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BP_PROCESS_WORMBASE(1)User Contributed Perl DocumentatioBP_PROCESS_WORMBASE(1)

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.

perl v5.24.1			  2017-07-08		BP_PROCESS_WORMBASE(1)

NAME | SYNOPSIS | DESCRIPTION | SEE ALSO | AUTHOR

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