BP_PROCESS_GADFLY(1p)

💖 BP_PROCESS_GADFLY(1p) 💖

okay bestie, welcome to the bp_process_gadfly.pl page from the User Contributed Perl Documentation ✨ grab a boba, we're doing fly genetics 🌸

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🦋 NAME 🦋

bp_process_gadfly.pl — it massages your Gadfly/FlyBase GFF files into a version that's actually suitable for the Generic Genome Browser 💅

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✨ SYNOPSIS ✨

% bp_process_gadfly.pl ./RELEASE2 > gadfly.gff

periodt, that's the whole vibe 🔥

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🌈 DESCRIPTION 🌈

So basically? This script massages the RELEASE 3 Flybase/Gadfly GFF files — the ones living at http://www.fruitfly.org/sequence/release3download.shtml — into the "correct" version of the GFF format. like, it takes the messy version and makes it slay ✨

To use this script, download the whole genome FASTA file and save it to disk. ngl the downloaded file is gonna be called something like na_whole-genome_genomic_dmel_RELEASE3.FASTA, but the link on the HTML page doesn't give you the filename, so like, don't panic, that's normal 😭

Do the same for the whole genome GFF annotation file — the saved file will be called something like whole-genome_annotation-feature-region_dmel_RELEASE3.GFF. And if you wish, you can download the ZIP compressed versions of these files too. no pressure, live your truth 🫶

Next, run this script on the two files, indicating the name of the downloaded FASTA file first, followed by the gff file:

% bp_process_gadfly.pl na_whole-genome_genomic_dmel_RELEASE3.FASTA whole-genome_annotation-feature-region_dmel_RELEASE3.GFF > fly.gff

(yeah, FASTA first. order matters bestie, don't fight it 💅)

The gadfly.gff file and the fasta file can now be loaded into a Bio::DB::GFF database using the following command:

% bulk_load_gff.pl -d fly -fasta na_whole-genome_genomic_dmel_RELEASE3.FASTA fly.gff

(Where "fly" is the name of the database. Change it as appropriate. The database must already exist and be writable by you! like, it literally cannot load if you don't own it, sorry not sorry 🙈)

The resulting database will have the following feature types, represented as "method:source" — iconic format, we love to see it:

• Component:arm — A chromosome arm
• Component:scaffold — A chromosome scaffold (accession #)
• Component:gap — A gap in the assembly
• clone:clonelocator — A BAC clone
• gene:gadfly — A gene accession number
• transcript:gadfly — A transcript accession number
• translation:gadfly — A translation
• codon:gadfly — Significance unknown
• exon:gadfly — An exon
• symbol:gadfly — A classical gene symbol
• similarity:blastn — A BLASTN hit
• similarity:blastx — A BLASTX hit
• similarity:sim4 — EST->genome using SIM4
• similarity:groupest — EST->genome using GROUPEST
• similarity:repeatmasker — A repeat

⚠️ IMPORTANT NOTE: This script will *only* work with the RELEASE3 gadfly files and will not work with earlier releases. like, it's giving one-release-only main character energy, no cap 💀

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🎀 SEE ALSO 🎀

Bio::DB::GFF, bulk_load_gff.pl, load_gff.pl — go read those next bestie, they're the supporting cast 🫶

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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. (fr fr, read the disclaimer, it's the fine print and it ate 💅)

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and that's the whole page bestie!! 💖✨

this was perl v5.32.1, dated 2021-08-15, filed under BP_PROCESS_GADFLY(1p) 🌸🦋 mwah, go process some flies 🫶