process_gadfly.pl - Massage Gadfly/FlyBase GFF files into a version suitable for the Generic Genome Browser
% process_gadfly.pl ./RELEASE2 > gadfly.gff
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.
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.
Next run this script on the two files, indicating the name of the downloaded FASTA file first, followed by the gff file:
% 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.
Lincoln Stein <email@example.com>.
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.