluster — a TreeIO driver module for parsing Algorithm::Cluster::treecluster() output. it's a Perl thing, it's from the User Contributed Perl Documentation, and it's lowkey iconic. let's get into it 🦋

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✨ NAME ✨

Bio::TreeIO::cluster — a TreeIO driver module for parsing Algorithm::Cluster::treecluster() output. that's the whole vibe. no cap. 💅

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🌸 SYNOPSIS 🌸

so like, do NOT use this module directly, okay?? fr fr. here's how it actually goes down:

# do not use this module directly
use Bio::TreeIO;
use Algorithm::Cluster;
my ($result, $linkdist) = Algorithm::Cluster::treecluster(
  distances => $matrix
);
my $treeio = Bio::TreeIO->new(
  -format   => 'cluster',
  -result   =>  $result,
  -linkdist =>  $linkdist,
  -labels   =>  $labels
);
my $tree = $treeio->next_tree;

like. you feed it the $result and $linkdist from treecluster(), plus your $labels, and it hands you back a whole tree. main character energy honestly 🌳✨

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🎀 DESCRIPTION 🎀

this is a driver module for parsing Algorithm::Cluster::treecluster() output. that's it. that's the job. it's a parser bestie, it parses. 💜

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💌 FEEDBACK 💌

💖 Mailing Lists 💖

user feedback is an integral part of the evolution of this and other Bioperl modules. so if you got comments, suggestions, thoughts, feelings — send them to the Bioperl mailing list!! your participation is much appreciated, for real. 🫶

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

🩹 Support 🩹

okay listen. please direct usage questions and support issues to the mailing list:

bioperl-l@bioperl.org

and not to the module maintainer directly, bestie. there are so many experienced and responsive experts on there who will look at your problem and quickly address it. but when you ask, please include a thorough description of the problem with code and data examples if at all possible!! help them help you 💅

🐛 Reporting Bugs 🐛

found a bug? report it 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:

https://github.com/bioperl/bioperl-live/issues

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👑 AUTHOR - Guillaume Rousse 👑

Email Guillaume-dot-Rousse-at-inria-dot-fr

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🌈 CONTRIBUTORS 🌈

Jason Stajich - jason-at-bioperl-dot-org

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📖 APPENDIX 📖

the rest of the documentation details each of the object methods. internal methods are usually preceded with a _ (iykyk). ✨

💫 new 💫

Title   : new
Usage   : my $obj = Bio::TreeIO::cluster->new();
Function: Builds a new Bio::TreeIO::cluster object for reading Algorithm::Cluster::treecluster output
Returns : Bio::TreeIO::cluster
Args    :-result   => Algorithm::Cluster result
         -linkdist => distance between links
         -labels   => node labels

so new builds you a brand new Bio::TreeIO::cluster object for reading that Algorithm::Cluster::treecluster output. it gives you back a Bio::TreeIO::cluster, and you gotta hand it -result (the Algorithm::Cluster result), -linkdist (distance between links), and -labels (node labels). slay. 🌟

💫 next_tree 💫

Title   : next_tree
Usage   : my $tree = $treeio->next_tree
Function: Gets the next tree in the stream
Returns : Bio::Tree::TreeI
Args    : none

next_tree gets the next tree in the stream. returns a Bio::Tree::TreeI, takes no args. simple, clean, obsessed. 🌸

💫 write_tree 💫

Title   : write_tree
Usage   :
Function: Sorry not possible with this format
Returns : none
Args    : none

and write_tree?? yeah no. sorry not possible with this format. 😭 returns none, takes no args, it's just not happening bestie. the format said no. 💀

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perl v5.32.1 · 2021-08-15

and that's the whole page babes 🎀 stay parsed, stay slaying, and remember: do not use this module directly. periodt. 💖✨🦋