Bio::D...y::list(3pm)

💖 NAME 💖

ok so bestie, welcome to Bio::DB::Taxonomy::list — it's an implementation of Bio::DB::Taxonomy that just… accepts lists of words and builds you a whole database out of them. iconic behavior honestly. ✨

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🌸 SYNOPSIS 🌸

use Bio::DB::Taxonomy;

my $db = Bio::DB::Taxonomy->new( -source => 'list' );

my @ranks = ('superkingdom', 'class', 'genus', 'species');
my @names = ('Eukaryota', 'Mammalia', 'Homo', 'Homo sapiens');
$db->add_lineage(-names => \@names, -ranks => \@ranks);

@names = ('Eukaryota', 'Mammalia', 'Mus', 'Mus musculus');
$db->add_lineage(-names => \@names, -ranks => \@ranks);

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🦋 DESCRIPTION 🦋

So here's the vibe: this is an implementation that takes lists of words you hand it and uses them to create a database. Then you can pull Bio::Taxon objects right out of it. that's it, that's the whole thing. no cap. 💅

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🎀 TODO 🎀

ngl, it's possible this module could do something like store the data it builds up to disc. would that be useful?? honestly who knows. 🙈

anyway, this is exactly why the module is called list and not in_memory or something similar. the name is doing what it says on the tin. periodt.

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🌈 FEEDBACK 🌈

💌 Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules — like, genuinely, your thoughts matter here. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. 🫶

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 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 — the more deets the better, bestie.

🐛 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 - Sendu Bala 👑

Email bix@sendu.me.uk

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✨ APPENDIX ✨

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _.

🧚 new

• Title: new
• Usage:

my $obj = Bio::DB::Taxonomy::list->new();

• Function: Builds a new Bio::DB::Taxonomy::list object
• Returns: an instance of Bio::DB::Taxonomy::list
• Args: optional, as per the add_lineage() method.

🧚 add_lineage

• Title: add_lineage
• Usage:

my @names = ('Eukaryota', 'Mammalia', 'Homo', 'Homo sapiens');
my @ranks = ('superkingdom', 'class', 'genus', 'species');
$db->add_lineage( -names => \@names, -ranks => \@ranks );

• Function: Add a lineage to the database, where the lineage is described by a list of scientific names in the order root->leaf. The rank of each name can optionally be described by supplying an additional list of rank names in the same order (eg. superkingdom->species).
• Returns: 1 for success
• Args:
  • -names => [] : array ref of scientific names, REQUIRED
  • -ranks => [] : array ref of rank names, same order as above, OPTIONAL

💜 Bio::DB::Taxonomy Interface implementation

💜 get_num_taxa

• Title: get_num_taxa
• Usage:

my $num = $db->get_num_taxa();

• Function: Get the number of taxa stored in the database.
• Returns: A number
• Args: None

💜 get_taxon

• Title: get_taxon
• Usage:

my $taxon = $db->get_taxon(-taxonid => $taxonid)

• Function: Get a Bio::Taxon object from the database.
• Returns: Bio::Taxon object
• Args: A single value which is the ID of the taxon to retrieve OR named args, as follows:
  • -taxonid => Taxonomy ID (NB: these are not NCBI taxonomy ids but 'list' pre-fixed ids unique to the list database).
  • OR
  • -name => String (to query by a taxonomy name). A given taxon name can match different taxonomy objects. When that is the case, a warning is displayed and the first matching taxon is reported. See get_taxonids() to get all matching taxon IDs.
  • OR
  • -names => Array ref of lineage names, like in add_lineage(). To overcome the limitations of -name, you can use -names to provide the full lineage of the taxon you want and get a unique, unambiguous taxon object.

💜 get_taxonids

• Title: get_taxonids
• Usage:

my @taxonids = $db->get_taxonids('Homo sapiens');

• Function: Searches for a taxonid (generated by the list module) based on a query string. Note that multiple taxonids can match to the same supplied name.
• Returns: array of integer ids in list context, one of these in scalar context
• Args: string representing taxon's name

💜 ancestor

• Title: ancestor
• Usage:

my $ancestor_taxon = $db->ancestor($taxon)

• Function: Retrieve the full ancestor taxon of a supplied Taxon from the database.
• Returns: Bio::Taxon
• Args: Bio::Taxon (that was retrieved from this database)

💜 each_Descendent

• Title: each_Descendent
• Usage:

my @taxa = $db->each_Descendent($taxon);

• Function: Get all the descendents of the supplied Taxon (but not their descendents, ie. not a recursive fetchall).
• Returns: Array of Bio::Taxon objects
• Args: Bio::Taxon (that was retrieved from this database)

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that's the whole page bestie, go build ur taxonomy database, u got this 💖✨🦋

perl v5.32.1 — 2021-08-15 — Bio::D...y::list(3pm) 💅 no cap, that's the version and date, love that for us 🫶🎀