Bio::TreeIO::pag(3pm)

💖 Bio::TreeIO::pag 💖

okay bestie, gather round — this is the manual page for Bio::TreeIO::pag (yes, the (3pm) one), from the User Contributed Perl Documentation collection. It's the Bio::TreeIO driver for the Pagel format, and we are gonna get you fluent in it in like, one scroll. no cap. 🦋

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✨ NAME ✨

Bio::TreeIO::pag — a Bio::TreeIO driver for Pagel format 🎀

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🌸 SYNOPSIS 🌸

okay so here's the vibe, code and all, exactly as it is:

use Bio::TreeIO;
my $in = Bio::TreeIO->new(-format => 'nexus',
                          -file   => 't/data/adh.mb_tree.nexus');

my $out = Bio::TreeIO->new(-format => 'pag');
while( my $tree = $in->next_tree ) {
  $out->write_tree($tree);
}

read a nexus file, write pag trees, loop, done. slay. 💅

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🧚 DESCRIPTION 🧚

So the whole point: this converts a Bio::TreeIO to Pagel format. That's it, that's the job. 🌈

More info lives here, and yes this is the real link, don't @ me:

http://www.evolution.reading.ac.uk/index.html

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💌 FEEDBACK 💌

📬 Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. (like, genuinely, they love hearing from you 🫶)

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

🆘 Support

Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

...rather than to the module maintainer directly. Bestie, this is not a snub, it's strategy: many experienced and reponsive experts will be able look at the problem and quickly address it. 👑

If you can, please include a thorough description of the problem with code and data examples if at all possible. 🙏 The more receipts you bring, the faster the fix.

🐛 Reporting Bugs

Report bugs to the Bioperl bug tracking system so they 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 - Jason Stajich 👑

Email: 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 _ — that underscore is the "backstage pass only" sign, iykyk. 🎟️

🆕 new

Title   : new
Usage   : my $obj = Bio::TreeIO::pag->new();
Function: Builds a new Bio::TreeIO::pag object
Returns : an instance of Bio::TreeIO::pag
Args    : -file/-fh for filename or filehandles
          -name_length for minimum name length (default = 10)

Builds a fresh new object, main character energy, and hands you an instance of Bio::TreeIO::pag. ✨

• -file / -fh — for filename or filehandles
• -name_length — for minimum name length (default = 10)

✍️ write_tree

Title   : write_tree
Usage   :
Function: Write a tree out in Pagel format
          Some options are only appropriate for bayesianmultistate and
          the simpler output is only proper for discrete
Returns : none
Args    : -no_outgroups => (number)
          -print_header => 0/1 (leave 0 for discrete, 1 for bayesianms)
          -special_node => special node - not sure what they wanted to do here
          -keep_outgroup => 0/1 (keep the outgroup node in the output)
          -outgroup_ancestor => Bio::Tree::Node (if we want to exclude or include the outgroup this is what we operate on)
          -tree_no       => a tree number label - only useful for BayesianMultistate

Writes a tree out in Pagel format. Heads up: some options are only appropriate for bayesianmultistate, and the simpler output is only proper for discrete. Returns nothing at all — no return value, no gift bag. 🙈

The args, one by one:

• -no_outgroups => (number) — a number, that's the whole spec, take it as given
• -print_header => 0/1 — leave 0 for discrete, 1 for bayesianms
• -special_node => special node — honestly? not sure what they wanted to do here 😭 it's a mystery, we're all just living in it
• -keep_outgroup => 0/1 — keep the outgroup node in the output
• -outgroup_ancestor => Bio::Tree::Node — if we want to exclude or include the outgroup, this is what we operate on
• -tree_no => a tree number label — only useful for BayesianMultistate

🌳 next_tree

Title   : next_tree
Usage   :
Function:
Example :
Returns :
Args    :

Literally no details documented here — the fields are all blank, bestie. It exists, that's the tea. 🍵

📏 name_length

Title   : name_length
Usage   : $self->name_length(20);
Function: set minimum taxon name length
Returns : integer (length of name)
Args    : integer

Sets the minimum taxon name length, hands back an integer which is the length of the name, and takes an integer as its arg. Clean, simple, iconic. 🎀

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and that's the whole page, bestie!! this was perl v5.32.1, dated 2021-08-15, and it's the Bio::TreeIO::pag(3pm) manual — go forth and write some pag trees 💖✨🦋🌸💅🫶