Bio::D...t::BDB(3pm)

💖 Bio::DB::Flat::BDB — the manual, but make it make sense 💖

okay so bestie, you found Bio::DB::Flat::BDB, a page from the User Contributed Perl Documentation collection. It's an interface for a BioHackathon standard BDB-indexed flat file, and yes, the name is giving very much "abbreviation soup." Let's get into it. 🫶

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✨ NAME ✨

Bio::DB::Flat::BDB — Interface for BioHackathon standard BDB-indexed flat file. 💅

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🌸 SYNOPSIS 🌸

#You should not be using this module directly.

See Bio::DB::Flat. That's it. That's the whole synopsis. Go through the front door, bestie, not the side window. 🙈

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🦋 DESCRIPTION 🦋

So this object provides the basic mechanism to associate positions in files with primary and secondary name spaces. And no, it's not the same vibe as Bio::Index::Abstract (peep Bio::Index::Abstract if you're curious) — this one is specialized to work with the BerkeleyDB-indexed "common" flat file format that got worked out at the 2002 BioHackathon. iconic honestly. ⭐

This object is the guts to the mechanism, and it's the specific objects that inherit from it that actually put it to work. main character energy, but backstage. 🎀

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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 one of the Bioperl mailing lists. Your participation is much appreciated. fr fr, 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.

ngl, going straight to the maintainer's DMs instead of the list is a vibe killer — the list has the experts, and they're ready. 😭

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 email or the web:

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

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👑 AUTHOR - Lincoln Stein 👑

Email - lstein@cshl.org

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🔥 SEE ALSO 🔥

• Bio::DB::Flat,

(yeah there's a comma and then nothing else. we love a dramatic pause. 💀)

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📖 APPENDIX 📖

The rest of the documentation details each of the object methods. Internal methods are usually preceded with an "_" (underscore). iykyk. 🧚

get_PrimarySeq_stream 🌀

Title   : get_PrimarySeq_stream
Usage   : $stream = get_PrimarySeq_stream
Function: Makes a Bio::DB::SeqStreamI compliant object
          which provides a single method, next_primary_seq
Returns : Bio::DB::SeqStreamI
Args    : none

so you get back a Bio::DB::SeqStreamI-compliant object with exactly one method to its name: next_primary_seq. minimalism. slay. ✨

get_all_primary_ids 🎀

Title   : get_all_primary_ids
Usage   : @ids = $seqdb->get_all_primary_ids()
Function: gives an array of all the primary_ids of the
          sequence objects in the database.
Example :
Returns : an array of strings
Args    : none

every primary_id in the database, handed to you as an array of strings. no args, no drama. 💜

To Be Implemented in Subclasses ⚠️

The following methods MUST be implemented by subclasses.

bestie this is a hard requirement, not a suggestion. no cap. 🚨

May Be Overridden in Subclasses 🌈

The following methods MAY be overridden by subclasses.

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and that's the whole page, periodt. this was Bio::D...t::BDB(3pm) from perl v5.32.1, dated 2021-08-15 — go forth and index your flat files, gorgeous. 💖✨🎀