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revision 1.4, Thu Dec 10 19:31:12 2009 UTC revision 1.6, Mon Sep 20 21:38:53 2010 UTC
# Line 9  Line 9 
9  use Data::Dumper;  use Data::Dumper;
10  use Getopt::Long;  use Getopt::Long;
11    
12  my $usage = "Usage: $0 [--verbose] [--test] username password < contig-id-list\n";  my $usage = "Usage: $0 [--determineFamily] [--url server-url] [--nonActive] [--verbose] [--test] username password < contig-id-list\n";
13    
14  my $verbose;  my $verbose;
15  my $use_test_server = 0;  my $use_test_server = 0;
16    my $non_active = 0;
17    my $url;
18    my $determine_family = 0;
19  if (!GetOptions('verbose' => \$verbose,  if (!GetOptions('verbose' => \$verbose,
20                    "nonActive" => \$non_active,
21                    "url=s" => \$url,
22                    "determineFamily" => \$determine_family,
23                  'test' => \$use_test_server))                  'test' => \$use_test_server))
24  {  {
25      die $usage;      die $usage;
# Line 23  Line 29 
29    
30  my $username = shift;  my $username = shift;
31  my $password = shift;  my $password = shift;
32    my $opts = {};
33  my $rast = RASTserver->new($username, $password, { -test => $use_test_server});  if ($url)
34    {
35        $opts->{-server} = $url;
36    }
37    if ($use_test_server)
38    {
39        $opts->{-test} = 1;
40    }
41    my $rast = RASTserver->new($username, $password, $opts);
42    
43  my @input_ids = <STDIN>;  my @input_ids = <STDIN>;
44  chomp @input_ids;  chomp @input_ids;
# Line 123  Line 137 
137          -geneticCode => $biggest->{genetic_code},          -geneticCode => $biggest->{genetic_code},
138          -keepGeneCalls => 0,          -keepGeneCalls => 0,
139          -geneCaller => 'RAST',          -geneCaller => 'RAST',
140            -nonActive => $non_active,
141            -determineFamily => $determine_family,
142      };      };
143    
144      print "Submitting job to RAST for contigs @$ids with these parameters:\n";      print "Submitting job to RAST for contigs @$ids with these parameters:\n";

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