int main()
{
std::string pathBegin = "/home/nax/Work/biolab/TestingIn/";
unsigned numMixtures = 1;
std::vector<double> sphi_init(numMixtures, 2);
std::vector<std::vector<unsigned> > mixtureDefinitionMatrix;
// SIMULATE GENOME: RFP
Genome genome;
//if(testEqualityGenome(genome, genome)){
// my_print("So far so good\n");
//}
//exit(1);
genome.readRFPData(pathBegin + "rfp_file_20positions_20genes.csv", false);
exit(0);
/*genome.readFasta(pathBegin + "RibModelDev/data/singleMixture/genome_2000.fasta", false);
std::vector<unsigned> geneAssignment(genome.getGenomeSize());
for (unsigned i = 0u; i < genome.getGenomeSize(); i++)
{
geneAssignment[i] = 0u;
}
PAParameter parameter(sphi_init, numMixtures, geneAssignment, mixtureDefinitionMatrix, true, "allUnique");
PAModel model;
//ROCParameter parameter(sphi_init, numMixtures, geneAssignment, mixtureDefinitionMatrix, true, "allUnique");
//ROCModel model;
model.setParameter(parameter);
model.simulateGenome(genome);
genome.writeRFPData(pathBegin + "labbooks/Denizhan.Pak/Log_Files/sim_genomes/PASim.csv", true);
genome.writeRFPData(pathBegin + "labbooks/Denizhan.Pak/Log_Files/sim_genomes/PANotSim.csv", false);
exit(1);*/
// UNIT TESTING
//testUtility();
//testSequenceSummary();
//testGene();
//testGenome(pathBegin + "RibModelFramework/tests/testthat/UnitTestingData");
//testCovarianceMatrix();
//testParameter();
//testParameterWithFile(pathBegin + "HollisFile.txt");
//testPAParameter();
//testMCMCAlgorithm();
//exit(0);
std::string modelToRun = "PANSE"; //can be RFP, ROC or FONSE
bool withPhi = false;
bool fromRestart = false;
my_print("Initializing MCMCAlgorithm object---------------\n");
unsigned samples = 100;
unsigned thinning = 100;
int useSamples = 1000;
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 == "PANSE")
{
my_print("Initializing Genome object--------------------------\n");
Genome genome;
//genome.readRFPData(pathBegin + "RibModelDev/data/rfp/rfp.counts.by.codon.and.gene.GSE63789.wt.csv");
genome.readRFPData(pathBegin + "PopPAData.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 PANSEParameter object--------------------\n\n");
PANSEParameter parameter;
//parameter.writeBasicRestartFile("/Users/hollisbui/HollisFile.txt");
if (fromRestart)
{
PANSEParameter tmp(pathBegin + "RibModelFramework/10_restartFile.rst");
parameter = tmp;
}
else
{
std::string mixDef = Parameter::allUnique;
PANSEParameter 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 PAModel object--------------------------\n");
PANSEModel 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()
{
std::string pathBegin = "/Users/hollisbui/";
unsigned numMixtures = 1;
std::vector<double> sphi_init(numMixtures, 2);
std::vector<std::vector<unsigned>> mixtureDefinitionMatrix;
/*
// SIMULATE GENOME: PA
Genome genome;
genome.readRFPData(pathBegin + "TODO");
std::vector<unsigned> geneAssignment(genome.getGenomeSize());
for (unsigned i = 0u; i < genome.getGenomeSize(); i++)
geneAssignment[i] = 0u;
PAParameter parameter(sphi_init, numMixtures, geneAssignment, mixtureDefinitionMatrix, true, "allUnique");
std::vector<std::string> files;
files.push_back(pathBegin + "miscGilchrist/runMe/HollisTestingData/RFPAlphaValues.csv");
parameter.initMutationSelectionCategories(files, 1, PAParameter::alp);
files[0] = pathBegin + "miscGilchrist/runMe/HollisTestingData/RFPLambdaPrimeValues.csv";
parameter.initMutationSelectionCategories(files, 1, PAParameter::lmPri);
std::vector<double> phi = parameter.readPhiValues(pathBegin + "miscGilchrist/runMe/HollisTestingData/RFPPhiValues.csv");
//std::vector<double> phi = tmp.readPhiValues("/Users/roxasoath1/Desktop/TONEWTON/RFPPsiValues.csv");
parameter.InitializeSynthesisRate(phi);
PAModel model;
model.setParameter(parameter);
model.simulateGenome(genome);
genome.writeRFPData(pathBegin + "miscGilchrist/runMe/HollisTestingOut/hbuiSimGenome5.30.17.csv", true);
exit(1);
*/
// UNIT TESTING
//testUtility();
//testSequenceSummary();
//testGene();
//testGenome(pathBegin + "RibModelFramework/tests/testthat/UnitTestingData");
//testCovarianceMatrix();
//testParameter();
//testMCMCAlgorithm();
//exit(0);
std::string modelToRun = "PA"; //can be PA, ROC or FONSE
bool withPhi = false;
bool fromRestart = false;
my_print("Initializing MCMCAlgorithm object---------------\n");
unsigned samples = 1000;
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");
my_print("Initializing Genome object--------------------------\n");
Genome genome;
if (modelToRun == "ROC")
{
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;
}
}
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 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(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 == "PA")
{
genome.readRFPData(pathBegin + "labnotebooks/Hollis.Bui/RunnableScriptsAndData/June2017PAModelPop/PopPADataOneGene.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;
}
}
my_print("Done!------------------------\n\n\n");
my_print("Initializing PAParameter object--------------------\n\n");
PAParameter parameter;
parameter.writeBasicRestartFile(pathBegin + "RibModelFramework/HollisRestartFile.txt");
if (fromRestart)
{
PAParameter tmp(pathBegin + "RibModelFramework/10_restartFile.rst");
parameter = tmp;
}
else
{
std::string mixDef = Parameter::allUnique;
PAParameter 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);
tmp.InitializeSynthesisRate(genome, sphi_init[0]);
parameter = tmp;
parameter.writeEntireRestartFile(pathBegin + "RibModelFramework/HollisRestartFile2.txt");
}
my_print("Done!--------------------------------\n\n\n");
my_print("Initializing PAModel object--------------------------\n");
PAModel 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");
std::vector<double> alphaList (61,0);
std::vector<double> lambdaPrimeList (61,0);
std::vector<double> waitingTimes (61,0);
std::vector<double> waitRates (61,0);
std::vector<std::string> codonList = SequenceSummary::codons();
unsigned cat = 0u;
for (unsigned i = 0u; i < 61; i++)
{
std::string codon = codonList[i];
alphaList[i] = parameter.getCodonSpecificPosteriorMean(cat, samples / 2, codon, 0, false);
//alphaTrace <- trace$getCodonSpecificParameterTraceByMixtureElementForCodon(1, codon, 0, FALSE)
//alpha.ci[i,] <- quantile(alphaTrace[(samples * 0.5):samples], probs = c(0.025,0.975))
lambdaPrimeList[i] = parameter.getCodonSpecificPosteriorMean(cat, samples / 2, codon, 1, false);
//lambdaPrimeTrace <- trace$getCodonSpecificParameterTraceByMixtureElementForCodon(1, codon, 1, FALSE)
//lambdaPrime.ci[i,] <- quantile(lambdaPrimeTrace[(samples * 0.5):samples], probs = c(0.025,0.975))
waitingTimes[i] = alphaList[i] / lambdaPrimeList[i];
waitRates[i] = (1.0/waitingTimes[i]);
my_print("For codon %, alpha is %, lambda prime is %, and waitingTime is %.\n", codonList[i], alphaList[i],
lambdaPrimeList[i], waitingTimes[i]);
}
} //END OF PA
else if (modelToRun == "FONSE")
{
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;
}
}
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()
{
std::cout << "Initializing MCMCAlgorithm object---------------" << std::endl;
int samples = 2000;
int thinning = 1000;
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, 100, false, true, true);
mcmc.setRestartFileSettings(std::string("test"), 100, true);
//mcmc.setRestartFileSettings("RestartFile.txt", 20, true);
std::cout << "Done!-------------------------------\n\n\n";
std::cout << "initialize Genome object--------------------------" << std::endl;
bool withPhi = true;
Genome genome;
genome.readFasta("/home/clandere/CodonUsageBias/R_roctest/bioinf_test_data/second_run/genome1/sim_oneMix_id_1_csp_-1_1_sphi_0.5.fasta");
//genome.readFasta("F:/GitHub/RibModelDev/data/twoMixtures/simulatedAllUniqueR.fasta");
//genome.readFasta("E:/RibosomeModel/RibModelDev/data/twoMixtures/simulatedAllUniqueR_unevenMixtures.fasta");
if(withPhi)
{
genome.readObservedPhiValues("/home/clandere/CodonUsageBias/R_roctest/bioinf_test_data/second_run/genome1/sim_oneMix_id_1_sphi_0.5_aphi_1_seps_1.csv", false);
//genome.readObservedPhiValues("E:/RibosomeModel/RibModelDev/data/twoMixtures/simulatedAllUniqueR_phi_unevenMixtures.csv", false);
}
std::cout << "Done!-------------------------------\n\n\n";
std::cout << "Initializing shared parameter variables---------------\n";
std::cout << "Done!-------------------------------\n\n\n";
std::cout << "Initializing shared parameter variables---------------\n";
std::vector<unsigned> geneAssignment(genome.getGenomeSize());
unsigned numMixtures = 1;
std::vector<double> sphi_init(numMixtures, 1);
/* For 2 mixture */
for (unsigned i = 0u; i < genome.getGenomeSize(); i++)
{
//geneAssignment[i] = ( ((double)rand() / (double)RAND_MAX) < 0.5 ? 0u : 1u );
geneAssignment[i] = 0u;
}
std::vector<std::vector<unsigned>> mixtureDefinitionMatrix;
std::cout << "Done!------------------------\n\n\n";
std::cout << "initialize ROCParameter object" << std::endl;
std::string mixDef = ROCParameter::allUnique;
ROCParameter parameter(sphi_init, numMixtures, geneAssignment, mixtureDefinitionMatrix, true, mixDef);
for (unsigned i = 0u; i < numMixtures; i++)
{
unsigned selectionCategry = parameter.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("F:/GitHub/RibModelDev/data/twoMixtures/simulated_mutation0.csv");
//files[1] = std::string("F:/GitHub/RibModelDev/data/twoMixtures/simulated_mutation1.csv");
files[0] = std::string("/home/clandere/CodonUsageBias/R_roctest/bioinf_test_data/second_run/genome1/sim_oneMix_mutation_id_1_csp_-1_1_sphi_0.5.csv");
//files[1] = std::string("/home/clandere/CodonUsageBias/RibosomeModel/RibModelDev/data/twoMixtures/simulated_mutation1.csv");
parameter.initMutationCategories(files, parameter.getNumMutationCategories());
files.resize(1);
//files[0] = std::string("F:/GitHub/RibModelDev/data/twoMixtures/simulated_selection0.csv");
//files[1] = std::string("F:/GitHub/RibModelDev/data/twoMixtures/simulated_selection1.csv");
files[0] = std::string("/home/clandere/CodonUsageBias/R_roctest/bioinf_test_data/second_run/genome1/sim_oneMix_selection_id_1_csp_-1_1_sphi_0.5.csv");
//files[1] = std::string("/home/clandere/CodonUsageBias/RibosomeModel/RibModelDev/data/twoMixtures/simulated_selection1.csv");
parameter.initSelectionCategories(files, parameter.getNumSelectionCategories());
parameter.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 initialize ROCParameter object" << std::endl;
std::cout << "Initializing ROCModel object\n";
ROCModel model(withPhi);
model.setParameter(parameter);
std::cout << "starting MCMC for ROC" << std::endl;
mcmc.run(genome, model, 1, 0);
std::cout << std::endl << "Finished MCMC for ROC" << std::endl;
std::cout << std::endl << "Exiting" << std::endl;
}
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.readRFPData("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 PAParameter object--------------------\n" << std::endl;
PAParameter parameter;
if (fromRestart)
{
PAParameter tmp("/Users/roxasoath1/Desktop/RibModelFramework/DevRscripts/10restartFile.rst");
parameter = tmp;
}
else
{
std::string mixDef = Parameter::allUnique;
PAParameter 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 PAModel object--------------------------\n";
PAModel 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()
{
if (1)
{
//testSequenceSummary();
//testGene();
testGenome("/Users/roxasoath1/Desktop/RibModelDevScripts/RibModelDev/data/UnitTestingData");
/*
Genome genome;
genome.readRFPData("/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;
PAParameter 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, PAParameter::alp);
files[0] = "/Users/roxasoath1/Desktop/TONEWTON/RFPLambdaPrimeValues.csv";
tmp.initMutationSelectionCategories(files, 1, PAParameter::lmPri);
std::vector<double> phi = tmp.readPhiValues("/Users/roxasoath1/Desktop/TONEWTON/RFPPsiValues.csv");
tmp.InitializeSynthesisRate(phi);
PAModel model;
model.setParameter(tmp);
std::cout <<"init done\n";
model.simulateGenome(genome);
std::cout <<"writing file\n";
genome.writeRFPData("/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.readRFPData("/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 PAParameter object--------------------\n" << std::endl;
PAParameter parameter;
if (fromRestart)
{
PAParameter tmp("/Users/roxasoath1/Desktop/RibModelFramework/10_restartFile.rst");
parameter = tmp;
}
else
{
std::string mixDef = Parameter::allUnique;
PAParameter 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 PAModel object--------------------------\n";
PAModel 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;
}
}
int main()
{
std::cout << "Initializing MCMCAlgorithm object---------------" << std::endl;
int samples = 200;
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, 100, false, true, true);
mcmc.setRestartFileSettings(std::string("test"), 100, true);
//mcmc.setRestartFileSettings("RestartFile.txt", 20, true);
std::cout << "Done!-------------------------------\n\n\n";
std::cout << "initialize Genome object--------------------------" << std::endl;
bool withPhi = false;
Genome genome;
genome.readFasta("/home/clandere/CodonUsageBias/RibosomeModel/RibModelDev/data/twoMixtures/simulatedMutationSharedR.fasta");
//genome.readFasta("F:/GitHub/RibModelDev/data/twoMixtures/simulatedAllUniqueR.fasta");
//genome.readFasta("E:/RibosomeModel/RibModelDev/data/twoMixtures/simulatedAllUniqueR_unevenMixtures.fasta");
if(withPhi)
{
genome.readObservedPhiValues("F:/GitHub/RibModelDev/data/twoMixtures/simulatedAllUniqueR_phi_withPhiSet.csv", false);
//genome.readObservedPhiValues("E:/RibosomeModel/RibModelDev/data/twoMixtures/simulatedAllUniqueR_phi_unevenMixtures.csv", false);
}
std::cout << "Done!-------------------------------\n\n\n";
std::cout << "Initializing shared parameter variables---------------\n";
std::cout << "Done!-------------------------------\n\n\n";
std::cout << "Initializing shared parameter variables---------------\n";
std::vector<unsigned> geneAssignment(genome.getGenomeSize());
unsigned numMixtures = 2;
std::vector<double> sphi_init(numMixtures, 1);
/* For 2 mixture */
for (unsigned i = 0u; i < genome.getGenomeSize(); i++)
{
geneAssignment[i] = ( ((double)rand() / (double)RAND_MAX) < 0.5 ? 0u : 1u );
}
std::vector<std::vector<unsigned>> mixtureDefinitionMatrix;
std::cout << "Done!------------------------\n\n\n";
std::cout << "initialize ROCParameter object" << std::endl;
std::string mixDef = ROCParameter::mutationShared;
ROCParameter parameter(sphi_init, numMixtures, geneAssignment, mixtureDefinitionMatrix, true, mixDef);
for (unsigned i = 0u; i < numMixtures; i++)
{
unsigned selectionCategry = parameter.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("F:/GitHub/RibModelDev/data/twoMixtures/simulated_mutation0.csv");
//files[1] = std::string("F:/GitHub/RibModelDev/data/twoMixtures/simulated_mutation1.csv");
files[0] = std::string("/home/clandere/CodonUsageBias/RibosomeModel/RibModelDev/data/twoMixtures/simulated_mutation0.csv");
//files[1] = std::string("/home/clandere/CodonUsageBias/RibosomeModel/RibModelDev/data/twoMixtures/simulated_mutation1.csv");
parameter.initMutationCategories(files, parameter.getNumMutationCategories());
files.resize(2);
//files[0] = std::string("F:/GitHub/RibModelDev/data/twoMixtures/simulated_selection0.csv");
//files[1] = std::string("F:/GitHub/RibModelDev/data/twoMixtures/simulated_selection1.csv");
files[0] = std::string("/home/clandere/CodonUsageBias/RibosomeModel/RibModelDev/data/twoMixtures/simulated_selection0.csv");
files[1] = std::string("/home/clandere/CodonUsageBias/RibosomeModel/RibModelDev/data/twoMixtures/simulated_selection1.csv");
parameter.initSelectionCategories(files, parameter.getNumSelectionCategories());
parameter.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 initialize ROCParameter object" << std::endl;
std::cout << "Initializing ROCModel object\n";
ROCModel model(withPhi);
model.setParameter(parameter);
std::cout << "starting MCMC for ROC" << std::endl;
mcmc.run(genome, model, 1, 0);
std::cout << std::endl << "Finished MCMC for ROC" << std::endl;
double temp[] = { 0.025, 0.5, 0.975 };
std::vector<double> probs(temp, temp + sizeof(temp) / sizeof(double));
//std::vector<double> quants = parameter.getCodonSpecificQuantile(1, 100, std::string("GCA"), 0, probs, true);
std::string codon = std::string("TTT");
double a = parameter.getCodonSpecificPosteriorMean(0u, 50u, codon, 0u, true);
double b = parameter.getCodonSpecificPosteriorMean(0u, 50u, codon, 1u, true);
double c = parameter.getCodonSpecificPosteriorMean(1u, 50u, codon, 0u, true);
double d = parameter.getCodonSpecificPosteriorMean(1u, 50u, codon, 1u, true);
std::cout << std::endl << "Exiting" << std::endl;
}