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

✨ NAME ✨

Bio::DB::GFF::Adaptor::biofetch_oracle — it's giving cache BioFetch objects in a Bio::DB::GFF database 💖 (yes bestie, that's the whole vibe of this module, and we're gonna walk through it together)

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🌸 SYNOPSIS 🌸

Proof of principle. Not for production use.

fr fr, they said it right there in the synopsis. Not a drill. Do not ship this to prod. 🙈

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🦋 DESCRIPTION 🦋

Okay so here's the tea 🍓: this adaptor is a proof-of-principle. It exists to fetch BioFetch sequences into a Bio::DB::GFF database as needed — and rn it currently uses a hard-coded EMBL database, which is a choice, but it's the choice they made. 💅

What does that buy you? It lets the Generic Genome Browser be used as a Genbank/EMBL browser. Iconic behavior honestly. 👑

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💜 AUTHOR 💜

Lincoln Stein <lstein@cshl.org>. 🫶

Copyright 2002 Cold Spring Harbor Laboratory.

This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. (periodt. that's the license, and she's generous ✨)

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🎀 new 🎀

• Title — new
• Usage — $db = Bio::DB::GFF->new(-adaptor=>'biofetch_oracle', -preferred_tags => \%preferred, @args)
• Function — create a new adaptor
• Returns — a Bio::DB::GFF object
• Args —
  • -adaptor : required. Which adaptor to use; biofetch for mysql, biofetch_oracle for Oracle
  • -preferred_tags : optional. A hash of {classname => weight,...} used to determine the class and name of the feature when a choice of possible feature classes is available (e.g. a feature has both a 'gene' and a 'locus' tag). Common defaults are provided that work well for eukaryotic features (but not well for viral/prokaryotic)
  • see below for additional arguments.
• Status — Public

So this is the constructor for the adaptor, and the way it works is that Bio::DB::GFF->new calls it automatically for you — you don't have to do the intro yourself, she's already friends with everybody. 💅

On top of the arguments that are common among all adaptors, these class-specific arguments are recognized:

• -dsn — the DBI data source, e.g. 'dbi:mysql:ens0040'
• -user — username for authentication
• -pass — the password for authentication
• -proxy — [['http','ftp'],'http://proxy:8080']
• -create — initialize the database

-dsn, -user and -pass indicate the local database to cache results in, and are as per Bio::DB::GFF::Adaptor::dbi. 🌈

The -proxy argument lets you set the biofetch web proxy, and it uses the same syntax described for the proxy() method of Bio::DB::WebDBSeqI — except that here the argument must be passed as an array reference. Lowkey the one gotcha in this whole page, so don't let it catch you slippin'. 😭

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okay that's the whole page bestie, you ate that 💅

signing off from perl v5.30.0, dated 2020-01-13, straight out of Bio::D...oracle(3pm) — mwah 🎀✨🦋