int main()
{
unsigned index;
bool fromRestart = false;
std::string modelToRun = "FONSE";
bool withPhi = false;
std::cout << "Initializing MCMCAlgorithm object---------------" << std::endl;
int samples = 100;
int thinning = 10;
int useSamples = 100;
unsigned numMixtures = 1;
std::cout << "\t# Samples: " << samples << "\n";
std::cout << "\tThinning: " << thinning << "\n";
std::cout << "\t # Samples used: " << useSamples << "\n";
MCMCAlgorithm mcmc = MCMCAlgorithm(samples, thinning, 10, true, true, false);
mcmc.setRestartFileSettings("RestartFile.txt", 20, true);
std::cout << "Done!-------------------------------\n\n\n";
if (modelToRun == "FONSE") {
std::cout << "initialize Genome object--------------------------" << std::endl;
Genome genome;
std::cout << "Reading fasta file\n";
genome.readFasta("C:/Users/Alan/Documents/GitHub/RibModelDev/data/FONSE/nse2000.fasta");
std::cout << "Done!-------------------------------\n\n\n";
std::cout << "Initializing shared parameter variables---------------\n";
std::vector<unsigned> geneAssignment(genome.getGenomeSize());
std::vector<double> sphi_init(numMixtures, 1);
/* For 1 mixture */
for (unsigned i = 0u; i < genome.getGenomeSize(); i++)
{
geneAssignment[i] = 0u;
}
std::vector<std::vector<unsigned>> mixtureDefinitionMatrix;
std::cout << "Done!------------------------\n\n\n";
//ROCParameter parameter;
FONSEParameter parameter;
std::cout << "initialize Parameter object" << std::endl;
std::string mixDef = Parameter::allUnique;
if (fromRestart)
{
FONSEParameter tmp("C:/Users/Alan/Documents/GitHub/RibModelDev/DevRScripts/10restartfile.rst");
parameter = tmp;
}
else
{
//ROCParameter tmp(sphi_init, nu/mMixtures, geneAssignment, mixtureDefinitionMatrix, true, mixDef);
FONSEParameter tmp(sphi_init, numMixtures, geneAssignment, mixtureDefinitionMatrix, true, mixDef);
for (unsigned i = 0u; i < numMixtures; i++)
{
unsigned selectionCategry = tmp.getSelectionCategory(i);
std::cout << "Sphi_init for selection category " << selectionCategry << ": " << sphi_init[selectionCategry] << std::endl;
}
std::cout << "\t# mixtures: " << numMixtures << "\n";
std::cout << "\tmixture definition: " << mixDef << "\n";
//std::vector<std::string> files(1);
//files[0] = std::string("C:/Users/Jeremy/Documents/GitHub/RibModelDev/data/FONSE/Scereviciae.mut.csv");
//tmp.initMutationCategories(files, tmp.getNumMutationCategories());
//tmp.InitializeSynthesisRate(genome, sphi_init[0]);
std::vector<double> phiVals = parameter.readPhiValues("C:/Users/Alan/Documents/GitHub/RibModelDev/data/FONSE/nse2000.phi.csv");
tmp.InitializeSynthesisRate(phiVals);
parameter = tmp;
}
std::cout << "done initialize Parameter object" << std::endl;
std::cout << "Initializing Model object\n";
bool withPhi = true;
FONSEModel model;
//ROCModel model(withPhi);
model.setParameter(parameter);
std::cout << "starting MCMC for FONSE" << std::endl;
mcmc.run(genome, model, 1, 0);
std::cout << std::endl << "Finished MCMC for FONSE" << std::endl;
}
else if (modelToRun == "RFP")
{
std::cout << "Initializing Genome object--------------------------" << std::endl;
Genome genome;
genome.readRFPFile("C:/Users/Jeremy/Documents/GitHub/RibModelDev/data/rfp/rfp.counts.by.codon.and.gene.GSE63789.wt.csv");
std::cout << "Done!-------------------------------\n\n\n";
std::cout << "Initializing shared parameter variables---------------\n";
std::vector<unsigned> geneAssignment(genome.getGenomeSize());
std::vector<double> sphi_init(numMixtures, 1);
if (numMixtures == 1)
{
for (unsigned i = 0u; i < genome.getGenomeSize(); i++)
{
geneAssignment[i] = 0u;
}
}
else if (numMixtures == 3)
{
for (unsigned i = 0u; i < genome.getGenomeSize(); i++)
{
if (i < 961) geneAssignment[i] = 0u;
else if (i < 1418) geneAssignment[i] = 1u;
else geneAssignment[i] = 0u;
}
}
std::vector<std::vector<unsigned>> mixtureDefinitionMatrix;
std::cout << "Done!------------------------\n\n\n";
std::cout << "Initializing RFPParameter object--------------------\n" << std::endl;
RFPParameter parameter;
if (fromRestart)
{
RFPParameter tmp("/Users/roxasoath1/Desktop/RibModelFramework/DevRscripts/10restartFile.rst");
parameter = tmp;
}
else
{
std::string mixDef = Parameter::allUnique;
RFPParameter tmp(sphi_init, numMixtures, geneAssignment, mixtureDefinitionMatrix, true, mixDef);
for (unsigned i = 0u; i < numMixtures; i++) {
unsigned selectionCategry = tmp.getSelectionCategory(i);
std::cout << "Sphi_init for selection category " << selectionCategry << ": " <<
sphi_init[selectionCategry] << std::endl;
}
std::cout << "\t# mixtures: " << numMixtures << "\n";
std::cout << "\tmixture definition: " << mixDef << "\n";
tmp.InitializeSynthesisRate(genome, sphi_init[0]);
parameter = tmp;
}
std::cout << "Done!--------------------------------\n\n\n" << std::endl;
std::cout << "Initializing RFPModel object--------------------------\n";
RFPModel model;
model.setParameter(parameter);
std::cout << "Done!----------------------------------\n\n\n" << std::endl;
std::cout << "Running MCMC.............\n" << std::endl;
mcmc.run(genome, model, 1, 0);
std::cout << "Done!----------------------------------\n\n\n" << std::endl;
} //END OF RFP
if (modelToRun == "ROC")
{
std::cout << "Initializing Genome object--------------------------" << std::endl;
Genome genome;
genome.readFasta("C:/Users/Alan/Documents/GitHub/RibModelDev/data/realGenomes/Skluyveri.fasta");
if (withPhi)
{
genome.readObservedPhiValues("/Users/roxasoath1/Desktop/RibModelFramework/ribModel/data/simulatedAllUniqueR_phi.csv", false);
}
std::cout << "Done!-------------------------------\n\n\n";
std::cout << "Initializing shared parameter variables---------------\n";
std::vector<unsigned> geneAssignment(genome.getGenomeSize());
std::vector<double> sphi_init(numMixtures, 1);
if (numMixtures == 1)
{
for (unsigned i = 0u; i < genome.getGenomeSize(); i++)
{
geneAssignment[i] = 0u;
}
}
else if (numMixtures == 3)
{
for (unsigned i = 0u; i < genome.getGenomeSize(); i++)
{
if (i < 961) geneAssignment[i] = 0u;
else if (i < 1418) geneAssignment[i] = 1u;
else geneAssignment[i] = 0u;
}
}
std::vector<std::vector<unsigned>> mixtureDefinitionMatrix;
std::cout << "Done!------------------------\n\n\n";
std::cout << "Initializing ROCParameter object--------------------\n" << std::endl;
ROCParameter parameter;
if (fromRestart)
{
ROCParameter tmp("/Users/roxasoath1/Desktop/RibModelFramework/DevRscripts/10restartFile.rst");
parameter = tmp;
}
else
{
std::string mixDef = ROCParameter::allUnique;
ROCParameter tmp(sphi_init, numMixtures, geneAssignment, mixtureDefinitionMatrix, true, mixDef);
for (unsigned i = 0u; i < numMixtures; i++)
{
unsigned selectionCategry = tmp.getSelectionCategory(i);
std::cout << "Sphi_init for selection category " << selectionCategry << ": " << sphi_init[selectionCategry] << std::endl;
}
std::cout << "\t# mixtures: " << numMixtures << "\n";
std::cout << "\tmixture definition: " << mixDef << "\n";
/*std::vector<std::string> files(2);
files[0] = std::string("F:/GitHub/RibModelDev/data/twoMixtures/simulated_mutation0.csv");
files[1] = std::string("F:/GitHub/RibModelDev/data/twoMixtures/simulated_mutation1.csv");
tmp.initMutationCategories(files, tmp.getNumMutationCategories());
files[0] = std::string("F:/GitHub/RibModelDev/data/twoMixtures/simulated_selection0.csv");
files[1] = std::string("F:/GitHub/RibModelDev/data/twoMixtures/simulated_selection1.csv");
tmp.initSelectionCategories(files, tmp.getNumSelectionCategories());
tmp.InitializeSynthesisRate(genome, sphi_init[0]);
*/
//std::vector<double> phiVals = parameter.readPhiValues("/home/clandere/CodonUsageBias/RibosomeModel/RibModelFramework/ribModel/data/Skluyveri_ChrA_ChrCleft_phi_est.csv");
//parameter.InitializeSynthesisRate(phiVals);
parameter = tmp;
}
std::cout << "Done!--------------------------------\n\n\n" << std::endl;
std::cout << "Initializing ROCModel object--------------------------\n";
ROCModel model;
model.setParameter(parameter);
std::cout << "Done!----------------------------------\n\n\n" << std::endl;
std::cout << "Running MCMC.............\n" << std::endl;
std::cout << numMixtures << std::endl;
mcmc.run(genome, model, 1, 0);
std::cout << "Done!----------------------------------\n\n\n" << std::endl;
} //END OF ROC
}
int main()
{
std::string pathBegin = "/Users/hollisbui/";
unsigned numMixtures = 1;
std::vector<double> sphi_init(numMixtures, 2);
std::vector<std::vector<unsigned>> mixtureDefinitionMatrix;
// SIMULATE GENOME: RFP
/*
Genome genome;
//genome.readFasta(pathBegin + "HollisTestingData/s288c.genome.fasta");
genome.readRFPFile(pathBegin + "HollisTestingData/rfp.counts.by.codon.and.gene.GSE63789.wt.csv");
std::vector<unsigned> geneAssignment(genome.getGenomeSize());
for (unsigned i = 0u; i < genome.getGenomeSize(); i++)
{
geneAssignment[i] = 0u;
}
RFPParameter parameter(sphi_init, numMixtures, geneAssignment, mixtureDefinitionMatrix, true, "allUnique");
std::vector<std::string> files;
files.push_back(pathBegin + "HollisTestingData/RFPAlphaValues.csv");
parameter.initMutationSelectionCategories(files, 1, RFPParameter::alp);
files[0] = pathBegin + "HollisTestingData/RFPLambdaPrimeValues.csv";
parameter.initMutationSelectionCategories(files, 1, RFPParameter::lmPri);
std::vector<double> phi = parameter.readPhiValues(pathBegin + "HollisTestingData/RFPPhiValues.csv");
//std::vector<double> phi = tmp.readPhiValues("/Users/roxasoath1/Desktop/TONEWTON/RFPPsiValues.csv");
parameter.InitializeSynthesisRate(phi);
RFPModel model;
model.setParameter(parameter);
model.simulateGenome(genome);
genome.writeRFPFile(pathBegin + "HollisTestingOut/HollisSimulatedGenome2.csv", true);
exit(1);
*/
// UNIT TESTING
//testUtility();
//testSequenceSummary();
//testGene();
//testGenome(pathBegin + "RibModelFramework/tests/testthat/UnitTestingData");
//testCovarianceMatrix();
testParameter();
//testParameterWithFile(pathBegin + "HollisFile.txt");
//testTrace();
//testRFPParameter();
//testMCMCAlgorithm();
exit(0);
std::string modelToRun = "RFP"; //can be RFP, ROC or FONSE
bool withPhi = false;
bool fromRestart = false;
my_print("Initializing MCMCAlgorithm object---------------\n");
unsigned samples = 10;
unsigned thinning = 10;
int useSamples = 100;
my_print("\t# Samples: %\n", samples);
my_print("\tThinning: %\n", thinning);
my_print("\t # Samples used: %\n", useSamples);
MCMCAlgorithm mcmc = MCMCAlgorithm(samples, thinning, 10, true, true, true);
//mcmc.setRestartFileSettings(pathBegin + "RestartFile.txt", 20, true);
my_print("Done!-------------------------------\n\n\n");
if (modelToRun == "ROC")
{
my_print("Initializing Genome object--------------------------\n");
Genome genome;
genome.readFasta(pathBegin + "RibModelDev/data/twoMixtures/simulatedAllUniqueR.fasta");
if (withPhi)
{
genome.readObservedPhiValues(pathBegin + "RibModelFramework/ribModel/data/simulatedAllUniqueR_phi.csv", false);
}
my_print("Done!-------------------------------\n\n\n");
my_print("Initializing shared parameter variables---------------\n");
std::vector<unsigned> geneAssignment(genome.getGenomeSize());
std::vector<double> sphi_init(numMixtures, 1);
if (numMixtures == 1)
{
for (unsigned i = 0u; i < genome.getGenomeSize(); i++)
{
geneAssignment[i] = 0u;
}
}
else if (numMixtures == 3)
{
for (unsigned i = 0u; i < genome.getGenomeSize(); i++)
{
if (i < 961) geneAssignment[i] = 0u;
else if (i < 1418) geneAssignment[i] = 1u;
else geneAssignment[i] = 0u;
}
}
std::vector<std::vector<unsigned>> mixtureDefinitionMatrix;
my_print("Done!------------------------\n\n\n");
my_print("Initializing ROCParameter object--------------------\n\n");
ROCParameter parameter;
if (fromRestart)
{
ROCParameter tmp(pathBegin + "RibModelFramework/DevRscripts/10restartFile.rst");
parameter = tmp;
}
else
{
std::string mixDef = ROCParameter::allUnique;
ROCParameter tmp(sphi_init, numMixtures, geneAssignment, mixtureDefinitionMatrix, true, mixDef);
for (unsigned i = 0u; i < numMixtures; i++)
{
unsigned selectionCategry = tmp.getSelectionCategory(i);
my_print("Sphi_init for selection category %: %\n", selectionCategry, sphi_init[selectionCategry]);
}
my_print("\t# mixtures: %\n", numMixtures);
my_print("\tmixture definition: %\n", mixDef);
std::vector<std::string> files(2);
files[0] = std::string(pathBegin + "RibModelDev/data/twoMixtures/simulated_mutation0.csv");
files[1] = std::string(pathBegin + "RibModelDev/data/twoMixtures/simulated_mutation1.csv");
tmp.initMutationCategories(files, tmp.getNumMutationCategories());
files[0] = std::string(pathBegin + "RibModelDev/data/twoMixtures/simulated_selection0.csv");
files[1] = std::string(pathBegin + "RibModelDev/data/twoMixtures/simulated_selection1.csv");
tmp.initSelectionCategories(files, tmp.getNumSelectionCategories());
tmp.InitializeSynthesisRate(genome, sphi_init[0]);
//std::vector<double> phiVals =
// parameter.readPhiValues(pathBegin + "RibModelDev/data/realGenomes/Skluyveri_ChrA_ChrCleft_phi_est.csv");
//parameter.InitializeSynthesisRate(phiVals);
parameter = tmp;
}
my_print("Done!--------------------------------\n\n\n");
my_print("Initializing ROCModel object--------------------------\n");
ROCModel model;
model.setParameter(parameter);
my_print("Done!----------------------------------\n\n\n");
my_print("Running MCMC.............\n\n");
mcmc.run(genome, model, 1, 0);
my_print("Done!----------------------------------\n\n\n");
} //END OF ROC
else if (modelToRun == "RFP")
{
my_print("Initializing Genome object--------------------------\n");
Genome genome;
genome.readRFPFile(pathBegin + "RibModelDev/data/rfp/rfp.counts.by.codon.and.gene.GSE63789.wt.csv");
my_print("Done!-------------------------------\n\n\n");
my_print("Initializing shared parameter variables---------------\n");
std::vector<unsigned> geneAssignment(genome.getGenomeSize());
std::vector<double> sphi_init(numMixtures, 1);
if (numMixtures == 1)
{
for (unsigned i = 0u; i < genome.getGenomeSize(); i++)
{
geneAssignment[i] = 0u;
}
}
else if (numMixtures == 3)
{
for (unsigned i = 0u; i < genome.getGenomeSize(); i++)
{
if (i < 961) geneAssignment[i] = 0u;
else if (i < 1418) geneAssignment[i] = 1u;
else geneAssignment[i] = 0u;
}
}
std::vector<std::vector<unsigned>> mixtureDefinitionMatrix;
my_print("Done!------------------------\n\n\n");
my_print("Initializing RFPParameter object--------------------\n\n");
RFPParameter parameter;
//parameter.writeBasicRestartFile("/Users/hollisbui/HollisFile.txt");
if (fromRestart)
{
RFPParameter tmp(pathBegin + "RibModelFramework/10_restartFile.rst");
parameter = tmp;
}
else
{
std::string mixDef = Parameter::allUnique;
RFPParameter tmp(sphi_init, numMixtures, geneAssignment, mixtureDefinitionMatrix, true, mixDef);
for (unsigned i = 0u; i < numMixtures; i++)
{
unsigned selectionCategry = tmp.getSelectionCategory(i);
my_print("Sphi_init for selection category %: %\n", selectionCategry, sphi_init[selectionCategry]);
}
my_print("\t# mixtures: %\n", numMixtures);
my_print("\tmixture definition: %\n", mixDef);
tmp.InitializeSynthesisRate(genome, sphi_init[0]);
parameter = tmp;
//parameter.writeEntireRestartFile("/Users/hollisbui/HollisFile2.txt");
}
my_print("Done!--------------------------------\n\n\n");
my_print("Initializing RFPModel object--------------------------\n");
RFPModel model;
model.setParameter(parameter);
my_print("Done!----------------------------------\n\n\n");
my_print("Running MCMC.............\n\n");
mcmc.run(genome, model, 1, 0);
my_print("Done!----------------------------------\n\n\n");
} //END OF RFP
else if (modelToRun == "FONSE")
{
my_print("initialize Genome object--------------------------\n");
Genome genome;
genome.readFasta(pathBegin + "RibModelDev/data/singleMixture/genome_2000.fasta");
my_print("Done!-------------------------------\n\n\n");
my_print("Initializing shared parameter variables---------------\n");
std::vector<unsigned> geneAssignment(genome.getGenomeSize());
std::vector<double> sphi_init(numMixtures, 1);
if (numMixtures == 1)
{
for (unsigned i = 0u; i < genome.getGenomeSize(); i++)
{
geneAssignment[i] = 0u;
}
}
else if (numMixtures == 3)
{
for (unsigned i = 0u; i < genome.getGenomeSize(); i++)
{
if (i < 961) geneAssignment[i] = 0u;
else if (i < 1418) geneAssignment[i] = 1u;
else geneAssignment[i] = 0u;
}
}
std::vector<std::vector<unsigned>> mixtureDefinitionMatrix;
my_print("Done!------------------------\n\n\n");
FONSEParameter parameter;
my_print("initialize Parameter object\n");
if (fromRestart)
{
FONSEParameter tmp(pathBegin + "RibModelDev/DevRscripts/10restartFile.rst");
parameter = tmp;
}
else
{
std::string mixDef = ROCParameter::allUnique;
FONSEParameter tmp(sphi_init, numMixtures, geneAssignment, mixtureDefinitionMatrix, true, mixDef);
for (unsigned i = 0u; i < numMixtures; i++)
{
unsigned selectionCategory = tmp.getSelectionCategory(i);
my_print("Sphi_init for selection category %: %\n", selectionCategory, sphi_init[selectionCategory]);
}
my_print("\t# mixtures: %\n", numMixtures);
my_print("\tmixture definition: %\n", mixDef);
std::vector<std::string> files(1);
files[0] = std::string(pathBegin + "RibModelDev/data/singleMixture/genome_2000.mutation.csv");
tmp.initMutationCategories(files, tmp.getNumMutationCategories());
tmp.InitializeSynthesisRate(genome, sphi_init[0]);
//std::vector<double> phiVals = parameter.readPhiValues(
// pathBegin + "RibModelDev/data/realGenomes/Skluyveri_ChrA_ChrCleft_phi_est.csv");
//parameter.InitializeSynthesisRate(phiVals);
parameter = tmp;
my_print("done initialize Parameter object\n");
}
my_print("Initializing Model object\n");
FONSEModel model;
model.setParameter(parameter);
my_print("Done!------------------------\n\n\n");
my_print("starting MCMC for ROC\n");
mcmc.run(genome, model, 4, 0);
my_print("\nFinished MCMC for ROC\n");
}
}
int main()
{
if (1)
{
//testSequenceSummary();
//testGene();
testGenome("/Users/roxasoath1/Desktop/RibModelDevScripts/RibModelDev/data/UnitTestingData");
/*
Genome genome;
genome.readRFPFile("/Users/roxasoath1/Desktop/RibModelDevScripts/RibModelDev/data/rfp/rfp.counts.by.codon.and.gene.GSE63789.wt.csv");
std::vector<unsigned> geneAssignment(genome.getGenomeSize());
for (unsigned i = 0u; i < genome.getGenomeSize(); i++)
{
geneAssignment[i] = 0u;
}
unsigned numMixtures = 1;
std::vector<double> sphi_init(numMixtures, 2);
std::vector<std::vector<unsigned>> mixtureDefinitionMatrix;
RFPParameter tmp(sphi_init, numMixtures, geneAssignment, mixtureDefinitionMatrix, true, "allUnique");
std::vector<std::string> files;
files.push_back("/Users/roxasoath1/Desktop/TONEWTON/RFPAlphaValues.csv");
tmp.initMutationSelectionCategories(files, 1, RFPParameter::alp);
files[0] = "/Users/roxasoath1/Desktop/TONEWTON/RFPLambdaPrimeValues.csv";
tmp.initMutationSelectionCategories(files, 1, RFPParameter::lmPri);
std::vector<double> phi = tmp.readPhiValues("/Users/roxasoath1/Desktop/TONEWTON/RFPPsiValues.csv");
tmp.InitializeSynthesisRate(phi);
RFPModel model;
model.setParameter(tmp);
std::cout <<"init done\n";
model.simulateGenome(genome);
std::cout <<"writing file\n";
genome.writeRFPFile("/Users/roxasoath1/Desktop/RibModelDevScripts/RibModelDev/data/rfp/simulatedRFPData.csv", true);
*/
exit(1);
}
std::string modelToRun = "RFP"; //can also be ROC or FONSE
bool withPhi = false;
bool fromRestart = true;
unsigned numMixtures = 1;
std::cout << "Initializing MCMCAlgorithm object---------------" << std::endl;
int samples = 10;
int thinning = 10;
int useSamples = 100;
std::cout << "\t# Samples: " << samples << "\n";
std::cout << "\tThinning: " << thinning << "\n";
std::cout << "\t # Samples used: " << useSamples << "\n";
MCMCAlgorithm mcmc = MCMCAlgorithm(samples, thinning, 10, true, true, true);
mcmc.setRestartFileSettings("RestartFile.txt", 20, true);
std::cout << "Done!-------------------------------\n\n\n";
if (modelToRun == "ROC")
{
std::cout << "Initializing Genome object--------------------------" << std::endl;
Genome genome;
genome.readFasta("/Users/roxasoath1/Desktop/RibModelDevScripts/RibModelDev/data/twoMixtures/simulatedAllUniqueR.fasta");
if (withPhi)
{
genome.readObservedPhiValues("/Users/roxasoath1/Desktop/RibModelFramework/ribModel/data/simulatedAllUniqueR_phi.csv", false);
}
std::cout << "Done!-------------------------------\n\n\n";
std::cout << "Initializing shared parameter variables---------------\n";
std::vector<unsigned> geneAssignment(genome.getGenomeSize());
std::vector<double> sphi_init(numMixtures, 1);
if (numMixtures == 1)
{
for (unsigned i = 0u; i < genome.getGenomeSize(); i++)
{
geneAssignment[i] = 0u;
}
}
else if (numMixtures == 3)
{
for (unsigned i = 0u; i < genome.getGenomeSize(); i++)
{
if (i < 961) geneAssignment[i] = 0u;
else if (i < 1418) geneAssignment[i] = 1u;
else geneAssignment[i] = 0u;
}
}
std::vector<std::vector<unsigned>> mixtureDefinitionMatrix;
std::cout << "Done!------------------------\n\n\n";
std::cout << "Initializing ROCParameter object--------------------\n" << std::endl;
ROCParameter parameter;
if (fromRestart)
{
ROCParameter tmp("/Users/roxasoath1/Desktop/RibModelFramework/DevRscripts/10restartFile.rst");
parameter = tmp;
}
else
{
std::string mixDef = ROCParameter::allUnique;
ROCParameter tmp(sphi_init, numMixtures, geneAssignment, mixtureDefinitionMatrix, true, mixDef);
for (unsigned i = 0u; i < numMixtures; i++)
{
unsigned selectionCategry = tmp.getSelectionCategory(i);
std::cout << "Sphi_init for selection category " << selectionCategry << ": " << sphi_init[selectionCategry] << std::endl;
}
std::cout << "\t# mixtures: " << numMixtures << "\n";
std::cout << "\tmixture definition: " << mixDef << "\n";
std::vector<std::string> files(2);
files[0] = std::string("F:/GitHub/RibModelDev/data/twoMixtures/simulated_mutation0.csv");
files[1] = std::string("F:/GitHub/RibModelDev/data/twoMixtures/simulated_mutation1.csv");
tmp.initMutationCategories(files, tmp.getNumMutationCategories());
files[0] = std::string("F:/GitHub/RibModelDev/data/twoMixtures/simulated_selection0.csv");
files[1] = std::string("F:/GitHub/RibModelDev/data/twoMixtures/simulated_selection1.csv");
tmp.initSelectionCategories(files, tmp.getNumSelectionCategories());
tmp.InitializeSynthesisRate(genome, sphi_init[0]);
//std::vector<double> phiVals = parameter.readPhiValues("/home/clandere/CodonUsageBias/RibosomeModel/RibModelFramework/ribModel/data/Skluyveri_ChrA_ChrCleft_phi_est.csv");
//parameter.InitializeSynthesisRate(phiVals);
}
std::cout << "Done!--------------------------------\n\n\n" << std::endl;
std::cout << "Initializing ROCModel object--------------------------\n";
ROCModel model;
model.setParameter(parameter);
std::cout << "Done!----------------------------------\n\n\n" << std::endl;
std::cout << "Running MCMC.............\n" << std::endl;
mcmc.run(genome, model, 1, 0);
std::cout << "Done!----------------------------------\n\n\n" << std::endl;
} //END OF ROC
else if (modelToRun == "RFP")
{
std::cout << "Initializing Genome object--------------------------" << std::endl;
Genome genome;
genome.readRFPFile("/Users/roxasoath1/Desktop/RibModelDevScripts/RibModelDev/data/rfp/rfp.counts.by.codon.and.gene.GSE63789.wt.csv");
std::cout << "Done!-------------------------------\n\n\n";
std::cout << "Initializing shared parameter variables---------------\n";
std::vector<unsigned> geneAssignment(genome.getGenomeSize());
std::vector<double> sphi_init(numMixtures, 1);
if (numMixtures == 1)
{
for (unsigned i = 0u; i < genome.getGenomeSize(); i++)
{
geneAssignment[i] = 0u;
}
}
else if (numMixtures == 3)
{
for (unsigned i = 0u; i < genome.getGenomeSize(); i++)
{
if (i < 961) geneAssignment[i] = 0u;
else if (i < 1418) geneAssignment[i] = 1u;
else geneAssignment[i] = 0u;
}
}
std::vector<std::vector<unsigned>> mixtureDefinitionMatrix;
std::cout << "Done!------------------------\n\n\n";
std::cout << "Initializing RFPParameter object--------------------\n" << std::endl;
RFPParameter parameter;
if (fromRestart)
{
RFPParameter tmp("/Users/roxasoath1/Desktop/RibModelFramework/10_restartFile.rst");
parameter = tmp;
}
else
{
std::string mixDef = Parameter::allUnique;
RFPParameter tmp(sphi_init, numMixtures, geneAssignment, mixtureDefinitionMatrix, true, mixDef);
for (unsigned i = 0u; i < numMixtures; i++) {
unsigned selectionCategry = tmp.getSelectionCategory(i);
std::cout << "Sphi_init for selection category " << selectionCategry << ": " <<
sphi_init[selectionCategry] << std::endl;
}
std::cout << "\t# mixtures: " << numMixtures << "\n";
std::cout << "\tmixture definition: " << mixDef << "\n";
tmp.InitializeSynthesisRate(genome, sphi_init[0]);
parameter = tmp;
}
std::cout << "Done!--------------------------------\n\n\n" << std::endl;
std::cout << "Initializing RFPModel object--------------------------\n";
RFPModel model;
model.setParameter(parameter);
std::cout << "Done!----------------------------------\n\n\n" << std::endl;
std::cout << "Running MCMC.............\n" << std::endl;
mcmc.run(genome, model, 1, 0);
std::cout << "Done!----------------------------------\n\n\n" << std::endl;
} //END OF RFP
else if (modelToRun == "FONSE")
{
std::cout << "initialize Genome object--------------------------" << std::endl;
Genome genome;
genome.readFasta("/Users/roxasoath1/Desktop/RibModelDevScripts/RibModelDev/data/FONSE/genome_2000.fasta");
std::cout << "Done!-------------------------------\n\n\n";
std::cout << "Initializing shared parameter variables---------------\n";
std::vector<unsigned> geneAssignment(genome.getGenomeSize());
std::vector<double> sphi_init(numMixtures, 1);
if (numMixtures == 1)
{
for (unsigned i = 0u; i < genome.getGenomeSize(); i++)
{
geneAssignment[i] = 0u;
}
}
else if (numMixtures == 3)
{
for (unsigned i = 0u; i < genome.getGenomeSize(); i++)
{
if (i < 961) geneAssignment[i] = 0u;
else if (i < 1418) geneAssignment[i] = 1u;
else geneAssignment[i] = 0u;
}
}
std::vector<std::vector<unsigned>> mixtureDefinitionMatrix;
std::cout << "Done!------------------------\n\n\n";
FONSEParameter parameter;
std::cout << "initialize Parameter object" << std::endl;
if (fromRestart)
{
FONSEParameter tmp("/Users/roxasoath1/Desktop/RibModelDevScripts/RibModelDev/DevRscripts/10restartFile.rst");
parameter = tmp;
}
else
{
std::string mixDef = ROCParameter::allUnique;
FONSEParameter tmp(sphi_init, numMixtures, geneAssignment, mixtureDefinitionMatrix, true, mixDef);
for (unsigned i = 0u; i < numMixtures; i++) {
unsigned selectionCategry = tmp.getSelectionCategory(i);
std::cout << "Sphi_init for selection category " << selectionCategry << ": " <<
sphi_init[selectionCategry] << std::endl;
}
std::cout << "\t# mixtures: " << numMixtures << "\n";
std::cout << "\tmixture definition: " << mixDef << "\n";
std::vector<std::string> files(1);
files[0] = std::string(
"/Users/roxasoath1/Desktop/RibModelDevScripts/RibModelDev/data/FONSE/genome_2000.mutation.csv");
tmp.initMutationCategories(files, tmp.getNumMutationCategories());
tmp.InitializeSynthesisRate(genome, sphi_init[0]);
//std::vector<double> phiVals = parameter.readPhiValues("/home/clandere/CodonUsageBias/RibosomeModel/RibModelFramework/ribModel/data/Skluyveri_ChrA_ChrCleft_phi_est.csv");
//parameter.InitializeSynthesisRate(phiVals);
parameter = tmp;
std::cout << "done initialize Parameter object" << std::endl;
}
std::cout << "Initializing Model object\n";
FONSEModel model;
model.setParameter(parameter);
std::cout << "starting MCMC for ROC" << std::endl;
mcmc.run(genome, model, 4, 0);
std::cout << std::endl << "Finished MCMC for ROC" << std::endl;
}
}
