1BP_PROCESS_WORMBASE(1)User Contributed Perl DocumentationBP_PROCESS_WORMBASE(1)
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NAME

6       process_wormbase.pl - Massage WormBase GFF files into a version suit‐
7       able for the Generic Genome Browser
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SYNOPSIS

10         % process_wormbase.pl ./WS61 > wormbase.gff
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DESCRIPTION

13       This script massages the Wormbase GFF files located at ftp://www.worm‐
14       base.org/pub/wormbase/GENE_DUMPS into a version of the GFF format suit‐
15       able for display by the generic genome browser.  It mainly adds com‐
16       ments to the annotations and designates certain well-spaced genetic
17       loci as framework landmarks.
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19       This script requires the AcePerl distribution, which is available on
20       CPAN (look for the "Ace" module).
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22       To use this script, get the WormBase GFF files from the FTP site listed
23       above and place them in a directory.  It might be a good idea to name
24       the directory after the current release, such as WS61.  You do not need
25       to uncompress the files.
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27       Then give that directory as the argument to this script and capture the
28       script's output to a file:
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30         % process_wormbase.pl ./WS61 > wormbase.gff
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32       It may take a while before you see output from this script, since it
33       must first fetch gene and protein database from the remote AceDB run‐
34       ning at www.wormbase.org.  The wormbase.gff file can then be loaded
35       into a Bio::DB::GFF database using the following command:
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37         % bulk_load_gff.pl -d <databasename> wormbase.gff
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SEE ALSO

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

43       Lincoln Stein <lstein@cshl.org>
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45       Copyright (c) 2002 Cold Spring Harbor Laboratory
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47       This library is free software; you can redistribute it and/or modify it
48       under the same terms as Perl itself.  See DISCLAIMER.txt for dis‐
49       claimers of warranty.
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53perl v5.8.8                       2007-05-07            BP_PROCESS_WORMBASE(1)
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