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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 v5.24.1			  2017-07-08		  BP_PROCESS_GADFLY(1)

NAME | SYNOPSIS | DESCRIPTION | SEE ALSO | AUTHOR

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