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revision 1.1, Tue Jul 17 19:11:59 2007 UTC revision 1.2, Fri Jul 20 15:05:54 2007 UTC
# Line 3  Line 3 
3  #  #
4  #  #
5  use strict;  use strict;
6  use FIG;  use FIGV;
7  use Scenario;  use Scenario;
8    
9  my ($genome_id) = @ARGV;  my ($genome_id,$orgdir) = @ARGV;
10    
11  my $debug = 0;  my $debug = 0;
 my $fig = new FIG;  
12    
13  unless (scalar (@ARGV) == 1)  
14    unless (scalar (@ARGV) >= 1)
15  {  {
16      print STDERR "usage: make_SBML_model <genome_id>\n";      print STDERR "usage: make_SBML_model <genome_id>\n";
17      exit(-1);      exit(-1);
18  }  }
19  chomp $genome_id;  chomp $genome_id;
20    my $fig;
21    if($orgdir)
22    {
23        $fig = new FIGV($orgdir);
24    }
25    else
26    {
27        $fig = new FIGV;
28    }
29    Scenario::set_fig($fig);
30  print STDERR "Creating SBML model for genome $genome_id\n" if($debug);  print STDERR "Creating SBML model for genome $genome_id\n" if($debug);
31  print STDERR "\tStage 1 - Loading Scenarios, model inputs and biomass\n" if($debug);  print STDERR "\tStage 1 - Loading Scenarios, model inputs and biomass\n" if($debug);
32  my @scenarios = @{Scenario->get_genome_scenarios($genome_id,1)};  my @scenarios = @{Scenario->get_genome_scenarios($genome_id,1)};
33  my $filebase = "$FIG_Config::var/Models/$genome_id/Analysis/";  my $filebase = $fig->model_directory($genome_id)."/Analysis/";
34    
35  my %input_cpds;  my %input_cpds;
36  open(INPUTS,$filebase."inputs.txt")  open(INPUTS,$filebase."inputs.txt")

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