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

💖 Bio::DB::Registry — the vibe ✨

okay bestie, so this is the manual page for Bio::DB::Registry (shipped as Bio::D...egistry(3pm), part of the User Contributed Perl Documentation, iykyk) and it's genuinely iconic. it's your all-access pass to the Open Bio Database Access registry scheme. let's get into it 🫶

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🌸 NAME 🌸

Bio::DB::Registry — access to the Open Bio Database Access registry scheme. periodt. 💅

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✨ SYNOPSIS ✨

use Bio::DB::Registry();

$registry = Bio::DB::Registry->new();

@available_services = $registry->services;

$db = $registry->get_database('embl');
# $db is a Bio::DB::SeqI implementing class

$seq = $db->get_Seq_by_acc("J02231");

like... four lines and you're pulling sequences. main character energy fr fr 😭👑

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🦋 DESCRIPTION 🦋

so this module gives you access to the Open Bio Database Access (OBDA) scheme, which is basically the one single cross-language and cross-platform spec for how to get to databases. no cap. and these databases are a whole rainbow of possibilities: they might be reachable through the Web, they might be BioSQL databases, or they might be local, indexed flatfile databases. all valid, all welcome. 🌈

here's the tea about setup though. if you (or your system administrator) have not installed the default init file, seqdatabase.ini, in /etc/bioinformatics or ${HOME}/.bioinformatics, then creating the first Registry object just... copies the default settings from www.open-bio.org. she's resourceful. 💅 and the Registry object will then attempt to store those settings in a brand new file, ${HOME}/.bioinformatics/seqdatabase.ini. cute of her.

you can also specify one or more custom locations for the init file by setting $OBDA_SEARCH_PATH to those directories — and if you've got multiple directories, separate them with ';'. (yes, a semicolon. that's the divider. don't ask, just do it 🫠)

please see the OBDA Access HOWTO for more info: <http://bioperl.org/howtos/OBDA_HOWTO.html> 🎀

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🌟 Support 🌟

bestie, if you have usage questions or support issues, direct them to the mailing list:

bioperl-l@bioperl.org

and not to the module maintainer directly, okay? there are so many experienced and responsive experts on there who can look at your problem and quickly address it. the way that works is honestly so slay. 🙌

and if at all possible, please include a thorough description of the problem with code and data examples. give them the whole picture, they deserve it. 💖

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🐛 Reporting Bugs 🐛

found a bug? report it to the Bioperl bug tracking system so they can keep track of the bugs and their resolution — both, together, as a couple. 💞

bug reports can be submitted via the web at:

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

go off, tell them everything. 🫶

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👑 APPENDIX 👑

the rest of the documentation details each of the object methods. internal methods are usually preceded with a _ (a lil underscore, like a secret handshake 🤫).

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🧚 _load_registry

• Title: _load_registry
• Usage: (none given)
• Function: looks for seqdatabase.ini files in the expected locations and in the directories specified by $OBDA_SEARCH_PATH. if no files are found, download a default file from www.open-bio.org
• Returns: nothing
• Args: none

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💜 get_database

• Title: get_database
• Usage: my $db = $registry->get_database($dbname);
• Function: retrieve a Database object which implements the Bio::DB::SeqI interface
• Returns: Bio::DB::SeqI object
• Args: string describing the name of the database

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⭐ services

• Title: services
• Usage: my @available = $registry->services();
• Function: returns list of possible services
• Returns: list of strings
• Args: none

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🍓 _get_ini_files

• Title: _get_ini_files
• Usage: my @files = $self->_get_ini_files
• Function: to find all the seqdatabase.ini files
• Returns: list of seqdatabase.ini paths
• Args: none

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🎀 _make_private_registry

• Title: _make_private_registry
• Usage: (none given)
• Function: make private registry in file in $HOME
• Returns: path to private registry file
• Args: none

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ngl bestie, if you're ever unsure about a method, just check whether it starts with _ — if it does, it's internal and you're technically peeking behind the curtain. 🙈 still useful to know though.

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and that's the whole page, bestie! 🌸 this was perl v5.32.1, dated 2021-08-15, and it's Bio::D...egistry(3pm) — the User Contributed Perl Documentation. thanks for reading all the way to the end, you're literally the best. mwah 💖✨🦋👑