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
7 suitable 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
14 ftp://www.wormbase.org/pub/wormbase/GENE_DUMPS into a version of the
15 GFF format suitable for display by the generic genome browser. It
16 mainly adds comments to the annotations and designates certain well-
17 spaced genetic 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
34 running 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
49 disclaimers of warranty.
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53perl v5.12.0 2010-04-29 BP_PROCESS_WORMBASE(1)