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BP_PROCESS_GADFLY(1)  User Contributed Perl Documentation BP_PROCESS_GADFLY(1)


NAME

       bp_process_gadfly.pl - Massage Gadfly/FlyBase GFF files into a version
       suitable for the Generic Genome Browser


SYNOPSIS

         % bp_process_gadfly.pl ./RELEASE2 > gadfly.gff


DESCRIPTION

       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:

        % 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.


SEE ALSO

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


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.

perl v5.20.2                      2015-09-15              BP_PROCESS_GADFLY(1)

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