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

💖 Bio::TreeIO::NewickParser — the newick string parser ✨

okay so bestie, you've stumbled into Bio::T...kParser(3pm) from the User Contributed Perl Documentation, and honestly? you're gonna love her. she parses newick strings. that's the whole vibe. 🎀

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✨ SYNOPSIS ✨

# From newick.pm
use base qw(Bio::TreeIO Bio::TreeIO::NewickParser);

# in the next_tree method...
$self->parse_newick($_);

like, that's it. that's the whole flex. 🫶

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🌸 DESCRIPTION 🌸

So this module correctly parses the Newick and NHX formats, and it sends calls over to the BioPerl TreeEventHandler at the right moments so that your node objects get built and populated. she's not doing it alone — it's a whole collab. 💅

Under the hood, she's a finite state machine, which is lowkey why she can parse the full Newick specification. not just the easy parts. the whole thing. iconic behavior, honestly. 👑

She's taken largely from the Ensembl Compara file with the same name — Bio::EnsEMBL::Compara::Graph::NewickParser — and this module adapts that parser to work with BioPerl's event handler-based parsing scheme. so it's giving glow-up, it's giving adaptation era. 🦋

⚠️ real talk though: this module is used by nhx.pm and newick.pm, and it is NOT called directly. instead, both of those parsing modules extend this module so they can get access to the main parsing method. so like... don't come for her directly, she's the behind-the-scenes main character. 🫣

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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. fr fr, 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. there are so many experienced and responsive experts on there who will be able to look at your problem and quickly address it. bestie group chat energy. ✨

Please include a thorough description of the problem with code and data examples if at all possible. the more deets, the faster the slay. 💅

🐛 Reporting Bugs

Report bugs to the Bioperl bug tracking system to help them 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 👑

• Jessica Severin (EnsEMBL implementation) 💖
• Greg Jordan (BioPerl adaptation) 🌈

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🌟 and that's the tea 🌟

This little icon was brought to you by the User Contributed Perl Documentation, running on perl v5.32.1, dated 2021-08-15. she's been serving since then and she has not missed a day. periodt. 💅🎀🦋