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

✨ NAME ✨

okay bestie, so Bio::D...iofetch(3pm) — that's the page you're on, and the actual thing it documents is Bio::DB::GFF::Adaptor::biofetch 💅 — and what it does is cache BioFetch objects in a Bio::DB::GFF database. that's it, that's the whole vibe.

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📖 SYNOPSIS 📖

Proof of principle.  Not for production use.

fr fr, that's the entire synopsis. no flags, no usage line, just a warning label 😭 iconic of them honestly.

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💖 DESCRIPTION 💖

so here's the tea 🫖: this adaptor is a proof-of-principle. it's used to fetch BioFetch sequences into a Bio::DB::GFF database as needed — and ngl, it currently uses a hard-coded EMBL database. which means you can use the Generic Genome Browser as a Genbank/EMBL browser 🌈. slay.

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👑 AUTHOR 👑

Lincoln Stein <lstein@cshl.org> — the icon, the legend, the main character 🎀

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 💜

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new

• Title: new
• Usage: $db = Bio::DB::GFF->new(-adaptor=>'biofetch',@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

This is the constructor for the adaptor, bestie — it gets called automatically by Bio::DB::GFF->new, you don't have to do it yourself 💅. 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']
• -source — source to use for loaded features ('EMBL')

okay so let's break that down 🧚:

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

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. don't forget the arrayref, i'm begging you 😭

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and that's the whole page!! this was perl v5.30.0, dated 2020-01-13, and it came to you via the User Contributed Perl Documentation crew 🎀 no cap, go forth and cache responsibly 💖✨🦋