NAME¶
bp_process_wormbase.pl - Massage WormBase GFF files into a version suitable for
the Generic Genome Browser
SYNOPSIS¶
% bp_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:
% bp_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.