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revision 1.5, Fri Jul 27 18:54:34 2007 UTC revision 1.7, Wed Nov 12 18:29:31 2008 UTC
# Line 29  Line 29 
29  print STDERR "Creating SBML model for genome $genome_id\n" if($debug);  print STDERR "Creating SBML model for genome $genome_id\n" if($debug);
30  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);
31  my @scenarios = @{Scenario->get_genome_scenarios($genome_id,1)};  my @scenarios = @{Scenario->get_genome_scenarios($genome_id,1)};
32  my $filebase = $fig->model_directory($genome_id)."/Analysis/";  my $filebase = $fig->scenario_directory($genome_id)."/Analysis/";
33    
34  my %input_cpds;  my %input_cpds;
35  open(INPUTS,$filebase."inputs.txt")  open(INPUTS,$filebase."inputs.txt")
# Line 166  Line 166 
166      {      {
167          print OUT " G  $id\n"; #regular cellular          print OUT " G  $id\n"; #regular cellular
168          push @all_cpds, $id;          push @all_cpds, $id;
169            $id = substr($id,1);
170            print OUT " G  E$id\n"; #extra cellular
171            push @all_cpds, "E".$id;
172      }      }
173  }  }
174    
# Line 273  Line 276 
276          next;          next;
277      }      }
278      my $temp  = substr($cid,1);      my $temp  = substr($cid,1);
279      if(!$input_cpds{$cid} && !$output_cpds{$cid} && !$biomass_cpds{$cid})      if(!$input_cpds{$cid} && !$output_cpds{$cid})
280      {      {
281          print OUT "    T$temp    E$temp              1\n";          print OUT "    T$temp    E$temp              1\n";
282          print OUT "    T$temp    C$temp             -1\n";          print OUT "    T$temp    C$temp             -1\n";
283      }      }
284      elsif(!$output_cpds{$cid} && !$biomass_cpds{$cid})      if(!$output_cpds{$cid})
285      {      {
286          print OUT "    S$temp    E$temp             -1\n";          print OUT "    S$temp    E$temp             -1\n";
287      }      }
# Line 319  Line 322 
322      print OUT " UP RBOUND    T$cid            1000\n";      print OUT " UP RBOUND    T$cid            1000\n";
323      print OUT " UP RBOUND    S$cid            1000\n";      print OUT " UP RBOUND    S$cid            1000\n";
324  }  }
 #sink reactions here eh.  
325    
326    
327  print OUT "ENDATA\n";  print OUT "ENDATA\n";

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