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

💖 Bio::DB::Taxonomy::silva — the Silva taxonomy era 💖

okay bestie, so this is a Perl manpage, Bio::DB::Taxonomy::silva(3pm), straight outta the User Contributed Perl Documentation section. she's giving bioinformatics, she's giving taxonomy, she's giving memory hungry. let's get into it ✨

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🌸 NAME 🌸

Bio::DB::Taxonomy::silva — bestie, we're using the Silva taxonomy. that's the whole vibe. 💅

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🦋 SYNOPSIS 🦋

okay so here's how you summon her:

use Bio::DB::Taxonomy;

my $db = Bio::DB::Taxonomy->new(
   -source   => 'silva',
   -taxofile => 'SSURef_108_tax_silva_trunc.fasta',
);

look at that. clean. effortless. main character energy fr fr 🌟

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👑 DESCRIPTION 👑

so this is an implementation of Bio::DB::Taxonomy that stores and accesses the Silva taxonomy. iconic behaviour honestly.

internally, Bio::DB::Taxonomy::silva keeps the taxonomy in memory by using Bio::DB::Taxonomy::list. so like, heads up bestie: the IDs assigned to the taxonomy nodes — e.g. sv72 — are arbitrary. they are NOT the pre-defined IDs that NCBI assigns to taxons. no cap. also, no rank names and no common names get assigned to the taxa of Bio::DB::Taxonomy::silva. so if you were looking for common names, she's not serving that today 🙈

the latest Silva taxonomy (2011) contains about 126,000 taxa and occupies about 124 MB of memory once it's parsed into a Bio::DB::Taxonomy::silva object. that's... a lot. obviously it can take a little while to load. go get a snack, hydrate, do a face mask, she'll be ready when she's ready 💅

the taxonomy file SSURef_108_tax_silva_trunc.fasta that this module uses is available from:

<http://www.arb-silva.de/no_cache/download/archive/release_108/Exports/>

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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. literally, they want to hear 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. many experienced and reponsive experts will be able look at the problem and quickly address it. please include a thorough description of the problem with code and data examples if at all possible. give them the whole picture bestie, they're not mind readers 💖

🐛 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 - Florent Angly ⭐

florent.angly@gmail.com

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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
Usage   : my $obj = Bio::DB::Taxonomy::silva->new();
Function: Builds a new Bio::DB::Taxonomy::silva object
Returns : an instance of Bio::DB::Taxonomy::silva
Args    : -taxofile  => name of the FASTA file containing the taxonomic information,
                        typically 'SSURef_108_tax_silva_trunc.fasta' (mandatory)

so you're building a fresh Bio::DB::Taxonomy::silva object, she returns an instance of Bio::DB::Taxonomy::silva, and the -taxofile arg is the name of the FASTA file with the taxonomic info inside — typically SSURef_108_tax_silva_trunc.fasta. and bestie, it's mandatory. not optional. do not skip it. 🚨

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and that's the whole page, bestie! this was Bio::D...:silva(3pm) from perl v5.32.1, dated 2021-08-15 — go forth and taxonomy responsibly 💜✨🌸