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1 : gdpusch 1.1 # -*- perl -*-
2 :    
3 :     #
4 :     # This is a SAS Component
5 :     #
6 :    
7 :     ########################################################################
8 :     # Copyright (c) 2003-2008 University of Chicago and Fellowship
9 :     # for Interpretations of Genomes. All Rights Reserved.
10 :     #
11 :     # This file is part of the SEED Toolkit.
12 :     #
13 :     # The SEED Toolkit is free software. You can redistribute
14 :     # it and/or modify it under the terms of the SEED Toolkit
15 :     # Public License.
16 :     #
17 :     # You should have received a copy of the SEED Toolkit Public License
18 :     # along with this program; if not write to the University of Chicago
19 :     # at info@ci.uchicago.edu or the Fellowship for Interpretation of
20 :     # Genomes at veronika@thefig.info or download a copy from
21 :     # http://www.theseed.org/LICENSE.TXT.
22 :     ########################################################################
23 :    
24 : gdpusch 1.2 my $usage = "svr_seed_table SEED_OrgDir > org.tab";
25 :    
26 : gdpusch 1.3 =head1 svr_seed_to_table SEED_OrgDir > org.tab
27 : gdpusch 1.2
28 :     Extract a tab-separated feature table from a SEED Genome Directory.
29 :     Table format is:
30 :    
31 :     Feature_ID Location Function
32 :    
33 :     =cut
34 :    
35 : gdpusch 1.1 use strict;
36 :     use warnings;
37 :    
38 :     use SeedV;
39 :    
40 :     my ($org_dir) = @ARGV;
41 : gdpusch 1.2 if ($org_dir =~ m/^-{1,2}help/o) {
42 :     print STDERR " usage: $usage\n";
43 :     exit(0);
44 :     }
45 :    
46 : gdpusch 1.1 (-d $org_dir) || die "Organism directory \'$org_dir\' does not exist";
47 :    
48 :     my $seedV = SeedV->new($org_dir);
49 :     $seedV->write_features_for_comparison(\*STDOUT);
50 :    
51 :     exit(0);

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