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

okay so you've landed on the manual page for Bio::T...yloBase(3pm) — yeah that's her full name, and yeah it's giving "my government name got cropped by the terminal" 💀 — and she lives in the User Contributed Perl Documentation. Sit down, hydrate, we're going through every single line together. No skips. No cap. 💖

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🌸 NAME 🌸

Bio::Tools::Run::Phylo::PhyloBase — the base module for phylo wrappers. That's the whole thing. She's the blueprint, the foundation, the mother of the phylo wrapper family. 👑

✨ SYNOPSIS ✨

use base qw(Bio::Tools::Run::Phylo::PhyloBase);

Literally one line, bestie. Inherit from her and you're in. 💅

🦋 DESCRIPTION 🦋

Here's the tea: this module exists to be used by Bio::Tools::Run::Phylo modules as their base, standing in wherever Bio::Tools::Run::WrapperBase would normally go.

She's based on WrapperBase — respect where respect is due, she's standing on business — but she brings extra: additional phylo-related private helper subs. That's her whole thing. Private. Phylo-flavoured. Helpers. Periodt. 🫶

💌 FEEDBACK 💌

📬 Mailing Lists

User feedback is an integral part of the evolution of this module and every other Bioperl module, fr fr. Send your comments and suggestions — preferably to the Bioperl mailing list. Your participation is much appreciated, genuinely, we eat it up every time. 🍓

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

🆘 Support 🆘

Please direct your usage questions and support issues to the mailing list:

bioperl-l@bioperl.org

Not to the module maintainer directly, bestie, I'm begging you 🙈 — there are so many experienced and responsive experts on the list who will be able to look at your problem and address it quickly. Please include a thorough description of the problem, with code and data examples if at all possible. Yes, thorough. Yes, examples. It's giving effort and we love that for you. ✨

🐛 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/

👑 AUTHOR - Sendu Bala 👑

Email bix@sendu.me.uk. Iconic behaviour. Thank you for your service, king. 🎀

📖 APPENDIX 📖

The rest of this documentation goes through each of the object methods in detail. Internal methods are usually preceded with a _ — that underscore is the "we're in the private section, bestie" signal. 🔥

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💠 _alignment

• Title: _alignment
• Usage:

$aln = $obj->_alignment()

• Function: Get or set an alignment object — and if you want, she'll generate one straight from a file for you. ✨
• Returns: Bio::Align::AlignI (probably a Bio::SimpleAlign)
• Args:
  • nothing at all if you're just getting
  • OR a filename & the input format of the alignment file to set from a file — the format defaults to guess
  • OR a Bio::Align::AlignI to set

💠 _write_alignment

• Title: _write_alignment
• Usage:

$obj->_write_alignment()

• Function: Writes the alignment object that _alignment() returned out to a temp file, in whatever format you asked for. 🎀
• Returns: filename
• Args: a string describing the format (default 'fasta'), plus any other options you want passed along to AlignIO

💠 _tree

• Title: _tree
• Usage:

$tree = $obj->_tree()

• Function: Get or set a tree object — and if you want, she'll generate one from a file or a database for you. 🌈
• Returns: Bio::Tree::TreeI
• Args: nothing at all to get, OR to set:
  • OR a filename & the input format of the tree file — the format defaults to guess — to set from a file
  • OR a Bio::Tree::TreeI
  • OR a Bio::DB::Taxonomy, for when _alignment() has been set and the sequences in the alignment have ids matching species in the taxonomy database

💠 _write_tree

• Title: _write_tree
• Usage:

$obj->_write_tree()

• Function: Writes the tree object that _tree() returned out to a temp file, in whatever format you asked for. 💜
• Returns: filename
• Args: a string describing the format (default 'newick')

💠 _get_seq_names

• Title: _get_seq_names
• Usage:

@names = $obj->_get_seq_names()

• Function: Gets all the sequence names (from id()) of the sequences in the alignment. Heads up: _alignment() has to be set before you call this. 🙈
• Returns: a list of strings (seq ids)
• Args: none

💠 _get_node_names

• Title: _get_node_names
• Usage:

@names = $obj->_get_node_names()

• Function: Gets all the node names (from id()) of the nodes in the tree. Heads up: _tree has to be set before you call this. 🙈
• Returns: a list of strings (node ids)
• Args: none

💠 _check_names

• Title: _check_names
• Usage:

if ($obj->_check_names) { ... }

• Function: Figures out whether every single sequence in the alignment file has a corresponding node in the tree file. Both _alignment() and _tree() have to be set before you call this. 🌸
• Returns: boolean — and she'll also warn you about the specific problems when she returns false, so read the warnings, bestie, they're literally telling you what's wrong 😭
• Args: none

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and that's the whole page!! go forth and build your phylo wrappers, you're gonna slay. 🦋

this has been Bio::T...yloBase(3pm) from perl v5.32.1, dated 2021-08-15 — mwah, take care of her, she's iconic 💅✨