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.\"
.IX Title "BP_PROCESS_GADFLY 1p"
.TH BP_PROCESS_GADFLY 1p "2020-10-28" "perl v5.30.3" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
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.SH "NAME"
bp_process_gadfly.pl \- Massage Gadfly/FlyBase GFF files into a version suitable for the Generic Genome Browser
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 1
\&  % bp_process_gadfly.pl ./RELEASE2 > gadfly.gff
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
This script massages the \s-1RELEASE 3\s0 Flybase/Gadfly \s-1GFF\s0 files located at
http://www.fruitfly.org/sequence/release3download.shtml into the \*(L"correct\*(R"
version of the \s-1GFF\s0 format.
.PP
To use this script, download the whole genome \s-1FASTA\s0 file and save it
to disk.  (The downloaded file will be called something like
\&\*(L"na_whole\-genome_genomic_dmel_RELEASE3.FASTA\*(R", but the link on the
\&\s-1HTML\s0 page doesn't give the filename.)  Do the same for the whole
genome \s-1GFF\s0 annotation file (the saved file will be called something
like \*(L"whole\-genome_annotation\-feature\-region_dmel_RELEASE3.GFF\*(R".)  If
you wish you can download the \s-1ZIP\s0 compressed versions of these files.
.PP
Next run this script on the two files, indicating the name of the
downloaded \s-1FASTA\s0 file first, followed by the gff file:
.PP
.Vb 1
\& % bp_process_gadfly.pl na_whole\-genome_genomic_dmel_RELEASE3.FASTA whole\-genome_annotation\-feature\-region_dmel_RELEASE3.GFF > fly.gff
.Ve
.PP
The gadfly.gff file and the fasta file can now be loaded into a Bio::DB::GFF database
using the following command:
.PP
.Vb 1
\&  % bulk_load_gff.pl \-d fly \-fasta na_whole\-genome_genomic_dmel_RELEASE3.FASTA fly.gff
.Ve
.PP
(Where \*(L"fly\*(R" is the name of the database.  Change it as appropriate.
The database must already exist and be writable by you!)
.PP
The resulting database will have the following feature types
(represented as \*(L"method:source\*(R"):
.PP
.Vb 10
\&  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
.Ve
.PP
\&\s-1IMPORTANT NOTE:\s0 This script will *only* work with the \s-1RELEASE3\s0 gadfly
files and will not work with earlier releases.
.SH "SEE ALSO"
.IX Header "SEE ALSO"
Bio::DB::GFF, bulk_load_gff.pl, load_gff.pl
.SH "AUTHOR"
.IX Header "AUTHOR"
Lincoln Stein, lstein@cshl.org
.PP
Copyright (c) 2002 Cold Spring Harbor Laboratory
.PP
This library is free software; you can redistribute it and/or modify
it under the same terms as Perl itself.  See \s-1DISCLAIMER\s0.txt for
disclaimers of warranty.