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

💖 Bio::TreeIO::nexus — the tea ☕

okay bestie, so this is Bio::TreeIO::nexus, a TreeIO driver module for parsing Nexus tree output from PAUP. It lives in the User Contributed Perl Documentation and fr fr it's giving "I read your PAUP trees so you don't have to" 💅

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✨ SYNOPSIS ✨

like, the whole vibe in four lines:

use Bio::TreeIO;
my $in = Bio::TreeIO->new(-file => 't/data/cat_tre.tre');
while( my $tree = $in->next_tree ) {
}

that's it. that's the whole thing. loop over your trees, live your life 🦋

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🌸 DESCRIPTION 🌸

So this is a driver module for parsing PAUP Nexus tree format — which, no cap, is basically just a remapping of trees. lowkey simple, highkey useful 🫶

🎀 Comments 🎀

Here's the cute part: the nexus format lets you drop node comments inside square brackets. Normally those comments (which get implemented as tags for nodes) are there to give a name to an internal node or to record the bootstrap value, but bestie, other uses are possible. sky's the limit ✨

Now — the FigTree program by Andrew Rambaut adds all these rendering parameters inside comments, and it flags those comments by starting them with &!. Iconic behaviour tbh. The parameters implemented here are:

• label
• color

that's the list. those two. periodt 💅

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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 — genuinely, they mean it 😭

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. The way that there are many experienced and reponsive experts who will be able look at the problem and quickly address it… obsessed. Please include a thorough description of the problem with code and data examples if at all possible 🙏

🐛 Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us 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-open-bio-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
Args    : -header    => boolean  default is true
                        print/do not print #NEXUS header
          -translate => boolean default is true
                        print/do not print Node Id translation to a number

so like, -header is a boolean and the default is true — it controls whether you print/do not print the #NEXUS header. And -translate is a boolean too, default is true, controlling whether you print/do not print Node Id translation to a number. two little switches, both defaulting to yes 🎀

🌟 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

gets the next tree in the stream, hands you back a Bio::Tree::TreeI, takes no args. she just delivers 💅

🔥 write_tree

Title   : write_tree
Usage   : $treeio->write_tree($tree);
Function: Writes a tree onto the stream
Returns : none
Args    : Bio::Tree::TreeI

writes a tree onto the stream. takes a Bio::Tree::TreeI, returns none. in and out, no drama 🫶

💜 header

Title   : header
Usage   : $obj->header($newval)
Function:
Example :
Returns : value of header (a scalar)
Args    : on set, new value (a scalar or undef, optional)

returns the value of header (a scalar). on set, it takes the new value (a scalar or undef, optional). yes the Function and Example fields are literally empty, we're not gonna pretend otherwise 🙈

🦋 translate_node

Title   : translate_node
Usage   : $obj->translate_node($newval)
Function:
Example :
Returns : value of translate_node (a scalar)
Args    : on set, new value (a scalar or undef, optional)

returns the value of translate_node (a scalar). on set, new value (a scalar or undef, optional). same energy as header, different name, we love a consistent queen ✨

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and that's the whole page bestie!! 💖 no notes. this was perl v5.32.1, dated 2021-08-15, and it's part of Bio::T...:nexus(3pm) — User Contributed Perl Documentation. slay, go parse some trees 🌈🎀👑