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.IX Title "BP_PROCESS_WORMBASE 1p"
.TH BP_PROCESS_WORMBASE 1p "2018-10-27" "perl v5.26.2" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
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.SH "NAME"
bp_process_wormbase.pl \- Massage WormBase GFF files into a version suitable for the Generic Genome Browser
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 1
\&  % bp_process_wormbase.pl ./WS61 > wormbase.gff
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
This script massages the Wormbase \s-1GFF\s0 files located at
ftp://www.wormbase.org/pub/wormbase/GENE_DUMPS into a version of the
\&\s-1GFF\s0 format suitable for display by the generic genome browser.  It
mainly adds comments to the annotations and designates certain
well-spaced genetic loci as framework landmarks.
.PP
This script requires the AcePerl distribution, which is available on
\&\s-1CPAN\s0 (look for the \*(L"Ace\*(R" module).
.PP
To use this script, get the WormBase \s-1GFF\s0 files from the \s-1FTP\s0 site
listed above and place them in a directory.  It might be a good idea
to name the directory after the current release, such as \s-1WS61.\s0  You do
not need to uncompress the files.
.PP
Then give that directory as the argument to this script and capture
the script's output to a file:
.PP
.Vb 1
\&  % bp_process_wormbase.pl ./WS61 > wormbase.gff
.Ve
.PP
It may take a while before you see output from this script, since it
must first fetch gene and protein database from the remote AceDB
running at www.wormbase.org.
The wormbase.gff file can then be loaded into a Bio::DB::GFF database
using the following command:
.PP
.Vb 1
\&  % bulk_load_gff.pl \-d <databasename> wormbase.gff
.Ve
.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.