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

💖 NAME 💖

Bio::DB::ReferenceI — a RandomAccessI-ish abstract interface that pulls Reference data out of a sequence database and hands you back Bio::Annotation::Reference objects 🦋

It's a Perl module, bestie. Manual page name is Bio::D...erenceI(3pm), in case you were wondering what tab you're staring at 💅

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✨ SYNOPSIS ✨

#
# get a database object somehow using a concrete class
#

$ref = $db->get_Reference_by_id('123456');

#
# $ref is a Bio::Annotation::Reference object
#

Like. Get a database object first, somehow, using a concrete class. Then boom, you get your ref back. That's the whole vibe 🎀

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🌸 DESCRIPTION 🌸

Okay so first things first: this is a pure interface class. Which means?? It does literally nothing on its own. All it does is define methods that other (concrete) classes will actually go implement. It's giving blueprint energy. It's giving "I'm the idea, you're the execution" 💀

The Bio::DB::ReferenceI class defines methods used to retrieve reference data from a sequence. That data comes back to you in the form of Bio::Annotation::Reference objects. ✨

At the moment it is just the ability to make Bio::Annotation::Reference objects from a name or unique id (id), an accession number (acc), and so on. Small but mighty, fr fr.

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🫶 CONTACT 🫶

Ewan Birney originally wrote Bio::DB::RandomAccessI, from which this class is based. Shoutout to the originator 👑

📬 Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. So send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated, no cap 🙏

bioperl-l@lists.open-bio.org               - General discussion
http://bioperl.org/Support.html  - 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. Real talk: there are so many experienced and reponsive experts on there who will look at your problem and address it fast. Please include a thorough description of the problem with code and data examples if at all possible — give them the whole picture, bestie 🧚

🐛 Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track 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 👑

Email cjfields at bioperl 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 🫣).

⭐ get_Reference_by_id

Title   : get_Reference_by_id
Usage   : $ref = $db->get_Reference_by_id('123456')
Function: Gets a Bio::Annotation::Reference-implementing object by its name (id)
Returns : a Bio::Annotation::Reference object or undef if not found
Args    : the id (as a string) of a sequence

Grab a Bio::Annotation::Reference-implementing object by its name (id). You get the object back, or undef if it's not found. Args? Just the id, as a string. Simple, iconic 💅

⭐ get_Reference_by_acc

Title   : get_Reference_by_acc
Usage   : $ref = $db->get_Reference_by_acc('X77802');
Function: Gets a Bio::Annotation::Reference object by accession number
Returns : A Bio::Annotation::Reference object or undef if not found
Args    : accession number (as a string)
Throws  : "more than one sequences correspond to this accession"
           if the accession maps to multiple primary ids and
           method is called in a scalar context

Get a Bio::Annotation::Reference object by accession number. Returns the object, or undef if it's not found. Arg is the accession number as a string.

⚠️ Heads up bestie: this one can throw "more than one sequences correspond to this accession" if the accession maps to multiple primary ids and you called the method in a scalar context. So like, don't do that, or do and be ready 😭

⭐ get_Reference_by_version

Title   : get_Reference_by_version
Usage   : $ref = $db->get_Reference_by_version('X77802.1');
Function: Gets a Bio::Annotation::Reference object by sequence version
Returns : A Bio::Annotation::Reference object
Args    : accession.version (as a string)
Throws  : "acc.version does not exist" exception

Get a Bio::Annotation::Reference object by sequence version. Returns a Bio::Annotation::Reference object (yes, an actual object, no undef mention here, she's confident ✨). Arg is accession.version as a string.

⚠️ And this one throws the "acc.version does not exist" exception if that version isn't a thing. Periodt.

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That's the whole page, bestie — documented by the User Contributed Perl Documentation crew, running on perl v5.32.1, dated 2021-08-15, filed under Bio::D...erenceI(3pm). Go get your references. Slay 🎀✨💖