void ProcessWebInterfaceModels() {
string Filename(GetParameter("web interface model directory"));
Filename.append("ModelList.txt");
vector<string> Lines = ReadStringsFromFile(Filename,false);
//this database will hold a combination of all of the model compounds and reactions
Data* CompleteDatabase = new Data(0);
//the following structures will hold the data for the various models as they are read in
vector<Data*> Models;
vector< map<string, Identity*, std::less<string> > > ModelGenes;
map<string, vector<string>, std::less<string> > ReactionGenes;
map<string, vector<string>, std::less<string> > ReactionModels;
map<string, vector<string>, std::less<string> > CompoundModels;
//Reading in the models and storing the data in the above structures
for (int i=1; i < int(Lines.size()); i++) {
cout << i << endl;
//Parsing the model list line
vector<string>* Strings = StringToStrings(Lines[i], "\t");
if (Strings->size() >= 4) {
Filename.assign(GetParameter("web interface model directory"));
Filename.append((*Strings)[3]);
}
//Loading each model from the combined model file
if (FileExists(Filename)) {
map<string, Identity*, std::less<string> > CurrentGeneData;
ModelGenes.push_back(CurrentGeneData);
Data* NewData = new Data(0);
Models.push_back(NewData);
NewData->AddData("NAME",(*Strings)[0].data(),STRING);
NewData->AddData("AUTHORS",(*Strings)[1].data(),STRING);
NewData->AddData("ORGANISMS NAME",(*Strings)[2].data(),STRING);
NewData->AddData("FILENAME",(*Strings)[3].data(),STRING);
NewData->LoadSystem(Filename);
//Loading additional data on compounds and reactions from the centralized database
int TotalTransported = 0;
for (int j=0; j < NewData->FNumSpecies(); j++) {
if (NewData->GetSpecies(j)->FExtracellular()) {
TotalTransported++;
}
NewData->GetSpecies(j)->LoadSpecies(NewData->GetSpecies(j)->GetData("DATABASE",STRING));
CompoundModels[NewData->GetSpecies(j)->Query("CGI_ID")].push_back((*Strings)[0]);
if (CompleteDatabase->FindSpecies("DATABASE;CGI_ID",NewData->GetSpecies(j)->Query("CGI_ID").data()) == NULL && CompleteDatabase->FindSpecies("DATABASE;CGI_ID",NewData->GetSpecies(j)->GetData("DATABASE",STRING).data()) == NULL) {
CompleteDatabase->AddSpecies(NewData->GetSpecies(j));
}
}
//Note that the reaction equation that was read in was cleared in favor of the database equation... this could lead to problems
int TotalReactionsWithGenes = 0;
for (int j=0; j < NewData->FNumReactions(); j++) {
NewData->GetReaction(j)->LoadReaction(NewData->GetReaction(j)->GetData("DATABASE",STRING));
ReactionModels[NewData->GetReaction(j)->Query("CGI_ID")].push_back((*Strings)[0]);
//Capturing the gene data for entry into the gene hash
vector<string> GeneData = NewData->GetReaction(j)->GetAllData("ASSOCIATED PEG",DATABASE_LINK);
if (GeneData.size() > 0) {
TotalReactionsWithGenes++;
}
for (int k=0; k < int(GeneData.size()); k++) {
//Adding the gene to the reaction gene hash
string GeneName((*Strings)[2]);
GeneName.append(":");
GeneName.append(GeneData[k]);
ReactionGenes[NewData->GetReaction(j)->Query("CGI_ID")].push_back(GeneName);
//Finding the gene and creating a new gene if the gene does not currently exist
Identity* CurrentGene = ModelGenes[ModelGenes.size()-1][GeneData[k]];
if (CurrentGene == NULL) {
CurrentGene = new Identity;
ModelGenes[ModelGenes.size()-1][GeneData[k]] = CurrentGene;
}
//Adding the reaction data to the gene data
CurrentGene->AddData("REACTIONS",NewData->GetReaction(j)->Query("CGI_ID").data(),STRING);
vector<string> EnzymeData = NewData->GetReaction(j)->GetAllData("ENZYME",DATABASE_LINK);
for (int l=0; l < int(EnzymeData.size()); l++) {
CurrentGene->AddData("ENZYME",EnzymeData[l].data(),STRING);
}
EnzymeData = NewData->GetReaction(j)->GetAllData("PATHWAYS",STRING);
for (int l=0; l < int(EnzymeData.size()); l++) {
CurrentGene->AddData("PATHWAY",EnzymeData[l].data(),STRING);
}
}
//Adding all unique reactions to the complete database
if (CompleteDatabase->FindReaction("DATABASE;CGI_ID",NewData->GetReaction(j)->Query("CGI_ID").data()) == NULL && CompleteDatabase->FindReaction("DATABASE;CGI_ID",NewData->GetReaction(j)->GetData("DATABASE",STRING).data()) == NULL) {
CompleteDatabase->AddReaction(NewData->GetReaction(j));
}
}
//Searching the model for dead compounds and reactions
NewData->FindDeadEnds();
NewData->AddData("TRANSPORTED COMPOUNDS",double(TotalTransported));
NewData->AddData("REACTION WITH GENES",double(TotalReactionsWithGenes));
}
delete Strings;
}
//Printing the combined compounds table
Filename.assign(GetParameter("web interface model directory"));
Filename.append("AllCompoundsTable.txt");
ofstream CompleteOutput;
if (!OpenOutput(CompleteOutput,Filename)) {
return;
}
CompleteOutput << "ID SHORTNAME NAMES STATUS IN MODEL MODELS FORMULA MASS CHARGE(pH7) DELTA G(kcal/mol) PATHWAY DATABASE LINKS REACTIONS" << endl;
for (int i=0; i < CompleteDatabase->FNumSpecies(); i++) {
CompleteOutput << CompleteDatabase->GetSpecies(i)->Query("CGI_ID") << "\t";
CompleteOutput << CompleteDatabase->GetSpecies(i)->Query("SHORTNAME") << "\t";
CompleteOutput << StringReplace(CompleteDatabase->GetSpecies(i)->GetAllDataString("NAME",STRING).data(),"\t",", ") << "\t";
CompleteOutput << "Not in model" << "\t";
vector<string> ModelList = CompoundModels[CompleteDatabase->GetSpecies(i)->Query("CGI_ID")];
for (int j=0; j < int(ModelList.size()-1); j++) {
CompleteOutput << ModelList[j] << ", ";
}
CompleteOutput << ModelList[ModelList.size()-1] << "\t"; CompleteOutput << CompleteDatabase->GetSpecies(i)->FFormula() << "\t";
CompleteOutput << CompleteDatabase->GetSpecies(i)->FMW() << "\t";
CompleteOutput << CompleteDatabase->GetSpecies(i)->FCharge() << "\t";
CompleteOutput << CompleteDatabase->GetSpecies(i)->FEstDeltaG() << "\t";
CompleteOutput << StringReplace(CompleteDatabase->GetSpecies(i)->GetAllDataString("PATHWAYS",STRING).data(),"\t",", ") << "\t";
CompleteOutput << StringReplace(CompleteDatabase->GetSpecies(i)->GetCombinedData(DATABASE_LINK).data(),"\t",", ") << "\t";
CompleteOutput << StringReplace(CompleteDatabase->GetSpecies(i)->Query("REACTIONS").data(),"\t",", ") << endl;
}
CompleteOutput.close();
//Printing the combined reactions table
Filename.assign(GetParameter("web interface model directory"));
Filename.append("AllReactionsTable.txt");
if (!OpenOutput(CompleteOutput,Filename)) {
return;
}
CompleteOutput << "ID SHORTNAME NAMES STATUS IN MODEL MODELS DEFINITION EQUATION EC NUMBER ASSIGNED FUNCTIONS ASSIGNED GENES DELTA G(kcal/mol) PATHWAY PREVIOUS REACTIONS NEXT REACTIONS" << endl;
for (int i=0; i < CompleteDatabase->FNumReactions(); i++) {
CompleteOutput << CompleteDatabase->GetReaction(i)->Query("CGI_ID") << "\t";
CompleteOutput << CompleteDatabase->GetReaction(i)->Query("SHORTNAME") << "\t";
CompleteOutput << StringReplace(CompleteDatabase->GetReaction(i)->GetAllDataString("NAME",STRING).data(),"\t",", ") << "\t";
CompleteOutput << "Not in model" << "\t";
vector<string> ModelList = ReactionModels[CompleteDatabase->GetReaction(i)->Query("CGI_ID")];
for (int j=0; j < int(ModelList.size()-1); j++) {
CompleteOutput << ModelList[j] << ", ";
}
CompleteOutput << ModelList[ModelList.size()-1] << "\t";
CompleteOutput << CompleteDatabase->GetReaction(i)->Query("DEFINITION") << "\t";
CompleteOutput << CompleteDatabase->GetReaction(i)->CreateReactionEquation("CGI_ID") << "\t";
CompleteOutput << StringReplace(CompleteDatabase->GetReaction(i)->GetAllDataString("ENZYME",DATABASE_LINK).data(),"\t",", ") << "\t";
CompleteOutput << "No data" << "\t";
vector<string> AssignedGenes = ReactionGenes[CompleteDatabase->GetReaction(i)->Query("CGI_ID")];
if (AssignedGenes.size() >= 1) {
for (int j=0; j < int(AssignedGenes.size()-1); j++) {
CompleteOutput << AssignedGenes[j] << ", ";
}
CompleteOutput << AssignedGenes[AssignedGenes.size()-1] << "\t";
} else {
CompleteOutput << "None" << "\t";
}
CompleteOutput << CompleteDatabase->GetReaction(i)->FEstDeltaG() << "\t";
CompleteOutput << StringReplace(CompleteDatabase->GetReaction(i)->Query("PATHWAYS").data(),"\t",", ") << "\t";
CompleteOutput << StringReplace(CompleteDatabase->GetReaction(i)->Query("PREVIOUS").data(),"\t",", ") << "\t";
CompleteOutput << StringReplace(CompleteDatabase->GetReaction(i)->Query("NEXT").data(),"\t",", ") << endl;
}
CompleteOutput.close();
//Printing the compounds, reactions, and genes tables for each model and the model table
Filename.assign(GetParameter("web interface model directory"));
Filename.append("ModelTable.txt");
if (!OpenOutput(CompleteOutput,Filename)) {
return;
}
CompleteOutput << "ID MODEL AUTHORS ORGANISMS NAME TOTAL COMPOUNDS TRANSPORTED COMPOUNDS DEAD COMPOUNDS TOTAL REACTIONS REACTIONS WITH GENES DEAD REACTIONS NUMBER OF GENES" << endl;
for (int j=0; j < int(Models.size()); j++) {
//Printing the model data into the model table
CompleteOutput << Models[j]->GetData("NAME",STRING) << "\t";
CompleteOutput << Models[j]->GetData("AUTHORS",STRING) << "\t";
CompleteOutput << Models[j]->GetData("ORGANISMS NAME",STRING) << "\t";
CompleteOutput << Models[j]->FNumSpecies() << "\t";
CompleteOutput << Models[j]->GetDoubleData("TRANSPORTED COMPOUNDS") << "\t";
CompleteOutput << Models[j]->GetDoubleData("DEAD COMPOUNDS") << "\t";
CompleteOutput << Models[j]->FNumReactions() << "\t";
CompleteOutput << Models[j]->GetDoubleData("REACTION WITH GENES") << "\t";
CompleteOutput << Models[j]->GetDoubleData("DEAD REACTIONS") << "\t";
CompleteOutput << ModelGenes[j].size() << endl;
ofstream ModelOutput;
Filename.assign(GetParameter("web interface model directory"));
Filename.append(Models[j]->GetData("NAME",STRING));
Filename.append("CompoundsTable.txt");
if (!OpenOutput(ModelOutput,Filename)) {
return;
}
ModelOutput << "ID SHORTNAME NAMES STATUS IN MODEL MODELS FORMULA MASS CHARGE(pH7) DELTA G(kcal/mol) PATHWAY DATABASE LINKS REACTIONS" << endl;
for (int i=0; i < Models[j]->FNumSpecies(); i++) {
ModelOutput << Models[j]->GetSpecies(i)->Query("CGI_ID") << "\t";
ModelOutput << Models[j]->GetSpecies(i)->Query("SHORTNAME") << "\t";
ModelOutput << StringReplace(Models[j]->GetSpecies(i)->GetAllDataString("NAME",STRING).data(),"\t",", ") << "\t";
ModelOutput << Models[j]->GetSpecies(i)->GetData("CLASS",STRING) << "\t";
vector<string> ModelList = ReactionModels[Models[j]->GetSpecies(i)->Query("CGI_ID")];
if (ModelList.size() > 0) {
for (int k=0; k < int(ModelList.size()-1); k++) {
ModelOutput << ModelList[k] << ", ";
}
ModelOutput << ModelList[ModelList.size()-1] << "\t";
} else {
ModelOutput << "No data" << "\t";
}
ModelOutput << Models[j]->GetSpecies(i)->FFormula() << "\t";
ModelOutput << Models[j]->GetSpecies(i)->FMW() << "\t";
ModelOutput << Models[j]->GetSpecies(i)->FCharge() << "\t";
ModelOutput << Models[j]->GetSpecies(i)->FEstDeltaG() << "\t";
ModelOutput << StringReplace(Models[j]->GetSpecies(i)->GetAllDataString("PATHWAYS",STRING).data(),"\t",", ") << "\t";
ModelOutput << StringReplace(Models[j]->GetSpecies(i)->GetCombinedData(DATABASE_LINK).data(),"\t",", ") << "\t";
ModelOutput << StringReplace(Models[j]->GetSpecies(i)->Query("REACTIONS").data(),"\t",", ") << endl;
}
ModelOutput.close();
Filename.assign(GetParameter("web interface model directory"));
Filename.append(Models[j]->GetData("NAME",STRING));
Filename.append("ReactionsTable.txt");
if (!OpenOutput(ModelOutput,Filename)) {
return;
}
ModelOutput << "ID SHORTNAME NAMES STATUS IN MODEL MODELS DEFINITION EQUATION EC NUMBER ASSIGNED FUNCTIONS ASSIGNED GENES DELTA G(kcal/mol) PATHWAY PREVIOUS REACTIONS NEXT REACTIONS" << endl;
for (int i=0; i < Models[j]->FNumReactions(); i++) {
ModelOutput << Models[j]->GetReaction(i)->Query("CGI_ID") << "\t";
ModelOutput << Models[j]->GetReaction(i)->Query("SHORTNAME") << "\t";
ModelOutput << StringReplace(Models[j]->GetReaction(i)->GetAllDataString("NAME",STRING).data(),"\t",", ") << "\t";
ModelOutput << Models[j]->GetReaction(i)->GetData("CLASS",STRING) << "\t";
vector<string> ModelList = ReactionModels[Models[j]->GetReaction(i)->Query("CGI_ID")];
if (ModelList.size() > 0) {
for (int k=0; k < int(ModelList.size()-1); k++) {
ModelOutput << ModelList[k] << ", ";
}
ModelOutput << ModelList[ModelList.size()-1] << "\t";
}else {
ModelOutput << "No data" << "\t";
}
ModelOutput << Models[j]->GetReaction(i)->Query("DEFINITION") << "\t";
ModelOutput << Models[j]->GetReaction(i)->CreateReactionEquation("CGI_ID") << "\t";
ModelOutput << StringReplace(Models[j]->GetReaction(i)->GetAllDataString("ENZYME",DATABASE_LINK).data(),"\t",", ") << "\t";
ModelOutput << "No data" << "\t";
vector<string> AssignedGenes = ReactionGenes[Models[j]->GetReaction(i)->Query("CGI_ID")];
if (AssignedGenes.size() >= 1) {
bool First = true;
for (int k=0; k < int(AssignedGenes.size()); k++) {
if (AssignedGenes[k].length() > Models[j]->GetData("ORGANISMS NAME",STRING).length() && AssignedGenes[k].substr(0,Models[j]->GetData("ORGANISMS NAME",STRING).length()).compare(Models[j]->GetData("ORGANISMS NAME",STRING)) == 0) {
if (!First) {
ModelOutput << ", ";
}
First = false;
ModelOutput << AssignedGenes[k].substr(Models[j]->GetData("ORGANISMS NAME",STRING).length()+1,AssignedGenes[k].length()-Models[j]->GetData("ORGANISMS NAME",STRING).length()-1);
}
}
ModelOutput << "\t";
} else {
ModelOutput << "None" << "\t";
}
ModelOutput << Models[j]->GetReaction(i)->FEstDeltaG() << "\t";
ModelOutput << StringReplace(Models[j]->GetReaction(i)->Query("PATHWAYS").data(),"\t",", ") << "\t";
ModelOutput << StringReplace(Models[j]->GetReaction(i)->Query("PREVIOUS").data(),"\t",", ") << "\t";
ModelOutput << StringReplace(Models[j]->GetReaction(i)->Query("NEXT").data(),"\t",", ") << endl;
}
ModelOutput.close();
Filename.assign(GetParameter("web interface model directory"));
Filename.append(Models[j]->GetData("NAME",STRING));
Filename.append("GenesTable.txt");
if (!OpenOutput(ModelOutput,Filename)) {
return;
}
ModelOutput << "ID SHORTNAME NAMES ASSIGNED FUNCTIONS STATUS IN ORGANISM PARALOGS COORDINATES DIRECTIONALITY EC NUMBER PATHWAY REACTIONS" << endl;
for (map<string, Identity*, std::less<string> >::iterator MapIT = ModelGenes[j].begin(); MapIT != ModelGenes[j].end(); MapIT++) {
ModelOutput << MapIT->first << "\t";
ModelOutput << MapIT->first << "\t";
ModelOutput << MapIT->first << "\t";
ModelOutput << "No data" << "\t";
ModelOutput << "No data" << "\t";
ModelOutput << "No data" << "\t";
ModelOutput << "No data" << "\t";
ModelOutput << "No data" << "\t";
ModelOutput << StringReplace(MapIT->second->GetAllDataString("ENZYME",STRING).data(),"\t",", ") << "\t";
ModelOutput << StringReplace(MapIT->second->GetAllDataString("PATHWAY",STRING).data(),"\t",", ") << "\t";
ModelOutput << StringReplace(MapIT->second->GetAllDataString("REACTIONS",STRING).data(),"\t",", ") << endl;
}
ModelOutput.close();
}
CompleteOutput.close();
}
void LoadDatabaseFile(const char* DatabaseFilename) {
if (GetParameter("Network output location").compare("none") != 0 && GetParameter("Network output location").length() > 0) {
if (GetParameter("os").compare("windows") == 0) {
system(("move "+GetDatabaseDirectory(GetParameter("database"),"output directory")+GetParameter("output folder")+" "+GetParameter("Network output location")).data());
} else {
system(("cp -r "+GetDatabaseDirectory(GetParameter("database"),"output directory")+GetParameter("output folder")+" "+GetParameter("Network output location")).data());
}
}
//Getting filename that all compound and reaction data will be saved into
string Filename(DatabaseFilename);
if (Filename.length() == 0) {
Filename = AskString("Input filename for database: ");
}
//Creating datastructure for all program data
Data* NewData = new Data(0);
NewData->ClearData("NAME",STRING);
NewData->AddData("NAME",RemoveExtension(RemovePath(Filename)).data(),STRING);
//Loading data from file
if (NewData->LoadSystem(Filename) == FAIL) {
delete NewData;
return;
}
//Performing a variety of tasks according to the parameters in the parameters files including KEGG lookup, reaction and compound printing etc.
NewData->PerformAllRequestedTasks();
// Test for Adjustment of DeltaGs for PH for COMPOUNDS
bool TestCpds = 0;
if (TestCpds){
double IonicS = 0.25;
FErrorFile() << "Std Transformed Gibbs Energy of Formation vs pH" << endl;
for (int i=0; i < NewData->FNumSpecies(); i++){
string CompoundID = NewData->GetSpecies(i)->GetData("DATABASE",STRING); // gets the cpdID
string Name = NewData->GetSpecies(i)->GetData("NAME",STRING); // gets the name of the cpd
Species* Temp = NewData->FindSpecies("DATABASE",CompoundID.data());
//if (CompoundID.compare("cpd00003") == 0 || CompoundID.compare("cpd00004") == 0 || CompoundID.compare("cpd00002") == 0) {
double AdjDeltaG5 = Temp->AdjustedDeltaG(IonicS,5,298.15);
double AdjDeltaG5_kJ = 4.184*AdjDeltaG5;
double AdjDeltaG6 = Temp->AdjustedDeltaG(IonicS,6,298.15);
double AdjDeltaG6_kJ = 4.184*AdjDeltaG6;
double AdjDeltaG7 = Temp->AdjustedDeltaG(IonicS,7,298.15);
double AdjDeltaG7_kJ = 4.184*AdjDeltaG7;
double AdjDeltaG8 = Temp->AdjustedDeltaG(IonicS,8,298.15);
double AdjDeltaG8_kJ = 4.184*AdjDeltaG8;
double AdjDeltaG9 = Temp->AdjustedDeltaG(IonicS,9,298.15);
double AdjDeltaG9_kJ = 4.184*AdjDeltaG9;
FErrorFile() << CompoundID << "\t" << AdjDeltaG5_kJ << "\t" << AdjDeltaG6_kJ << "\t" << AdjDeltaG7_kJ << "\t" << AdjDeltaG8_kJ << "\t" << AdjDeltaG9_kJ << endl;
//}
}
FlushErrorFile();
}
// Test for Adjustment of DeltaGs for IONIC STRENGTH for COMPOUNDS
bool TestCpdsIS = 0;
if (TestCpdsIS){
FErrorFile() << "Std Transformed Gibbs Energy of Formation vs Ionic Strength" << endl;
for (int i=0; i < NewData->FNumSpecies(); i++){
string CompoundID = NewData->GetSpecies(i)->GetData("DATABASE",STRING); // gets the cpdID
string Name = NewData->GetSpecies(i)->GetData("NAME",STRING); // gets the name of the cpd
Species* Temp = NewData->FindSpecies("DATABASE",CompoundID.data());
double AdjDeltaG_IS0 = Temp->AdjustedDeltaG(0,7,298.15);
double AdjDeltaG_IS0_kJ = 4.184*AdjDeltaG_IS0;
double AdjDeltaG_IS10 = Temp->AdjustedDeltaG(0.1,7,298.15);
double AdjDeltaG_IS10_kJ = 4.184*AdjDeltaG_IS10;
double AdjDeltaG_IS25 = Temp->AdjustedDeltaG(0.25,7,298.15);
double AdjDeltaG_IS25_kJ = 4.184*AdjDeltaG_IS25;
FErrorFile() << CompoundID << "\t" << AdjDeltaG_IS0_kJ << "\t" << AdjDeltaG_IS10_kJ << "\t" << AdjDeltaG_IS25_kJ << endl;
}
FlushErrorFile();
}
// Test for Adjustment of DeltaGs for pH for REACTIONS
bool TestRxns = 0;
if (TestRxns){
double IonicS = 0.25;
//double pH = 7;
FErrorFile() << "Std Transformed Gibbs Energy of Reaction (kJmol-1) vs pH" << endl;
for (int i=0; i < NewData->FNumReactions(); i++){
Reaction* Rxn = NewData->GetReaction(i);
string RxnID = Rxn->GetData("DATABASE",STRING);
string Name = Rxn->GetData("NAME",STRING);
double DG5 = Rxn->FEstDeltaG(5,IonicS)*4.184;
double DG6 = Rxn->FEstDeltaG(6,IonicS)*4.184;
double DG7 = Rxn->FEstDeltaG(7,IonicS)*4.184;
double DG8 = Rxn->FEstDeltaG(8,IonicS)*4.184;
double DG9 = Rxn->FEstDeltaG(9,IonicS)*4.184;
FErrorFile() << RxnID << "\t" << DG5 << "\t" << DG6 << "\t" << DG7 << "\t" << DG8 << "\t" << DG9 << endl;
}
FlushErrorFile();
}
// Test for Adjustment of DeltaGs for IONIC STRENGTH for REACTIONS
bool TestRxnsIS = 0;
if (TestRxnsIS){
FErrorFile() << "Std Transformed Gibbs Energy of Reaction (kJmol-1) vs Ionic Strength" << endl;
for (int i=0; i < NewData->FNumReactions(); i++){
Reaction* Rxn = NewData->GetReaction(i);
string RxnID = Rxn->GetData("DATABASE",STRING);
string Name = Rxn->GetData("NAME",STRING);
double DG_IS0 = Rxn->FEstDeltaG(7,0.25)*4.184;
double DG_IS10 = Rxn->FEstDeltaG(7,0.15)*4.184;
double DG_IS25 = Rxn->FEstDeltaG(7,0.25)*4.184;
FErrorFile() << RxnID << "\t" << DG_IS0 << "\t" << DG_IS10 << "\t" << DG_IS25 << endl;
}
// FlushErrorFile();
}
delete NewData;
};
