LOAD_GENBANK(1p)

📦
version 2.56 · 5 versions
, in ubuntu questing

🌸 NAME 🌸

load_genbank.pl — bestie, this is the little script that loads a Bio::DB::GFF database straight from GENBANK files. It lives in the User Contributed Perl Documentation corner of the LOAD_GENBANK(1p) manual, and it is so ready to be your new fave.

✨ SYNOPSIS ✨

% load_genbank.pl -d genbank -f localfile.gb
% load_genbank.pl -d genbank -a AP003256
🫶 quick heads up, bestie: the script bp_genbank2gff.pl in the BioPerl distribution is literally the same script as this one. Same vibes, different name. iykyk.

💅 DESCRIPTION 💅

okay so. This script loads a Bio::DB::GFF database with all the features chillin' inside either a local genbank file or an accession that gets fetched from genbank. It's giving ✨flexible✨.

There's a whole squad of command-line options that let you control which database to load and whether you're allowed to overwrite a database that already exists. Choose wisely, queen 👑.

ngl, this script currently only uses MySQL. It's a proof-of-principle situation — it could easily be extended to work with other RDMS that GFF supports through adaptors, but for now? MySQL only. periodt.

🎀 COMMAND-LINE OPTIONS 🎀

bestie, these options can be abbreviated to single-letter options. e.g. -d instead of --database. So cute, so efficient 💖.

  • --create — force creation and initialization of the database. it's giving "build it from scratch, no cap" 🏗️
  • --dsn <dsn> — the data source. default is dbi:mysql:test ✨
  • --user <user> — username for mysql authentication 🔑
  • --pass <password> — password for mysql authentication 🤫
  • --proxy <proxy> — proxy server to use for remote access 🌐
  • --file — arguments that follow are Genbank/EMBL file names (this is the default behavior) 📁
  • --accession — arguments that follow are genbank accession numbers 🔢
  • --stdout — write the converted GFF file to stdout rather than loading it 👀

🦋 SEE ALSO 🦋

  • Bio::DB::GFF
  • bulk_load_gff.pl
  • load_gff.pl

go read those, they're iconic too 🫶

🌈 AUTHOR 🌈

  • Scott Cain, cain@cshl.org
  • Lincoln Stein, lstein@cshl.org

Copyright (c) 2003 Cold Spring Harbor Laboratory

This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. See DISCLAIMER.txt for disclaimers of warranty.

and that's the whole page, bestie 💖 this lil' manual page came to you courtesy of perl v5.40.0, dated 2024-10-20, under the LOAD_GENBANK(1p) title. slay, go load some genbank files 🌸✨🦋

📦 where this page comes from