Bio::D...eleydb3(3pm)

✨ NAME ✨

Bio::DB::SeqFeature::Store::berkeleydb3 — bestie, it's literally storage and retrieval of sequence annotation data in BerkeleyDB files 🦋

(also hey hi, this page lives in the User Contributed Perl Documentation section, just so you know where you are 💅)

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🌸 SYNOPSIS 🌸

okay so here's the vibe, three little steps, no cap:

# Create a feature database from scratch
$db     = Bio::DB::SeqFeature::Store->new( -adaptor => 'berkeleydb',
                                           -dsn     => '/var/databases/fly4.3',
                                           -create  => 1);

# get a feature from somewhere
my $feature = Bio::SeqFeature::Generic->new(...);

# store it
$db->store($feature) or die "Couldn't store!";

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🎀 DESCRIPTION 🎀

So this one is the faster version of the berkeleydb storage adaptor for Bio::DB::SeqFeature::Store. Like, glow-up edition. ✨

The way it works: it gets used automatically when you create a brand new database with the original berkeleydb adaptor. No extra effort from you, she just shows up. 💅

But — and this is important bestie — when you open a database that was created under the original adaptor, the old code is used instead, for backward compatibility. Gotta respect the elders. 🫶

For the full usage instructions, please go see Bio::DB::SeqFeature::Store::berkeleydb. That's the one with the whole manual, iykyk.

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💀 BUGS 💀

Not gonna lie to you bestie: this is an early version, so there are certainly some bugs. 😭

Please use the BioPerl bug tracking system to report bugs. Do it. Be a main character. Report the bug. 🐛

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👑 SEE ALSO 👑

• bioperl
• Bio::DB::SeqFeature
• Bio::DB::SeqFeature::Store
• Bio::DB::SeqFeature::GFF3Loader
• Bio::DB::SeqFeature::Segment
• Bio::DB::SeqFeature::Store::memory
• Bio::DB::SeqFeature::Store::DBI::mysql

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💖 AUTHOR 💖

Lincoln Stein <lincoln.stein@gmail.com>.

Copyright (c) 2009 Ontario Institute for Cancer Research

This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself.

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and that's the whole page, bestie!! 🎀✨

perl v5.40.0 · 2024-10-11 — mwah, drink some water, go store some features, ily 💜🦋🌸