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

✨ NAME ✨

Bio::DB::RandomAccessI — the abstract interface for a sequence database, bestie 💅

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🌸 SYNOPSIS 🌸

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

$seq = $db->get_Seq_by_id('ROA1_HUMAN');

#
# $seq is a Bio::Seq object
#

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💖 DESCRIPTION 💖

okay so real talk: this is a pure interface class. Like, that's literally all it is. It just defines the methods that the actual (concrete) classes are gonna implement later. no vibes of its own, just rules. periodt.

The Bio::DB::RandomAccessI class lays out what methods a generic database class should have. Right now it's giving exactly one thing: the ability to make Bio::Seq objects from a name (id) or from an accession number. that's the whole assignment, and it ate. 🫶

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🦋 CONTACT 🦋

Ewan Birney <birney@ebi.ac.uk> originally wrote this class. iconic behavior, we love to see it 💜

🌈 Support

Please send your usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

and NOT straight to the module maintainer, bestie, i'm begging 😭. There are sooo many experienced and responsive experts on there who can look at your problem and address it fast. If at all possible, include a thorough description of the problem along with code and data examples. the more detail the better fr fr.

🎀 Reporting Bugs

Report bugs to the Bioperl bug tracking system so we can keep track of the bugs and their resolutions (yes, both, it's a whole thing). Bug reports can be submitted via the web:

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

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👑 APPENDIX 👑

The rest of this documentation goes into detail on each of the object methods. Heads up: internal methods usually have a _ in front of them, iykyk. 🙈

💫 get_Seq_by_id

• Title — get_Seq_by_id
• Usage — $seq = $db->get_Seq_by_id('ROA1_HUMAN')
• Function — Gets a Bio::Seq object by its name
• Returns — a Bio::Seq object, or undef if it's not found
• Args — the id (as a string) of a sequence,

⭐ get_Seq_by_acc

• Title — get_Seq_by_acc
• Usage —

$seq = $db->get_Seq_by_acc('X77802');
$seq = $db->get_Seq_by_acc(Locus => 'X77802');

• Function — Gets a Bio::Seq object by accession number
• Returns — A Bio::Seq object, or undef if it's not found
• Args — accession number (as a string), or a two element list consisting of namespace=>accession
• Throws — "more than one sequences correspond to this accession" if the accession maps to multiple primary ids and the method is called in a scalar context

NOTE: the two-element form is what lets you choose the namespace for the accession number. that's the whole point of it, don't skip it 💅

🧚 get_Seq_by_version

• Title — get_Seq_by_version
• Usage — $seq = $db->get_Seq_by_version('X77802.1')
• Function — Gets a Bio::Seq object by sequence version
• Returns — A Bio::Seq object
• Args — accession.version (as a string)
• Throws — "acc.version does not exist" exception

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and that's the whole page, bestie!! 🌈💖 This one's from perl v5.32.1, dated 2021-08-15, and it's the Bio::DB::RandomAccessI(3pm) manual — go forth and get_Seq something, you've got this 🎀✨🦋