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 scripts 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