BP_PROCESS_WORMBASE(1)User Contributed Perl DocumentatioBP_PROCESS_WORMBASE(1)NAME
process_wormbase.pl - Massage WormBase GFF files into a version
suitable for the Generic Genome Browser
SYNOPSIS
% process_wormbase.pl ./WS61 > wormbase.gff
DESCRIPTION
This script massages the Wormbase GFF files located at
ftp://www.wormbase.org/pub/wormbase/GENE_DUMPS into a version of the
GFF 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.
This script requires the AcePerl distribution, which is available on
CPAN (look for the "Ace" module).
To use this script, get the WormBase GFF files from the FTP 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 WS61. You do not need
to uncompress the files.
Then give that directory as the argument to this script and capture the
script's output to a file:
% process_wormbase.pl ./WS61 > wormbase.gff
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:
% bulk_load_gff.pl -d <databasename> wormbase.gff
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 v5.14.1 2011-07-22 BP_PROCESS_WORMBASE(1)
