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revision 1.5, Wed Jul 15 23:39:58 2009 UTC revision 1.16, Tue Mar 1 22:26:34 2011 UTC
# Line 16  Line 16 
16  # Genomes at veronika@thefig.info or download a copy from  # Genomes at veronika@thefig.info or download a copy from
17  # http://www.theseed.org/LICENSE.TXT.  # http://www.theseed.org/LICENSE.TXT.
18  #  #
19  use FIGMODEL;  #use FIGMODEL;
20    
21  package ModelSaplingLoader;  package ModelSaplingLoader;
22      use strict;      use strict;
23      use Tracer;      use Tracer;
24      use ERDB;      use ERDB;
     use HTTP::Date;  
25      use base 'BaseSaplingLoader';      use base 'BaseSaplingLoader';
26    
27  =head1 Sapling ModelLoader Load Group Class  =head1 Sapling Model Load Group Class
28    
29  =head2 Introduction  =head2 Introduction
30    
31  The ModelLoader Load Group includes all of the major mdl tables.  The Model Load Group includes a small set of tables that describe reactions and compounds
32    and how they relate to the models in the main model database.
33    
34  =head3 new  =head3 new
35    
36      my $sl = ModelLoaderSaplingLoader->new($erdb, $options, @tables);      my $sl = ModelSaplingLoader->new($erdb, $options, @tables);
37    
38  Construct a new ModelLoaderSaplingLoader object.  Construct a new ModelSaplingLoader object.
39    
40  =over 4  =over 4
41    
# Line 59  Line 59 
59      # Get the parameters.      # Get the parameters.
60      my ($class, $erdb, $options) = @_;      my ($class, $erdb, $options) = @_;
61      # Create the table list.      # Create the table list.
62      my @tables = sort qw(StructuralCue IsFoundIn Compound HasAliasOf AliasType HasReactionAliasOf Reaction Involves IsTriggeredBy RoleSet IsCombinationOf IsCategorizedInto EcNumber IsConsistentWith IsStimulatedBy  FeatureSet IsSetOf IsRequiredBy Model Encompasses IsModeledBy);      my @tables = qw(Compound Reaction EcNumber Model Media IsTriggeredBy
63                        IsCategorizedInto IsConsistentWith IsModeledBy Involves
64                        IsRequiredBy);
65      # Create the BaseSaplingLoader object.      # Create the BaseSaplingLoader object.
66      my $retVal = BaseSaplingLoader::new($class, $erdb, $options, @tables);      my $retVal = BaseSaplingLoader::new($class, $erdb, $options, @tables);
67        # Create the reaction tracking hash.
68        $retVal->{reactions} = {};
69      # Return it.      # Return it.
70      return $retVal;      return $retVal;
71  }  }
# Line 72  Line 76 
76    
77      $sl->Generate();      $sl->Generate();
78    
79  Generate the data for the mdl files.  Generate the data for the model files.
80    
81  =cut  =cut
82    
# Line 81  Line 85 
85      my ($self) = @_;      my ($self) = @_;
86      # Get the database object.      # Get the database object.
87      my $erdb = $self->db();      my $erdb = $self->db();
     # Get the source object.  
     my $fig = $self->source();  
88      # Is this the global section?      # Is this the global section?
     my $model = new FIGMODEL;  
89      if ($self->global()) {      if ($self->global()) {
90          #Loading the model entities and relationships          # Load the tables from the model dump files.
91          $self->LoadModels($model);          $self->LoadModelFiles();
         #Loading structural cues first  
         $self->LoadStructuralCues($model);  
         #Loading the compound entities and relationships  
         $self->LoadCompounds($model);  
         #Loading the reaction, and EC number entities and relationships  
         $self->LoadReactions($model);  
         #Loading the role set entity and relationships  
         $self->LoadRoleSets($model);  
92      } else {      } else {
93          # Get the section ID.          # Get the section ID.
94          my $genomeID = $self->section();          my $genomeID = $self->section();
# Line 103  Line 96 
96      }      }
97  }  }
98    
99  #This function loads all of the StructuralCue entities  =head3 LoadModelFiles
 sub LoadStructuralCues {  
     my ($self,$model) = @_;  
100    
101      #Getting the list of structural cue filenames      $sl->LoadModelFiles();
     my @CuesList = glob($model->{"Reaction database directory"}->[0]."cues/");  
     my %CuePriorities;  
     #TODO:NEED TO POPULATE THE PRIORITIES HASH  
     foreach my $CueFile (@CuesList) {  
         my $Object = FIGMODELObject->load($CueFile,"\t");  
         if (defined($Object) && defined($Object->{"NAME"}->[0])) {  
             my @LoadingArray = ($Object->{"NAME"}->[0],-1,0,0,"","","","");  
             if (defined($CuePriorities{$Object->{"NAME"}->[0]})) {  
                 $LoadingArray[1] = $CuePriorities{$Object->{"NAME"}->[0]};  
             }  
             if (defined($Object->{"SMALL_MOLECULE"}->[0])) {  
                 $LoadingArray[2] = $Object->{"SMALL_MOLECULE"}->[0];  
             }  
             if (defined($Object->{"CHARGE"}->[0])) {  
                 $LoadingArray[3] = $Object->{"CHARGE"}->[0];  
             }  
             if (defined($Object->{"FORMULA"}->[0])) {  
                 $LoadingArray[4] = $Object->{"FORMULA"}->[0];  
             }  
             if (defined($Object->{"ENERGY"}->[0])) {  
                 $LoadingArray[5] = $Object->{"ENERGY"}->[0];  
             }  
             if (defined($Object->{"ERROR"}->[0])) {  
                 $LoadingArray[6] = $Object->{"ERROR"}->[0];  
             }  
             if (defined($Object->{"STRUCTURAL_CUES"}->[0])) {  
                 $LoadingArray[7] = join(";",@{$Object->{"STRUCTURAL_CUES"}});  
             }  
             $self->PutE(StructuralCue => $LoadingArray[0], priority => $LoadingArray[1], smallMolecule => $LoadingArray[2], charge => $LoadingArray[3], formula => $LoadingArray[4],deltaG => $LoadingArray[5], deltaGerr => $LoadingArray[6], subgroups => $LoadingArray[7]);  
         }  
     }  
 }  
102    
103  sub LoadCompounds {  Load the data from the six model dump files.
     my ($self,$model) = @_;  
104    
105      #First getting the compound table which has a list of all compounds in the database as well as alot of compound information  =cut
     my $CompoundTable = $model->GetDBTable("COMPOUNDS");  
106    
107      #Adding the universal AliasType that will always exist  # hash of ubiquitous compounds.
108      $self->PutE(AliasType => "NAME", source => "NONE");  use constant UBIQUITOUS => {
109      $self->PutE(AliasType => "SEARCHNAME", source => "NONE");      cpd00001 => 'OH-',
110      $self->PutE(AliasType => "KEGG", source => "http://www.kegg.com/");      cpd00002 => 'ATP',
111      $self->PutE(AliasType => "ARGONNE", source => "OBSOLETE IDs");      cpd00003 => 'Nicotinamideadeninedinucleotide',
112        cpd00004 => 'Nicotinamideadeninedinucleotide-reduced',
113        cpd00005 => 'Nicotinamideadeninedinucleotidephosphate-reduced',
114        cpd00006 => 'Nicotinamideadeninedinucleotidephosphate',
115        cpd00007 => 'Oxygen',
116        cpd00008 => 'ADP',
117        cpd00009 => 'Orthophosphoric acid',
118        cpd00010 => 'CoenzymeA',
119        cpd00011 => 'Carbon dioxide',
120        cpd00012 => 'PPi',
121        cpd00018 => 'AMP',
122        cpd00020 => 'Pyruvic Acid',
123        cpd00022 => 'Acetyl-CoA',
124        cpd00025 => 'Hydrogen peroxide',
125        cpd00067 => 'H+',
126        cpd00971 => 'Sodium',
127        cpd15352 => '2-Demethylmenaquinone',
128        cpd15353 => '2-Demethylmenaquinol',
129        cpd15499 => 'Menaquinol',
130        cpd15500 => 'Menaquinone',
131        cpd15560 => 'Ubiquinone-8',
132        cpd15561 => 'Ubiquinol-8',
133    };
134    
135      #Cycling through the compound list and adding each individual compound entity  sub LoadModelFiles {
136      for (my $i=0; $i < $CompoundTable->size(); $i++) {      # Get the parameters.
137          my $Row = $CompoundTable->get_row($i);      my ($self) = @_;
138          if (defined($Row) && defined($Row->{"DATABASE"}->[0]) && $Row->{"DATABASE"}->[0] =~ m/cpd\d\d\d\d\d/) {      # Get the model dump file directory.
139              my $Object = FIGMODELObject->load($model->{"compound directory"}->[0].$Row->{"DATABASE"}->[0],"\t");      my $dir = $self->db()->LoadDirectory() . "/models";
140              my @LoadingArray = ($Row->{"DATABASE"}->[0],$Row->{"DATABASE"}->[0],0,"",0,"",0,10000000,10000000,"");      # First we read the compounds.
141              $self->Track(compoundRow => $LoadingArray[0], 1000);      my $ih = $self->CheckFile("$dir/CompoundName.txt", qw(CompoundID Name));
142              if (defined($Row->{"NAME"}->[0])) {      while (! eof $ih) {
143                  $LoadingArray[1] = $Row->{"NAME"}->[0];          # Get the next compound.
144              }          my ($id, $label) = $self->ReadLine($ih);
145              if (defined($Object->{"MASS"}->[0])) {          # Create a compound record for it.
146                  $LoadingArray[2] = $Object->{"MASS"}->[0];          $self->PutE(Compound => $id, label => $label, ubiquitous => (UBIQUITOUS->{$id} ? 1 : 0));
147              }      }
148              if (defined($Object->{"FORMULA"}->[0])) {      # Next, the compound-reactions relationship. We create the reactions here, too.
149                  $LoadingArray[3] = $Object->{"FORMULA"}->[0];      $ih = $self->CheckFile("$dir/CompoundReaction.txt", qw(CompoundID ReactionID
150              }                             Stoichiometry Cofactor));
151              if (defined($Object->{"CHARGE"}->[0])) {      while (! eof $ih) {
152                  $LoadingArray[4] = $Object->{"CHARGE"}->[0];          # Get the next link.
153              }          my ($compound, $reaction, $stoich, $cofactor) = $self->ReadLine($ih);
154              if (defined($Object->{"CHARGE"}->[0]) && defined($Object->{"FORMULA"}->[0])) {          # Insure the reaction exists.
155                  $LoadingArray[5] = FIGMODEL::ConvertToNeutralFormula($Object->{"FORMULA"}->[0],$Object->{"CHARGE"}->[0]);          $self->CreateReaction($reaction);
156              }          # Check for product or substrate.
157              if (-e $model->{"Argonne molfile directory"}->[0].$Row->{"DATABASE"}->[0].".mol" || -e $model->{"Argonne molfile directory"}->[0]."pH7/".$Row->{"DATABASE"}->[0].".mol") {          my $product;
158                  $LoadingArray[6] = 1;          if ($stoich < 0) {
159              }              $product = 0;
160              if (defined($Object->{"DELTAG"}->[0])) {              $stoich = -$stoich;
161                  $LoadingArray[7] = $Object->{"DELTAG"}->[0];          } else {
162              }              $product = 1;
             if (defined($Object->{"DELTAGERR"}->[0])) {  
                 $LoadingArray[8] = $Object->{"DELTAGERR"}->[0];  
             }  
             if (defined($Row->{"STRINGCODE"}->[0])) {  
                 $LoadingArray[9] = $Row->{"STRINGCODE"}->[0];  
             }  
             $self->PutE(Compound => $LoadingArray[0], label => $LoadingArray[1], mass => $LoadingArray[2], chargedFormula => $LoadingArray[3], charge => $LoadingArray[4],neutralFormula => $LoadingArray[5], hasMolfile => $LoadingArray[6], deltaG => $LoadingArray[7], deltaGerr => $LoadingArray[8], stringcode => $LoadingArray[9]);  
             #Adding the relationship between compound and structural cue  
             if (defined($Object->{"STRUCTURAL_CUES"})) {  
                 foreach my $Cue (@{$Object->{"STRUCTURAL_CUES"}}) {  
                     my @TempArray = split(/:/,$Cue);  
                     if (@TempArray == 2) {  
                         $self->PutR(IsFoundIn => $TempArray[0],$LoadingArray[0],count => $TempArray[1]);  
                     }  
                 }  
             }  
             #Adding the relationship between compound and alias type  
             if (defined($Object->{"NAME"})) {  
                 foreach my $Name (@{$Object->{"NAME"}}) {  
                     $self->PutR(HasAliasOf => $LoadingArray[0],"NAME",alias => $Name);  
                     my @SearchNames = FIGMODEL::ConvertToSearchNames($Name);  
                     foreach my $SearchName (@SearchNames) {  
                         $self->PutR(HasAliasOf => $LoadingArray[0],"SEARCHNAME",alias => $SearchName);  
                     }  
                 }  
             }  
             if (defined($Object->{"DBLINKS"})) {  
                 foreach my $Link (@{$Object->{"DBLINKS"}}) {  
                     my @TempArray = split(/:/,$Link);  
                     if (@TempArray >= 2) {  
                         if ($TempArray[0] ne "KEGG" && $TempArray[0] ne "ARGONNE") {  
                             $self->PutE(AliasType => $TempArray[0], source => "PUBLISHED MODEL");  
                         }  
                         if ($TempArray[0] eq "ARGONNE") {  
                             splice(@TempArray,1,1);  
                         }  
                         for (my $j=1; $j < @TempArray; $j++) {  
                             $self->PutR(HasAliasOf => $LoadingArray[0],$TempArray[0],alias => $TempArray[$j]);  
                         }  
                     }  
                 }  
163              }              }
164            # Connect the reaction to the compound.
165            $self->PutR(Involves => $reaction, $compound, product => $product,
166                        stoichiometry => $stoich, cofactor => $cofactor);
167        }
168        # Now we connect the reactions to roles.
169        $ih = $self->CheckFile("$dir/ReactionRole.txt", qw(ReactionID Role));
170        while (! eof $ih) {
171            # Get the next reaction/role pair. We don't need to create roles here because
172            # they are built in the Feature module.
173            my ($reaction, $role) = $self->ReadLine($ih);
174            # Insure the reaction exists.
175            $self->CreateReaction($reaction);
176            # Connect the reaction to the role.
177            $self->PutR(IsTriggeredBy => $reaction, $role);
178        }
179        # Now we create the models.
180        $ih = $self->CheckFile("$dir/ModelGenome.txt", qw(ModelID GenomeID));
181        while (! eof $ih) {
182            # Get the next model.
183            my ($model, $genome) = $self->ReadLine($ih);
184            # Create the model.
185            $self->PutE(Model => $model);
186            # Connect it to the genome. Again, the genomes are created elsewhere.
187            $self->PutR(IsModeledBy => $genome, $model);
188        }
189        # Next we connect the reactions to models.
190        $ih = $self->CheckFile("$dir/ModelReaction.txt", qw(ModelID ReactionID));
191        while (! eof $ih) {
192            # Get the next line.
193            my ($model, $reaction) = $self->ReadLine($ih);
194            # Only proceed if a reaction is present.
195            if ($reaction) {
196                # Insure the reaction exists.
197                $self->CreateReaction($reaction);
198                # Connect the reaction to the model.
199                $self->PutR(IsRequiredBy => $reaction, $model);
200          }          }
201      }      }
202  }  }
203    
204  sub LoadReactions {  =head3 StartFile
205      my ($self,$model) = @_;  
206      #First getting the reaction table which has a list of all reactions in the database as well as alot of reaction information      my $ih = $sl->CheckFile($fileName, @fieldNames);
207      my $ReactionTable = $model->GetDBTable("REACTIONS");  
208    Read the header record of the specified file and verify that the field names match
209    the names in the input list. If they do not, an error will be thrown; if they do, an
210    open file handle will be returned, positioned on the first data record.
211    
212      #Cycling through the compound list and adding each individual compound entity  =over 4
213      my $Count = 0;  
214      for (my $i=0; $i < $ReactionTable->size(); $i++) {  =item fileName
215          my $Row = $ReactionTable->get_row($i);  
216          if (defined($Row) && defined($Row->{"DATABASE"}->[0]) && $Row->{"DATABASE"}->[0] =~ m/rxn\d\d\d\d\d/) {  Name for the input file. The file is in standard tab-delimited format. The first record
217              my $Object = FIGMODELObject->load($model->{"reaction directory"}->[0].$Row->{"DATABASE"}->[0],"\t");  contains the field names and the remaining records contain the data.
218              my @LoadingArray = ($Row->{"DATABASE"}->[0],"","","","","",10000000,10000000,10000000,"R");  
219              $self->Track(reactionRow => $LoadingArray[0], 1000);  =item fieldNames
220              if (defined($Object->{"DEFINITION"}->[0])) {  
221                  $LoadingArray[1] = $Object->{"DEFINITION"}->[0];  List of the field names expected, in order.
222              }  
223              if (defined($Object->{"EQUATION"}->[0])) {  =item RETURN
224                  my ($Direction,$Equation,$ReverseEquation,$FullEquation,$EquationCompartment,$Error) = $model->ConvertEquationToCode($Object->{"EQUATION"}->[0],{"Test" => "Test"});  
225                  $LoadingArray[2] = $Equation;  Returns the open file handle if successful. If there is a mismatch, throws an error.
226              }  
227              if (defined($Object->{"OPERATOR"}->[0])) {  =back
228                  $LoadingArray[3] = $Object->{"OPERATOR"}->[0];  
229              }  =cut
230              if (defined($Object->{"PATHWAY"}->[0])) {  
231                  $LoadingArray[4] = join(";",@{$Object->{"PATHWAY"}});  sub CheckFile {
232              }      # Get the parameters.
233              if (defined($Row->{"KEGG MAPS"}->[0])) {      my ($self, $fileName, @fieldNames) = @_;
234                  $LoadingArray[5] = join(";",@{$Row->{"KEGG MAPS"}});      # Open the file.
235              }      my $retVal = Open(undef, "<$fileName");
236              if (defined($Object->{"DELTAG"}->[0])) {      $self->Add(files => 1);
237                  $LoadingArray[6] = $Object->{"DELTAG"}->[0];      # Read in the file header.
238              }      my @actualFields = Tracer::GetLine($retVal);
239              if (defined($Object->{"MMDELTAG"}->[0])) {      # This will be set to TRUE if there's a mismatch.
240                  $LoadingArray[7] = $Object->{"MMDELTAG"}->[0];      my $error = 0;
241              }      for (my $i = 0; $i <= $#fieldNames; $i++) {
242              if (defined($Object->{"DELTAGERR"}->[0])) {          if ($fieldNames[$i] ne $actualFields[$i]) {
243                  $LoadingArray[8] = $Object->{"DELTAGERR"}->[0];              Trace("Field match error: expected $fieldNames[$i], found $actualFields[$i].") if T(0);
244              }              $error = 1;
245              if (defined($Object->{"THERMODYNAMIC REVERSIBILITY"}->[0])) {          }
246                  my $code = $Object->{"THERMODYNAMIC REVERSIBILITY"}->[0];      }
247                  if ($code eq '<=>') {      # Was there an error?
248                      $LoadingArray[9] = "R";      if ($error) {
249                  } elsif ($code eq '<=') {          # Yes, so abort.
250                      $LoadingArray[9] = "B";          Confess("Invalid field name header in $fileName.");
                 } elsif ($code eq '=>') {  
                     $LoadingArray[9] = "F";  
                 }  
             }  
             $self->PutE(Reaction => $LoadingArray[0], definition => $LoadingArray[1], code => $LoadingArray[2], operator => $LoadingArray[3], pathway => $LoadingArray[4],keggMap => $LoadingArray[5], deltaG => $LoadingArray[6], MMdeltaG => $LoadingArray[7], deltaGerr => $LoadingArray[8], predictedReversibility => $LoadingArray[9]);  
             #Adding relationship between compounds and reactions  
             my ($Reactants,$Products) = $model->GetReactionSubstrateData($LoadingArray[0]);  
             if (! defined $Reactants) {  
                 $self->Add(missingReactants => 1);  
             } else {  
                 for (my $j=0; $j < @{$Reactants}; $j++) {  
                     $self->PutR(Involves => $LoadingArray[0],$Reactants->[$j]->{"DATABASE"}->[0],product => 0,stoichiometry => $Reactants->[$j]->{"COEFFICIENT"}->[0],main => 1,compartment => $Reactants->[$j]->{"COMPARTMENT"}->[0],discriminator => $Count);  
                     #TODO:Properly identify main reactants in reactions  
                     $Count++;  
                 }  
             }  
             if (! defined $Products) {  
                 $self->Add(missingProducts => 1);  
251              } else {              } else {
252                  for (my $j=0; $j < @{$Products}; $j++) {          # No, so trace the open.
253                      $self->PutR(Involves => $LoadingArray[0],$Products->[$j]->{"DATABASE"}->[0],product => 1,stoichiometry => $Products->[$j]->{"COEFFICIENT"}->[0],main => 1,compartment => $Products->[$j]->{"COMPARTMENT"}->[0],discriminator => $Count);          Trace("Processing $fileName.") if T(ERDBLoadGroup => 2);
                     #TODO:Properly identify main reactants in reactions  
                     $Count++;  
                 }  
             }  
             #Adding relationship between EC number and reactions  
             if (defined($Object->{"ENZYME"})) {  
                 foreach my $Enzyme (@{$Object->{"ENZYME"}}) {  
                    $self->PutE(EcNumber => $Enzyme, obsolete => 0, replacedby => "NONE");  
                    $self->PutR(IsCategorizedInto => $LoadingArray[0],$Enzyme,source => "KEGG");  
                 }  
             }  
             #Adding the relationship between reaction and alias type  
             if (defined($Object->{"NAME"})) {  
                 foreach my $Name (@{$Object->{"NAME"}}) {  
                     $self->PutR(HasReactionAliasOf => $LoadingArray[0],"NAME",alias => $Name);  
                 }  
             }  
             if (defined($Object->{"DBLINKS"})) {  
                 foreach my $Link (@{$Object->{"DBLINKS"}}) {  
                     my @TempArray = split(/:/,$Link);  
                     if (@TempArray >= 2) {  
                         if ($TempArray[0] ne "KEGG" && $TempArray[0] ne "ARGONNE") {  
                             $self->PutE(AliasType => $TempArray[0], source => "PUBLISHED MODEL");  
                         }  
                         if ($TempArray[0] eq "ARGONNE") {  
                             splice(@TempArray,1,1);  
                         }  
                         for (my $j=1; $j < @TempArray; $j++) {  
                             $self->PutR(HasReactionAliasOf => $LoadingArray[0],$TempArray[0],alias => $TempArray[$j]);  
                         }  
                     }  
                 }  
             }  
         }  
254      }      }
255        # Return the file handle.
256        return $retVal;
257  }  }
258    
259  sub LoadRoleSets {  =head3 ReadLine
     my ($self,$model) = @_;  
     my $sapling =$self->db();  
     my $RoleMappings = $model->GetDBTable("CURATED ROLE MAPPINGS");  
     my $NewSet;  
     my $SetHash;  
     my $LastComplex = -1;  
     my $LastReaction = "";  
     my $LastRole = "";  
     for (my $i=0; $i < $RoleMappings->size(); $i++) {  
         my $Row = $RoleMappings->get_row($i);  
         if (defined($Row) && defined($Row->{"REACTION"}->[0]) && defined($Row->{"ROLE"}->[0]) && defined($Row->{"COMPLEX"}->[0]) && defined($Row->{"MASTER"}->[0])) {  
             if ($Row->{"REACTION"}->[0] ne $LastReaction || $LastComplex ne $Row->{"COMPLEX"}->[0]) {  
                 if (defined($NewSet->{"ROLES"}) && defined($NewSet->{"REACTIONS"})) {  
                     my @RoleList = sort(keys(%{$NewSet->{"ROLES"}}));  
                     my @ReactionList = keys(%{$NewSet->{"REACTIONS"}});  
                     foreach my $Reaction (@ReactionList) {  
                         $SetHash->{join("+",@RoleList)}->{"REACTIONS"}->{$Reaction}->{"MASTER"}->[0] = $NewSet->{"REACTIONS"}->{$Reaction}->{"MASTER"}->[0];  
                         if (defined($NewSet->{"REACTIONS"}->{$Reaction}->{"SUBSYSTEMS"})) {  
                             foreach my $Subsystem (@{$NewSet->{"REACTIONS"}->{$Reaction}->{"SUBSYSTEMS"}}) {  
                                 if (defined($SetHash->{join("+",@RoleList)}->{"REACTIONS"}->{$Reaction}->{"SUBSYSTEMS"})) {  
                                     foreach my $OtherSubsystem (@{$SetHash->{join("+",@RoleList)}->{"REACTIONS"}->{$Reaction}->{"SUBSYSTEMS"}}) {  
                                         if ($Subsystem eq $OtherSubsystem) {  
                                             $Subsystem = "";  
                                             last;  
                                         }  
                                     }  
                                 }  
                                 if ($Subsystem ne "") {  
                                     push(@{$SetHash->{join("+",@RoleList)}->{"REACTIONS"}->{$Reaction}->{"SUBSYSTEMS"}},$Subsystem);  
                                 }  
                             }  
                         }  
                     }  
                     foreach my $Role (@RoleList) {  
                         $SetHash->{join("+",@RoleList)}->{"ROLES"}->{$Role} = 1;  
                     }  
                 }  
                 $NewSet = {};  
             }  
             $NewSet->{"ROLES"}->{$Row->{"ROLE"}->[0]} = 1;  
             $NewSet->{"REACTIONS"}->{$Row->{"REACTION"}->[0]}->{"MASTER"}->[0] = $Row->{"MASTER"}->[0];  
             if (defined($Row->{"SUBSYSTEM"}->[0])) {  
                 push(@{$NewSet->{"REACTIONS"}->{$Row->{"REACTION"}->[0]}->{"SUBSYSTEMS"}},$Row->{"SUBSYSTEM"}->[0]);  
             }  
             $LastRole = $Row->{"ROLE"}->[0];  
             $LastReaction = $Row->{"REACTION"}->[0];  
             $LastComplex = $Row->{"COMPLEX"}->[0];  
         }  
     }  
260    
261      my @RoleSets = keys(%{$SetHash});      my @fields = $sl->ReadLine($ih);
     foreach my $RoleSet (@RoleSets) {  
         my $Digested = $sapling->DigestKey($RoleSet);  
         $self->PutE(RoleSet => $Digested, source => "NONE");  
         my @ReactionList = keys(%{$SetHash->{$RoleSet}->{"REACTIONS"}});  
         foreach my $Reaction (@ReactionList) {  
             $self->PutR(IsTriggeredBy => $Reaction,$Digested, source => "NONE",master => $SetHash->{$RoleSet}->{"REACTIONS"}->{$Reaction}->{"MASTER"}->[0],subsystem => join(";",@{$SetHash->{$RoleSet}->{"REACTIONS"}->{$Reaction}->{"SUBSYSTEMS"}}));  
         }  
         my @RoleList = keys(%{$SetHash->{$RoleSet}->{"ROLES"}});  
         foreach my $Role (@RoleList) {  
             $self->PutR(IsCombinationOf => $Digested,$Role, local => 0);  
         }  
     }  
 }  
262    
263  sub LoadModels {  Read a line of data from an input file.
264      my ($self,$model) = @_;  
265      my $sapling = $self->db();  =over 4
266      ## TRS: Get hash of valid genome IDs.  
267      my $genomeHash = $sapling->GenomeHash();  =item ih
268      my $ModelList = $model->GetDBTable("MODEL LIST");  
269      my $ModelStats = $model->GetDBTable("MODEL STATS");  Open file handle for the input file.
270      for (my $i=0; $i < $ModelStats->size(); $i++) {  
271          my $Row = $ModelStats->get_row($i);  =item RETURN
272          if (defined($Row) && defined($Row->{"Model ID"}->[0])) {  
273              my @LoadingArray = ($Row->{"Model ID"}->[0],"","",0,0,0,"",0,0,0,0,0,0,0,0,0,0,0,0,"","",0,0,"",0,0);  Returns a list of the field values for the next record in the file.
274              if (defined($Row->{"Genome ID"}->[0]) && $genomeHash->{$Row->{"Genome ID"}->[0]}) {  
275                  if (defined($Row->{"Organism name"}->[0])) {  =back
276                      $LoadingArray[1] = $Row->{"Organism name"}->[0];  
277                  }  =cut
278                  if (defined($Row->{"Source"}->[0])) {  
279                      $LoadingArray[2] = $Row->{"Source"}->[0];  sub ReadLine {
280                  }      # Get the parameters.
281                  if (defined($Row->{"Total genes"}->[0])) {      my ($self, $ih) = @_;
282                      $LoadingArray[3] = $Row->{"Total genes"}->[0];      # Read the line.
283                  }      my @retVal = Tracer::GetLine($ih);
284                  if (defined($Row->{"Gram positive genes"}->[0])) {      # Count this record.
285                      $LoadingArray[4] = $Row->{"Gram positive genes"}->[0];      $self->Track(records => $retVal[0], 1000);
286                  }      # Return the data.
287                  if (defined($Row->{"Gram negative genes"}->[0])) {      return @retVal;
                     $LoadingArray[5] = $Row->{"Gram negative genes"}->[0];  
                 }  
                 if (defined($Row->{"Class"}->[0])) {  
                     $LoadingArray[6] = $Row->{"Class"}->[0];  
                 }  
                 if (defined($Row->{"Genes with functions"}->[0])) {  
                     $LoadingArray[7] = $Row->{"Genes with functions"}->[0];  
                 }  
                 if (defined($Row->{"Genes with reactions"}->[0])) {  
                     $LoadingArray[8] = $Row->{"Genes with reactions"}->[0];  
                 }  
                 if (defined($Row->{"Subsystem genes"}->[0])) {  
                     $LoadingArray[9] = $Row->{"Subsystem genes"}->[0];  
                 }  
                 if (defined($Row->{"Subsystem genes with reactions"}->[0])) {  
                     $LoadingArray[10] = $Row->{"Subsystem genes with reactions"}->[0];  
                 }  
                 if (defined($Row->{"Nonsubsystem genes"}->[0])) {  
                     $LoadingArray[11] = $Row->{"Nonsubsystem genes"}->[0];  
                 }  
                 if (defined($Row->{"Nonsubsystem genes with reactions"}->[0])) {  
                     $LoadingArray[12] = $Row->{"Nonsubsystem genes with reactions"}->[0];  
                 }  
                 if (defined($Row->{"Number of reactions"}->[0])) {  
                     $LoadingArray[13] = $Row->{"Number of reactions"}->[0];  
                 }  
                 if (defined($Row->{"Transport reaction"}->[0])) {  
                     $LoadingArray[14] = $Row->{"Transport reaction"}->[0];  
                 }  
                 if (defined($Row->{"Gap filling reactions"}->[0])) {  
                     $LoadingArray[15] = $Row->{"Gap filling reactions"}->[0];  
                 }  
                 if (defined($Row->{"Gap filling time"}->[0])) {  
                     $LoadingArray[16] = $Row->{"Gap filling time"}->[0];  
                 }  
                 if (defined($Row->{"Gap filling objective"}->[0])) {  
                     $LoadingArray[17] = $Row->{"Gap filling objective"}->[0];  
                 }  
                 if (defined($Row->{"Gap filling minimal objective"}->[0])) {  
                     $LoadingArray[18] = $Row->{"Gap filling minimal objective"}->[0];  
                 }  
                 if (defined($Row->{"Build date"}->[0])) {  
                     $LoadingArray[19] = $Row->{"Build date"}->[0];  
                 }  
                 if (defined($Row->{"Gap fill date"}->[0])) {  
                     $LoadingArray[20] = $Row->{"Gap fill date"}->[0];  
                 }  
                 if (defined($Row->{"Version"}->[0])) {  
                     $LoadingArray[21] = $Row->{"Version"}->[0];  
                 }  
                 if (defined($Row->{"Gap fill version"}->[0])) {  
                     $LoadingArray[22] = $Row->{"Gap fill version"}->[0];  
                 }  
                 if ($Row->{"Model ID"}->[0] =~ m/Core\d+\.\d+V\d+\.\d+/) {  
                     $LoadingArray[25] = 1;  
                 } elsif (defined($ModelList->get_row_by_key($Row->{"Model ID"}->[0],"MODEL ID"))) {  
                     if (defined($ModelList->get_row_by_key($Row->{"Model ID"}->[0],"MODEL ID")->{"DIRECTORY"}->[0])) {  
                         $LoadingArray[23] = $ModelList->get_row_by_key($Row->{"Model ID"}->[0],"MODEL ID")->{"DIRECTORY"}->[0];  
                     }  
                     if (defined($ModelList->get_row_by_key($Row->{"Model ID"}->[0],"MODEL ID")->{"JOB ID"}->[0]) && $ModelList->get_row_by_key($Row->{"Model ID"}->[0],"MODEL ID")->{"JOB ID"}->[0] ne "NONE") {  
                         $LoadingArray[24] = $ModelList->get_row_by_key($Row->{"Model ID"}->[0],"MODEL ID")->{"JOB ID"}->[0];  
                     }  
                 }  
                 for my $j (3,4,5,7,8,9,10,11,12,13,14,15,16,17,18,21,22,24,25) {  
                     $LoadingArray[$j] = 0 if ($LoadingArray[$j] =~ /[a-z]/i);  
                 }  
                 $self->PutE(Model => $LoadingArray[0], organismName => $LoadingArray[1], source => $LoadingArray[2], totalGenes => $LoadingArray[3], gramPositiveGenes => $LoadingArray[4],gramNegativeGenes => $LoadingArray[5], class => $LoadingArray[6], genesWithFunction => $LoadingArray[7], genesWithReactions => $LoadingArray[8], subsystemGenes => $LoadingArray[9], subsystemGenesWithReactions => $LoadingArray[10], nonsubsystemGenes => $LoadingArray[11], nonsubsystemGenesWithReactions => $LoadingArray[12], numberOfReactions => $LoadingArray[13], numberOfTransporters => $LoadingArray[14], gapFillingReactions => $LoadingArray[15], gapFillingTime => $LoadingArray[16], gapFillingObjective => $LoadingArray[17], gapFillingMinimalObjective => $LoadingArray[18], buildDate => $LoadingArray[19], gapFillDate => $LoadingArray[20], version => $LoadingArray[21], gapFillVersion => $LoadingArray[22], directory => $LoadingArray[23], jobid => $LoadingArray[24], obsolete => $LoadingArray[25]);  
                 #Adding the relationship between model and genome  
                 if (defined($Row->{"Genome ID"}->[0])) {  
                     $self->PutR(IsModeledBy => $Row->{"Genome ID"}->[0],$LoadingArray[0]);  
                 }  
                 #If the model is not obsolete, we add the relationships between model and reaction and featureset  
                 if ($LoadingArray[25] == 0) {  
                     #Loading the model from file  
                     my $ModelTable = $model->GetDBModel($LoadingArray[0]);  
                     for (my $j=0; $j < $ModelTable->size(); $j++) {  
                         my $RxnRow = $ModelTable->get_row($j);  
                         if (defined($RxnRow) && defined($RxnRow->{"LOAD"}->[0])) {  
                             my @SubLoadingArray = ("R","c","NONE",10,"V","NONE","UNKNOWN");  
                             if (defined($RxnRow->{"DIRECTIONALITY"}->[0])) {  
                                 my $code = $RxnRow->{"DIRECTIONALITY"}->[0];  
                                 if ($code eq '<=>') {  
                                     $SubLoadingArray[0] = 'R';  
                                 } elsif ($code eq '<=') {  
                                     $SubLoadingArray[0] = 'B';  
                                 } elsif ($code eq '=>') {  
                                     $SubLoadingArray[0] = 'F';  
                                 }  
                             }  
                             if (defined($RxnRow->{"COMPARTMENT"}->[0])) {  
                                 $SubLoadingArray[1] = $RxnRow->{"COMPARTMENT"}->[0];  
                             }  
                             if (defined($RxnRow->{"SUBSYSTEM"})) {  
                                 $SubLoadingArray[2] = join(";",@{$RxnRow->{"SUBSYSTEM"}});  
                             }  
                             if (defined($RxnRow->{"CONFIDENCE"}->[0])) {  
                                 $SubLoadingArray[3] = $RxnRow->{"CONFIDENCE"}->[0];  
                                 if ($SubLoadingArray[3] eq 'NONE') {  
                                     $SubLoadingArray[3] = 10;  
                                 }  
                             }  
                             if (defined($RxnRow->{"NOTES"})) {  
                                 $SubLoadingArray[5] = join(";",@{$RxnRow->{"NOTES"}});  
                             }  
                             if (defined($RxnRow->{"ASSOCIATED PEG"})) {  
                                 #Adding the role set entities  
                                 foreach my $FeatureSet (@{$RxnRow->{"ASSOCIATED PEG"}}) {  
                                     if ($FeatureSet =~ m/peg\.\d+/) {  
                                         my $DigestedKey = $sapling->DigestKey($FeatureSet);  
                                         $self->PutE(FeatureSet => $DigestedKey, source => "NONE");  
                                         #Adding the relationship between the reaction and roleset  
                                         $self->PutR(IsStimulatedBy => $RxnRow->{"LOAD"}->[0],$DigestedKey);  
                                         #Adding the relationship between the model and featureset  
                                         $self->PutR(Encompasses => $LoadingArray[0],$DigestedKey);  
                                         #Adding the relationship between FeatureSet and feature  
                                         my @PegArray = split(/\+/,$FeatureSet);  
                                         foreach my $Feature (@PegArray) {  
                                             if ($Feature =~ m/(peg\.\d+)/) {  
                                                 $self->PutR(IsSetOf => $DigestedKey,"fig|".$Row->{"Genome ID"}->[0].".".$1);  
                                             }  
                                         }  
                                     }  
                                 }  
                                 $SubLoadingArray[6] = join(";",@{$RxnRow->{"ASSOCIATED PEG"}});  
                             }  
                             $self->PutR(IsRequiredBy => $RxnRow->{"LOAD"}->[0],$LoadingArray[0], direction => $SubLoadingArray[0], compartment => $SubLoadingArray[1], confidence => $SubLoadingArray[3], class => $SubLoadingArray[4], notes => $SubLoadingArray[5], dependency => $SubLoadingArray[6]);  
                         }  
                     }  
                     #Clearing the model data from memmory  
                     undef $ModelTable;  
                     $model->ClearDBModel($LoadingArray[0],"DELETE");  
                 }  
             }  
288          }          }
289    
290    
291    =head3 CheckReaction
292    
293        $sl->CheckReaction($reaction);
294    
295    Insure we have created a rectord for the specified reaction.
296    
297    =over 4
298    
299    =item reaction
300    
301    ID of the reaction in question.
302    
303    =back
304    
305    =cut
306    
307    sub CreateReaction {
308        # Get the parameters.
309        my ($self, $reaction) = @_;
310        # Get the reaction hash.
311        my $reactionH = $self->{reactions};
312        # See if this reaction is new.
313        if (! $reactionH->{$reaction}) {
314            # It is, so create it.
315            $self->PutE(Reaction => $reaction);
316            # Insure we don't create it again.
317            $reactionH->{$reaction} = 1;
318      }      }
319  }  }
320    

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