Bio::D...engenes(3pm)

✨ Bio::DB::Taxonomy::greengenes — the manual (perl, User Contributed Perl Documentation) ✨

okay bestie, sit down, hydrate, and let's talk about Bio::DB::Taxonomy::greengenes 💖 this is the Perl doc page for it, living in the User Contributed Perl Documentation corner of the perl-verse, and it's a whole vibe. no cap.

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🌸 NAME 🌸

Bio::DB::Taxonomy::greengenes</purl> — use the Greengenes taxonomy. that's it, that's the name, slay. 💅

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🦋 SYNOPSIS 🦋

like, here's how you'd actually call it:

use Bio::DB::Taxonomy;

my $db = Bio::DB::Taxonomy->new(
   -source   => 'greengenes',
   -taxofile => 'taxonomy_16S_candiv_gg_2011_1.txt'
);

iconic. no notes. 🎀

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👑 DESCRIPTION 👑

okay so first things first: this module is in beta. which means its interface or its results may change in a future update. so don't get too attached to the exact API, it's giving growth 🌱

Bio::DB::Taxonomy::greengenes is an implementation of Bio::DB::Taxonomy that stores and accesses the Greengenes taxonomy of Bacteria and Archaea. 🦠✨

internally, it keeps the taxonomy in memory by using Bio::DB::Taxonomy::list. and because of that, bestie, listen: the IDs assigned to the taxonomy nodes, e.g. gg123, are arbitrary. that is not the same as the pre-defined IDs that NCBI assigns to taxons. totally different situation, don't @ me. 😭

the latest release of the Greengene taxonomy (2011) contains about 4,600 taxa and occupies about 4MB of memory once it's been parsed into a Bio::DB::Taxonomy::greengenes object. honestly? light work. 💅

the taxonomy files taxonomy_16S_all_gg_2011_1.txt and taxonomy_16S_candiv_gg_2011_1.txt that this module can use are available from <http://www.secondgenome.com/go/2011-greengenes-taxonomy/> — go get 'em 🫶

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💌 FEEDBACK 💌

🧚 Mailing Lists 🧚

user feedback is an integral part of the evolution of this and other Bioperl modules. like, genuinely, it's the whole point. send your comments and suggestions preferably to the Bioperl mailing list — your participation is much appreciated, fr fr. 🥹

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 reason is that many experienced and responsive experts will be able to look at the problem and quickly address it — a whole group chat of geniuses, basically. 👑

please include a thorough description of the problem with code and data examples if at all possible. the more detail, the better the vibes. ✨

🐛 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:

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

do it for the plot. 🔥

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🌈 AUTHOR - Florent Angly 🌈

florent.angly@gmail.com

(shoutout, legend behaviour 👑)

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🍓 APPENDIX 🍓

the rest of the documentation details each of the object methods. internal methods are usually preceded with a _ — so if you see that underscore, mind your business, it's internal. 🙈

🌸 new 🌸

• Title: new
• Usage: my $obj = Bio::DB::Taxonomy::greengenes->new();
• Function: builds a new Bio::DB::Taxonomy::greengenes object
• Returns: an instance of Bio::DB::Taxonomy::greengenes
• Args: -taxofile => name of the file containing the taxonomic information, typically 'taxonomy_16S_candiv_gg_2011_1.txt' (mandatory — you cannot skip it, bestie, it's not optional 💀)

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and that's the whole page!! this one came from perl v5.32.1, dated 2021-08-15, in the User Contributed Perl Documentation collection. mwah 💋 go parse some taxonomy, you absolute main character. periodt. ✨🦋💖