bp_process_wormbase.pl man page on DragonFly

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BP_PROCESS_WORMBASE(1)User Contributed Perl DocumentatioBP_PROCESS_WORMBASE(1)

       bp_process_wormbase.pl - Massage WormBase GFF files into a version
       suitable for the Generic Genome Browser

	 % bp_process_wormbase.pl ./WS61 > wormbase.gff

       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

       Bio::DB::GFF, bulk_load_gff.pl, load_gff.pl

       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 v5.20.2			  2015-09-15		BP_PROCESS_WORMBASE(1)

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