1BP_PROCESS_WORMBASE(1)User Contributed Perl DocumentationBP_PROCESS_WORMBASE(1)
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6 process_wormbase.pl - Massage WormBase GFF files into a version suit‐
7 able for the Generic Genome Browser
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10 % process_wormbase.pl ./WS61 > wormbase.gff
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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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40 Bio::DB::GFF, bulk_load_gff.pl, load_gff.pl
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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)