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revision 1.2, Tue Apr 7 14:13:11 2009 UTC revision 1.15, Mon Feb 28 20:27:17 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, $options, @tables);
37    
38  Construct a new ModelLoaderSaplingLoader object.  Construct a new ModelSaplingLoader object.
39    
40  =over 4  =over 4
41    
42  =item erdb  =item erdb
43    
44  [[SaplingPm]] object for the database being loaded.  L<Sapling> object for the database being loaded.
45    
46  =item options  =item options
47    
# Line 59  Line 59 
59      # Get the parameters.      # Get the parameters.
60      my ($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");      cpd00002 => 'ATP',
110      $self->PutE(AliasType => "KEGG", source => "http://www.kegg.com/");      cpd00008 => 'ADP',
111      $self->PutE(AliasType => "ARGONNE", source => "OBSOLETE IDs");      cpd00007 => 'Oxygen',
112        cpd00010 => 'CoenzymeA',
113        cpd00012 => 'PPi',
114        cpd15560 => 'Ubiquinone-8',
115        cpd15561 => 'Ubiquinol-8',
116        cpd15500 => 'Menaquinone',
117        cpd15499 => 'Menaquinol',
118        cpd00022 => 'Acetyl-CoA',
119        cpd00018 => 'AMP',
120        cpd00971 => 'Sodium',
121        cpd15352 => '2-Demethylmenaquinone',
122        cpd15353 => '2-Demethylmenaquinol'
123    
124      #Cycling through the compound list and adding each individual compound entity  };
125      for (my $i=0; $i < $CompoundTable->size(); $i++) {  
126          my $Row = $CompoundTable->get_row($i);  sub LoadModelFiles {
127          if (defined($Row) && defined($Row->{"DATABASE"}->[0]) && $Row->{"DATABASE"}->[0] =~ m/cpd\d\d\d\d\d/) {      # Get the parameters.
128              my $Object = FIGMODELObject->load($model->{"compound directory"}->[0].$Row->{"DATABASE"}->[0],"\t");      my ($self) = @_;
129              my @LoadingArray = ($Row->{"DATABASE"}->[0],$Row->{"DATABASE"}->[0],0,"",0,"",0,10000000,10000000,"");      # Get the model dump file directory.
130              if (defined($Row->{"NAME"}->[0])) {      my $dir = $self->db()->LoadDirectory() . "/models";
131                  $LoadingArray[1] = $Row->{"NAME"}->[0];      # First we read the compounds.
132              }      my $ih = $self->CheckFile("$dir/CompoundName.txt", qw(CompoundID Name));
133              if (defined($Object->{"MASS"}->[0])) {      while (! eof $ih) {
134                  $LoadingArray[2] = $Object->{"MASS"}->[0];          # Get the next compound.
135              }          my ($id, $label) = $self->ReadLine($ih);
136              if (defined($Object->{"FORMULA"}->[0])) {          # Create a compound record for it.
137                  $LoadingArray[3] = $Object->{"FORMULA"}->[0];          $self->PutE(Compound => $id, label => $label, ubiquitous => (UBIQUITOUS->{$id} ? 1 : 0));
138              }      }
139              if (defined($Object->{"CHARGE"}->[0])) {      # Next, the compound-reactions relationship. We create the reactions here, too.
140                  $LoadingArray[4] = $Object->{"CHARGE"}->[0];      $ih = $self->CheckFile("$dir/CompoundReaction.txt", qw(CompoundID ReactionID
141              }                             Stoichiometry Cofactor));
142              if (defined($Object->{"CHARGE"}->[0]) && defined($Object->{"FORMULA"}->[0])) {      while (! eof $ih) {
143                  $LoadingArray[5] = FIGMODEL::ConvertToNeutralFormula($Object->{"FORMULA"}->[0],$Object->{"CHARGE"}->[0]);          # Get the next link.
144              }          my ($compound, $reaction, $stoich, $cofactor) = $self->ReadLine($ih);
145              if (-e $model->{"Argonne molfile directory"}->[0].$Row->{"DATABASE"}->[0].".mol" || -e $model->{"Argonne molfile directory"}->[0]."pH7/".$Row->{"DATABASE"}->[0].".mol") {          # Insure the reaction exists.
146                  $LoadingArray[6] = 1;          $self->CreateReaction($reaction);
147              }          # Check for product or substrate.
148              if (defined($Object->{"DELTAG"}->[0])) {          my $product;
149                  $LoadingArray[7] = $Object->{"DELTAG"}->[0];          if ($stoich < 0) {
150              }              $product = 0;
151              if (defined($Object->{"DELTAGERR"}->[0])) {              $stoich = -$stoich;
152                  $LoadingArray[8] = $Object->{"DELTAGERR"}->[0];          } else {
153              }              $product = 1;
             if (defined($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]);  
                         }  
                     }  
                 }  
154              }              }
155            # Connect the reaction to the compound.
156            $self->PutR(Involves => $reaction, $compound, product => $product,
157                        stoichiometry => $stoich, cofactor => $cofactor);
158        }
159        # Now we connect the reactions to roles.
160        $ih = $self->CheckFile("$dir/ReactionRole.txt", qw(ReactionID Role));
161        while (! eof $ih) {
162            # Get the next reaction/role pair. We don't need to create roles here because
163            # they are built in the Feature module.
164            my ($reaction, $role) = $self->ReadLine($ih);
165            # Insure the reaction exists.
166            $self->CreateReaction($reaction);
167            # Connect the reaction to the role.
168            $self->PutR(IsTriggeredBy => $reaction, $role);
169        }
170        # Now we create the models.
171        $ih = $self->CheckFile("$dir/ModelGenome.txt", qw(ModelID GenomeID));
172        while (! eof $ih) {
173            # Get the next model.
174            my ($model, $genome) = $self->ReadLine($ih);
175            # Create the model.
176            $self->PutE(Model => $model);
177            # Connect it to the genome. Again, the genomes are created elsewhere.
178            $self->PutR(IsModeledBy => $genome, $model);
179        }
180        # Next we connect the reactions to models.
181        $ih = $self->CheckFile("$dir/ModelReaction.txt", qw(ModelID ReactionID));
182        while (! eof $ih) {
183            # Get the next line.
184            my ($model, $reaction) = $self->ReadLine($ih);
185            # Only proceed if a reaction is present.
186            if ($reaction) {
187                # Insure the reaction exists.
188                $self->CreateReaction($reaction);
189                # Connect the reaction to the model.
190                $self->PutR(IsRequiredBy => $reaction, $model);
191          }          }
192      }      }
193  }  }
194    
195  sub LoadReactions {  =head3 StartFile
196      my ($self,$model) = @_;  
197      #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);
198      my $ReactionTable = $model->GetDBTable("REACTIONS");  
199    Read the header record of the specified file and verify that the field names match
200    the names in the input list. If they do not, an error will be thrown; if they do, an
201    open file handle will be returned, positioned on the first data record.
202    
203      #Cycling through the compound list and adding each individual compound entity  =over 4
     my $Count = 0;  
     for (my $i=0; $i < $ReactionTable->size(); $i++) {  
         my $Row = $ReactionTable->get_row($i);  
         if (defined($Row) && defined($Row->{"DATABASE"}->[0]) && $Row->{"DATABASE"}->[0] =~ m/rxn\d\d\d\d\d/) {  
             my $Object = FIGMODELObject->load($model->{"reaction directory"}->[0].$Row->{"DATABASE"}->[0],"\t");  
             my @LoadingArray = ($Row->{"DATABASE"}->[0],"","","","","",10000000,10000000,10000000,"R");  
             if (defined($Object->{"DEFINITION"}->[0])) {  
                 $LoadingArray[1] = $Object->{"DEFINITION"}->[0];  
             }  
             if (defined($Object->{"EQUATION"}->[0])) {  
                 my ($Direction,$Equation,$ReverseEquation,$FullEquation,$EquationCompartment,$Error) = $model->ConvertEquationToCode($Object->{"EQUATION"}->[0],{"Test" => "Test"});  
                 $LoadingArray[2] = $Equation;  
             }  
             if (defined($Object->{"OPERATOR"}->[0])) {  
                 $LoadingArray[3] = $Object->{"OPERATOR"}->[0];  
             }  
             if (defined($Object->{"PATHWAY"}->[0])) {  
                 $LoadingArray[4] = join(";",@{$Object->{"PATHWAY"}});  
             }  
             if (defined($Row->{"KEGG MAPS"}->[0])) {  
                 $LoadingArray[5] = join(";",@{$Row->{"KEGG MAPS"}});  
             }  
             if (defined($Object->{"DELTAG"}->[0])) {  
                 $LoadingArray[6] = $Object->{"DELTAG"}->[0];  
             }  
             if (defined($Object->{"MMDELTAG"}->[0])) {  
                 $LoadingArray[7] = $Object->{"MMDELTAG"}->[0];  
             }  
             if (defined($Object->{"DELTAGERR"}->[0])) {  
                 $LoadingArray[8] = $Object->{"DELTAGERR"}->[0];  
             }  
             if (defined($Object->{"THERMODYNAMIC REVERSIBILITY"}->[0])) {  
                 my $code = $Object->{"THERMODYNAMIC REVERSIBILITY"}->[0];  
                 if ($code eq '<=>') {  
                     $LoadingArray[9] = "R";  
                 } elsif ($code eq '<=') {  
                     $LoadingArray[9] = "B";  
                 } elsif ($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]);  
             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++;  
             }  
             for (my $j=0; $j < @{$Products}; $j++) {  
                 $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);  
                 #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, obselete => 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]);  
                         }  
                     }  
                 }  
             }  
         }  
     }  
 }  
204    
205  sub LoadRoleSets {  =item fileName
     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 = $Row->{"COMPLEX"}->[0];  
         }  
     }  
206    
207      my @RoleSets = keys(%{$SetHash});  Name for the input file. The file is in standard tab-delimited format. The first record
208      foreach my $RoleSet (@RoleSets) {  contains the field names and the remaining records contain the data.
         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);  
         }  
     }  
 }  
209    
210  sub LoadModels {  =item fieldNames
211      my ($self,$model) = @_;  
212      my $sapling = $self->db();  List of the field names expected, in order.
213      ## TRS: Get hash of valid genome IDs.  
214      my $genomeHash = $sapling->GenomeHash();  =item RETURN
215      my $ModelList = $model->GetDBTable("MODEL LIST");  
216      my $ModelStats = $model->GetDBTable("MODEL STATS");  Returns the open file handle if successful. If there is a mismatch, throws an error.
217      for (my $i=0; $i < $ModelStats->size(); $i++) {  
218          my $Row = $ModelStats->get_row($i);  =back
219          if (defined($Row) && defined($Row->{"Model ID"}->[0])) {  
220              my @LoadingArray = ($Row->{"Model ID"}->[0],"","",0,0,0,"",0,0,0,0,0,0,0,0,0,0,0,0,"","",0,0,"",0,0);  =cut
221              if (defined($Row->{"Genome ID"}->[0]) && $genomeHash->{$Row->{"Genome ID"}->[0]}) {  
222                  if (defined($Row->{"Organism name"}->[0])) {  sub CheckFile {
223                      $LoadingArray[1] = $Row->{"Organism name"}->[0];      # Get the parameters.
224                  }      my ($self, $fileName, @fieldNames) = @_;
225                  if (defined($Row->{"Source"}->[0])) {      # Open the file.
226                      $LoadingArray[2] = $Row->{"Source"}->[0];      my $retVal = Open(undef, "<$fileName");
227                  }      $self->Add(files => 1);
228                  if (defined($Row->{"Total genes"}->[0])) {      # Read in the file header.
229                      $LoadingArray[3] = $Row->{"Total genes"}->[0];      my @actualFields = Tracer::GetLine($retVal);
230                  }      # This will be set to TRUE if there's a mismatch.
231                  if (defined($Row->{"Gram positive genes"}->[0])) {      my $error = 0;
232                      $LoadingArray[4] = $Row->{"Gram positive genes"}->[0];      for (my $i = 0; $i <= $#fieldNames; $i++) {
233                  }          if ($fieldNames[$i] ne $actualFields[$i]) {
234                  if (defined($Row->{"Gram negative genes"}->[0])) {              Trace("Field match error: expected $fieldNames[$i], found $actualFields[$i].") if T(0);
235                      $LoadingArray[5] = $Row->{"Gram negative genes"}->[0];              $error = 1;
236                  }          }
237                  if (defined($Row->{"Class"}->[0])) {      }
238                      $LoadingArray[6] = $Row->{"Class"}->[0];      # Was there an error?
239                  }      if ($error) {
240                  if (defined($Row->{"Genes with functions"}->[0])) {          # Yes, so abort.
241                      $LoadingArray[7] = $Row->{"Genes with functions"}->[0];          Confess("Invalid field name header in $fileName.");
242                  }      } else {
243                  if (defined($Row->{"Genes with reactions"}->[0])) {          # No, so trace the open.
244                      $LoadingArray[8] = $Row->{"Genes with reactions"}->[0];          Trace("Processing $fileName.") if T(ERDBLoadGroup => 2);
                 }  
                 if (defined($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");  
245                  }                  }
246        # Return the file handle.
247        return $retVal;
248              }              }
249    
250    =head3 ReadLine
251    
252        my @fields = $sl->ReadLine($ih);
253    
254    Read a line of data from an input file.
255    
256    =over 4
257    
258    =item ih
259    
260    Open file handle for the input file.
261    
262    =item RETURN
263    
264    Returns a list of the field values for the next record in the file.
265    
266    =back
267    
268    =cut
269    
270    sub ReadLine {
271        # Get the parameters.
272        my ($self, $ih) = @_;
273        # Read the line.
274        my @retVal = Tracer::GetLine($ih);
275        # Count this record.
276        $self->Track(records => $retVal[0], 1000);
277        # Return the data.
278        return @retVal;
279          }          }
280    
281    
282    =head3 CheckReaction
283    
284        $sl->CheckReaction($reaction);
285    
286    Insure we have created a rectord for the specified reaction.
287    
288    =over 4
289    
290    =item reaction
291    
292    ID of the reaction in question.
293    
294    =back
295    
296    =cut
297    
298    sub CreateReaction {
299        # Get the parameters.
300        my ($self, $reaction) = @_;
301        # Get the reaction hash.
302        my $reactionH = $self->{reactions};
303        # See if this reaction is new.
304        if (! $reactionH->{$reaction}) {
305            # It is, so create it.
306            $self->PutE(Reaction => $reaction);
307            # Insure we don't create it again.
308            $reactionH->{$reaction} = 1;
309      }      }
310  }  }
311    

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