BP_GENBANK2GFF(1p)

💖 BP_GENBANK2GFF(1p) 💖

okay bestie, welcome to bp_genbank2gff.pl — yes that's the whole name, and yes it slaps. it's a Perl script, it lives in the user-contributed Perl docs section of your manual, and it's about to load a whole GenBank file into a database like it's nothing. no cap. 🧬✨

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🌸 NAME 🌸

bp_genbank2gff.pl — literally just here to load a Bio::DB::GFF database from GENBANK files. that's the job. that's the whole vibe. 💅

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✨ SYNOPSIS ✨

the three ways you can pull up, fr fr:

% bp_genbank2gff.pl -d genbank -f localfile.gb
% bp_genbank2gff.pl -d genbank --accession AP003256
% bp_genbank2gff.pl --accession AP003256 --stdout

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🦋 DESCRIPTION 🦋

so what this script does is load a Bio::DB::GFF database with all the features that are chillin' inside either a local genbank file or an accession that it goes and fetches from genbank. and there's a whole menu of command-line options letting you pick which database gets loaded and whether you're allowed to just bulldoze an existing database that's already sitting there. choices, bestie. we love options. 👑

heads up though — the database has to already exist, and the current user needs to actually have the appropriate INSERT and UPDATE privileges. like, you can't just waltz in. 🙈

and the --create option? that one will initialize a brand new database with the appropriate schema — and it deletes any tables that were already there. so if there was stuff in there, it's gone gone. dramatic but true. 💀

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🎀 COMMAND-LINE OPTIONS 🎀

little pro tip: command-line options can be abbreviated to single-letter options. e.g. -d instead of --database. short queen energy.

• --create — force creation and initialization of database. fresh start, no notes.
• --dsn <dsn> — 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.
• --stdout — direct output to STDOUT.
• --adaptor <adaptor> — adaptor to use (eg dbi::mysql, dbi::pg, dbi::oracle).
• --viral — the genome you are loading is viral (changes tag choices).
• --source <source> — source field for features ['genbank'].

then, bestie, you pick EITHER one of these:

• --file — arguments that follow are Genbank/EMBL file names.
• --gb_folder — what follows is a folder full of gb files to process.
• --accession — arguments that follow are genbank accession numbers (not gi!).
• --acc_file — accession numbers (not gi!) in a file (one per line, no punc.).
• --acc_pipe — accession numbers (not gi!) from a STDIN pipe (one per line).

ok the not gi! thing is in there three whole times, so we're saying it three whole times. it's not gi. remember it. 💖

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🌈 SEE ALSO 🌈

go check out Bio::DB::GFF, bulk_load_gff.pl, and load_gff.pl. the whole friend group. 🫶

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👑 AUTHOR 👑

Scott Cain, cain@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.

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and that's the page, bestie 🎀 this was perl v5.30.0, dated 2020-01-13, filed under BP_GENBANK2GFF(1p) — mwah, iconic, go load some genomes. 💜🌸🦋