BP_PROCESS_GADFLY(1)

📦 version 1.7.8, in nixos 26.05, nixpkgs unstable

💖 BP_PROCESS_GADFLY(1) 💖

okay so this is a User Contributed Perl Documentation page, bestie, and it's all about bp_process_gadfly.pl. Buckle up, it's giving bioinformatics but make it cute. 🧬✨

🌸 NAME 🌸

bp_process_gadfly.pl — this script massages Gadfly/FlyBase GFF files into a version suitable for the Generic Genome Browser. Yes, "massages." That's the word. Slay. 💅

✨ SYNOPSIS ✨

  % bp_process_gadfly.pl ./RELEASE2 > gadfly.gff

🦋 DESCRIPTION 🦋

Okay so this script massages the RELEASE 3 Flybase/Gadfly GFF files located at http://www.fruitfly.org/sequence/release3download.shtml into the "correct" version of the GFF format. Periodt. 🎀

To use this script, download the whole genome FASTA file and save it to disk. The downloaded file will be called something like "na_whole-genome_genomic_dmel_RELEASE3.FASTA", but the link on the HTML page doesn't give the filename. 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". If you wish, you can download the ZIP compressed versions of these files. Lowkey convenient. 🫶

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

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!)

The resulting database will have the following feature types (represented as "method:source"):

  • 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. Not me warning you dramatically, but like… I am. 😭💀

🎀 SEE ALSO 🎀

Go peek at Bio::DB::GFF, bulk_load_gff.pl, and load_gff.pl. iykyk. 👑

🌈 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.

okay bye bestie 💖 this was BP_PROCESS_GADFLY(1) from perl v5.42.3, dated 2021-02-03. mwah. 🍓✨

📦 where this page comes from