BP_PRO...ORMBASE(1p)

💖 NAME 💖

bp_process_wormbase.pl — the little script that takes your WormBase GFF files and massages them into a version that's actually suitable for the Generic Genome Browser. bestie it's a glow-up for your data, no cap ✨

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🎀 SYNOPSIS 🎀

% bp_process_wormbase.pl ./WS61 > wormbase.gff

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🦋 DESCRIPTION 🦋

okay so picture this: this script takes the Wormbase GFF files that live over at ftp://www.wormbase.org/pub/wormbase/GENE_DUMPS and massages them into a version of the GFF format that's suitable for display by the generic genome browser. it's giving transformation sequence 💅

what does the massaging actually do, you ask? mainly two things:

• it adds comments to the annotations 💬
• it designates certain well-spaced genetic loci as framework landmarks 📍

heads up: this script requires the AcePerl distribution, which is available on CPAN (go look for the "Ace" module). no AcePerl, no vibes, periodt.

🌸 how to actually use it 🌸

1. get the WormBase GFF files from that FTP site listed above and place them in a directory.
2. honestly it might be a good idea to name the directory after the current release, such as WS61 — cute and organized, main character energy 👑
3. you do not need to uncompress the files. we love a low-effort step 🙈

then give that directory as the argument to this script and capture the script's output to a file:

% bp_process_wormbase.pl ./WS61 > wormbase.gff

⏳ real talk: it may take a while before you see output from this script, because it must first fetch the gene and protein database from the remote AceDB running at www.wormbase.org. so don't panic and don't refresh, she's just fetching, bestie 😭

once you've got it, the wormbase.gff file can then be loaded into a Bio::DB::GFF database using the following command:

% bulk_load_gff.pl -d <databasename> wormbase.gff

and that's the whole pipeline, slay 🫶

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🌈 SEE ALSO 🌈

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

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💜 AUTHOR 💜

Lincoln Stein <lstein@cshl.org>

Copyright (c) 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. See DISCLAIMER.txt for disclaimers of warranty.

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and that's the tea, bestie 🍓 this page came to you courtesy of perl v5.30.0, dated 2019-11-25 — iconic behavior, see you in the next one 💖✨