std::pair<Chromosome, Breeder::BreedStats> Breeder::breed(const Chromosome& mum, const Chromosome& dad, uint32_t crossOverPerMillion)
{
BreedStats stats;
stats.crossOvers = 0;
std::random_device rd;
std::uniform_int_distribution<> randomMillion(0, 999999);
std::uniform_int_distribution<> mumOrDad(0, 1);
bool startWithMum = mumOrDad(rd) == 0;
const Gene* currentGene = startWithMum ? &mum.gene() : &dad.gene();
const Gene* otherGene = startWithMum ? &dad.gene() : &mum.gene();
Gene resultingGene;
resultingGene.resize(currentGene->size());
for(uint32_t i = 0; i < resultingGene.size(); i++)
{
resultingGene[i] = (*currentGene)[i];
if(crossOverPerMillion > randomMillion(rd))
{
std::swap(currentGene, otherGene);
++stats.crossOvers;
}
}
return {Chromosome(mum.maxCistronIds(), mum.informationDensity(), mum.startSequence(), mum.stopSequence(), resultingGene), stats};
}
void Chromosome::replaceCistronValues(const std::vector<Cistron>& cistrons)
{
CistronMap cistronMap;
for(const auto& cistron : cistrons)
{
cistronMap.emplace(cistron.id(), cistron);
}
size_t start = 0;
while((start = mGene.find(mStartSequence, start)) != std::string::npos)
{
size_t stop = mGene.find(mStopSequence, start);
if(stop != std::string::npos)
{
size_t cistronStart = start + mStartSequence.size();
Cistron cistron(mGene.substr(cistronStart, stop - cistronStart), mMaxCistronIds, mInformationDensity);
if(cistronMap.count(cistron.id()))
{
Gene toInsert = mStartSequence;
toInsert.append(cistronMap.at(cistron.id()).gene());
toInsert.append(mStopSequence);
mGene.replace(start, toInsert.size(), toInsert);
}
}
start = stop;
}
}
void Host::RestoreHost(const string& sline)
{
stringstream ssline(sline);
ssline >> lociKIR;
ssline >> lociMHC;
ssline >>age;
ssline >> tuning;
ssline >> dead;
ssline >> mutationRateHost;
ssline >> inhibitoryKIRs;
ssline >> activatingKIRs;
int totalInfections;
ssline >> totalInfections;
/*use the streamstring from the position after "totalInfections"
*for that I copy the rest of the line into a string, and then reassign the streamstring with the content of
*for "restLine. For it to work, I have to clear the string first!
*/
string restLine;
getline(ssline,restLine);
ssline.clear();
ssline.str(restLine);
string infectionString;
int type; double inf_time; double immune_time; double clearance_time;
for(int i=0; i<totalInfections; i++)
{
Infection dummyInfection;
infectionString = dummyInfection.RestoreInfection(ssline);
infections.push_back(dummyInfection);
ssline.clear();
ssline.str(infectionString);
}
string geneString;
//cout <<"mhc string>>>>>"<<ssline.str() <<endl;
for(int i=0; i<lociMHC*TWO; i++)
{
Gene mhc;
geneString = mhc.RestoreGenes(ssline);
mhcGenes.push_back(mhc);
ssline.clear();
ssline.str(geneString);
}
string kirString;
for(int i=0; i<lociKIR*TWO; i++)
{
//cout <<"kir string>>>>>"<<ssline.str() <<endl;
KIRGene kir;
kirString = kir.RestoreGenes(ssline);
kirGenes.push_back(kir);
ssline.clear();
ssline.str(kirString);
}
}
void SmallWorld::initialize() {
for (int i = 0; i < bugNum; i++) {
Gene gene;
gene.initialize(minSpeed, maxSpeed, nodeNum * turn);
genes[i] = gene;
}
generations++;
}
void FONSEModel::calculateLogLikelihoodRatioPerGroupingPerCategory(std::string grouping, Genome& genome, std::vector<double> &logAcceptanceRatioForAllMixtures)
{
int numGenes = genome.getGenomeSize();
//int numCodons = SequenceSummary::GetNumCodonsForAA(grouping);
double likelihood = 0.0;
double likelihood_proposed = 0.0;
double mutation[5];
double selection[5];
double mutation_proposed[5];
double selection_proposed[5];
std::string curAA;
Gene *gene;
SequenceSummary *sequenceSummary;
unsigned aaIndex = SequenceSummary::AAToAAIndex(grouping);
#ifdef _OPENMP
//#ifndef __APPLE__
#pragma omp parallel for private(mutation, selection, mutation_proposed, selection_proposed, curAA, gene, sequenceSummary) reduction(+:likelihood,likelihood_proposed)
#endif
for (unsigned i = 0u; i < numGenes; i++)
{
gene = &genome.getGene(i);
sequenceSummary = gene->getSequenceSummary();
if (sequenceSummary->getAACountForAA(aaIndex) == 0) continue;
// which mixture element does this gene belong to
unsigned mixtureElement = parameter->getMixtureAssignment(i);
// how is the mixture element defined. Which categories make it up
unsigned mutationCategory = parameter->getMutationCategory(mixtureElement);
unsigned selectionCategory = parameter->getSelectionCategory(mixtureElement);
unsigned expressionCategory = parameter->getSynthesisRateCategory(mixtureElement);
// get phi value, calculate likelihood conditional on phi
double phiValue = parameter->getSynthesisRate(i, expressionCategory, false);
// get current mutation and selection parameter
parameter->getParameterForCategory(mutationCategory, FONSEParameter::dM, grouping, false, mutation);
parameter->getParameterForCategory(selectionCategory, FONSEParameter::dOmega, grouping, false, selection);
// get proposed mutation and selection parameter
parameter->getParameterForCategory(mutationCategory, FONSEParameter::dM, grouping, true, mutation_proposed);
parameter->getParameterForCategory(selectionCategory, FONSEParameter::dOmega, grouping, true, selection_proposed);
likelihood += calculateLogLikelihoodRatioPerAA(*gene, grouping, mutation, selection, phiValue);
likelihood_proposed += calculateLogLikelihoodRatioPerAA(*gene, grouping, mutation_proposed, selection_proposed, phiValue);
}
//likelihood_proposed = likelihood_proposed + calculateMutationPrior(grouping, true);
//likelihood = likelihood + calculateMutationPrior(grouping, false);
logAcceptanceRatioForAllMixtures[0] = (likelihood_proposed - likelihood);
}
/* -----------------------------------------------------------------------
* makeGeneVector():
*
* Returns a vector of n randomly generated genes of length CHROMOSOME_LENGTH. Gives each
* object in the vector a fitness level of 0 to start it out.
* -----------------------------------------------------------------------
*/
vector<Gene> makeGeneVector(int n)
{
vector<Gene> geneVector;
/* Make INITIAL_POPULATION amount of random genes and push it to firstNGenes */
for (int i = 0; i < INITIAL_POPULATION; i++)
{
Gene g;
g.setValues(makeRandomGene(), 0);
geneVector.push_back(g);
}
return geneVector;
}
genotypes::genotypes(int genomSize) {
Gene n;
for(int i = 0; i < genomSize; i++){
for(int j = 0; j < SEGMENT_SIZE; j++){
if(rand()%2){
n.flip(j);
}
}
genom.push_back(n);
n.reset();
}
}
unsigned int Neuron::loadWeights(Gene const &gene, unsigned int index)
{
unsigned int i(0);
for (auto &s : _inputs)
{
s.second = gene.getWeight(index + i);
i++;
}
return index + i;
}
bool operator<(const Gene& g) const {
if( (compareChar(chrom.c_str(), g.getChr().c_str()) < 0) ||
(hs == g.getHS() && entrez_ID < g.getEID()) ||
(hs == g.getHS() && entrez_ID == g.getEID() && start_p < g.getStart()) ||
(hs == g.getHS() && entrez_ID == g.getEID() && start_p == g.getStart() && stop_p < g.getStop())
)
return true;
else
return false;
}
Genome* SelfAdaptiveMutation::mutateProper(Genome* target) {
std::vector<Gene*> genes = target->getGenome();
std::vector<Gene*> results;
for (unsigned int i = 0; i < this->initialGenomeLength; i++)
results.push_back(genes[i]->copy());
double rhoZero = HierRNG::gaussian(0, 1);
for (unsigned int index: this->stdDevIndices) {
Gene* target = genes[index];
double stdDev = target->getIndex();
double tauResult = this->tauPrime * rhoZero
+ this->tau * HierRNG::gaussian(0, 1);
stdDev *= this->useTauPlusOneCorrection ?
pow(stdDev, tauResult) : exp(tauResult);
results.push_back(target->copy(stdDev));
}
for (unsigned int i = 0; i < this->initialGenomeLength; i++) {
Gene* original = results[i];
double newIndex = original->getIndex();
newIndex = newIndex
+ results[this->initialGenomeLength + i]->getIndex()
* HierRNG::gaussian(0, 1);
results[i] = original->copy(newIndex);
delete(original);
}
return new Genome(results, target->getSpeciesNode());
}
void main()
{
CDiophantine dp(1, 2, 3, 4, 30);
int ans;
ans = dp.Solve();
if (ans == -1)
{
cout << "No solution found." << endl;
}
else
{
Gene gn = dp.GetGene(ans);
cout << "The solution set to a+2b+3c+4d=30 is:\n";
cout << "a = " << gn.getAlleles()[0] << "." << endl;
cout << "b = " << gn.getAlleles()[1] << "." << endl;
cout << "c = " << gn.getAlleles()[2] << "." << endl;
cout << "d = " << gn.getAlleles()[3] << "." << endl;
}
getchar();
}
void genetic::Generation::Generate(const genetic::Generation& ancestor)
{
int& nCells = gainput.max_cells;
m_cells = vector<Cell>(nCells, Cell());
int iCell = 0;
// Chose Elites
for(; iCell < gainput.max_elite; ++iCell) m_cells[iCell] = ancestor.m_cells[iCell];
// Selection to Next Generation
while(iCell < nCells)
{
Gene child;
if(drand(1.0) > gainput.thre_cloning)
{
child = ancestor.Select().Gen();
}
else
{
Cell father(ancestor.Select());
Cell mother(ancestor.Select());
// if(father.Fitness() > mother.Fitness())
child = father.Gen() * mother.Gen();
// else
// child = mother.Gen() * father.Gen();
}
// Mutation
if(drand(1.0) < gainput.thre_mutation) child.pMutate();
if(drand(1.0) < gainput.thre_mutation) child.gMutate();
m_cells[iCell++] = Cell(child);
}
ComputeProbability();
}
void Gene::singleCross(Gene& g1,Gene& g2,unsigned position){
Gene g1temp = g1;
unsigned word = position / bits_per_word;
unsigned bit = position % bits_per_word;
unsigned byte_before = word * sizeof(g1.data[0]);
memcpy(g1temp.data, g2.data, byte_before);
memcpy(g2.data, g1.data, byte_before);
for(int i = 0 ; i < bit ; i++){
if( (g1.data[word] & (BIT_MASK << i)) != (g2.data[word] & (BIT_MASK << i)) ){
unsigned pos = i + word * bits_per_word;
g1temp.toggle(pos);
g2.toggle(pos);
}
}
g1 = g1temp;
};
double genetic::Evaluate(const double& scale, const double& np, const Gene& gene, const Matrix& K)
{
Matrix Kp;
Permute(K, gene.Sequence(), Kp);
double weight = 0.0;
for(int i = 0; i < Kp.Nrows(); ++i)
for(int j = i + 1; j < Kp.Ncols(); ++j)
{
double d = j - i;
// weight += Kp.element(i, j) * pow(d, np);
weight += Kp.element(i, j) * d * d;
}
return scale * weight;
}
void SmallWorld::breed() {
if (bugs.size() > 2) {
vector<Gene> tmp;
tmp.resize(bugs.size());
tmp[0] = bugs[0].getGene();
tmp[1] = bugs[1].getGene();
for (int i = 2; i < bugs.size() - 1; i++) {
Gene gene;
gene.crossover(tmp[0].dna, tmp[1].dna, nodeNum * turn);
for (int j = 0; j < int(nodeNum / 4); j++) {
gene.mutation(minSpeed, maxSpeed, probability);
}
tmp[i] = gene;
}
for (int i = bugs.size() - 2; i < bugs.size() - 1; i++) {
Gene gene;
gene.crossover(tmp[0].dna, tmp[1].dna, nodeNum * turn);
for (int j = 0; j < int(nodeNum / 4); j++) {
gene.mutation(minSpeed, maxSpeed, probability * 10);
}
tmp[i] = gene;
}
for (int i = bugs.size() - 1; i < bugs.size(); i++) {
Gene gene;
gene.initialize(minSpeed, maxSpeed, nodeNum * turn);
tmp[i] = gene;
}
genes.swap(tmp);
}
generations++;
}
void Neuron::saveWeights(Gene &gene) const
{
for (auto s : _inputs)
gene.addWeight(s.second);
}
void FONSEModel::calculateLogLikelihoodRatioPerGene(Gene& gene, unsigned geneIndex, unsigned k, double* logProbabilityRatio)
{
double likelihood = 0.0;
double likelihood_proposed = 0.0;
std::string curAA;
std::vector <unsigned> positions;
double mutation[5];
double selection[5];
SequenceSummary *seqsum = gene.getSequenceSummary();
// get correct index for everything
unsigned mutationCategory = parameter->getMutationCategory(k);
unsigned selectionCategory = parameter->getSelectionCategory(k);
unsigned expressionCategory = parameter->getSynthesisRateCategory(k);
double phiValue = parameter->getSynthesisRate(geneIndex, expressionCategory, false);
double phiValue_proposed = parameter->getSynthesisRate(geneIndex, expressionCategory, true);
/* This loop causes a compiler warning because i is an int, but openMP won't compile if I change i to unsigned.
Maybe worth looking into? */
#ifndef __APPLE__
#pragma omp parallel for private(mutation, selection, positions, curAA) reduction(+:likelihood,likelihood_proposed)
#endif
for (int i = 0; i < getGroupListSize(); i++)
{
curAA = getGrouping(i);
parameter->getParameterForCategory(mutationCategory, FONSEParameter::dM, curAA, false, mutation);
parameter->getParameterForCategory(selectionCategory, FONSEParameter::dOmega, curAA, false, selection);
likelihood += calculateLogLikelihoodRatioPerAA(gene, curAA, mutation, selection, phiValue);
likelihood_proposed += calculateLogLikelihoodRatioPerAA(gene, curAA, mutation, selection, phiValue_proposed);
}
//std::cout << logLikelihood << " " << logLikelihood_proposed << std::endl;
double stdDevSynthesisRate = parameter->getStdDevSynthesisRate(false);
double logPhiProbability = Parameter::densityLogNorm(phiValue, (-(stdDevSynthesisRate * stdDevSynthesisRate) / 2), stdDevSynthesisRate, true);
double logPhiProbability_proposed = Parameter::densityLogNorm(phiValue_proposed, (-(stdDevSynthesisRate * stdDevSynthesisRate) / 2), stdDevSynthesisRate, true);
double currentLogLikelihood = (likelihood + logPhiProbability);
double proposedLogLikelihood = (likelihood_proposed + logPhiProbability_proposed);
if (phiValue == 0) {
std::cout << "phiValue is 0\n";
}
if (phiValue_proposed == 0) {
std::cout << "phiValue_prop is 0\n";
}
logProbabilityRatio[0] = (proposedLogLikelihood - currentLogLikelihood) - (std::log(phiValue) - std::log(phiValue_proposed));
logProbabilityRatio[1] = currentLogLikelihood - std::log(phiValue_proposed);
if (std::isinf(logProbabilityRatio[1])) {
std::cout << "logprob1 inf\n";
}
logProbabilityRatio[2] = proposedLogLikelihood - std::log(phiValue);
if (std::isinf(logProbabilityRatio[2])) {
std::cout << "logprob2 inf\n";
}
//------------NOTE: Jeremy, Cedric changed the reverse jump to where we DON'T include it. I had my RFP
//LogLikelihood go to 0 because of now missing terms. I have added the code underneath to where we calculate it---/
logProbabilityRatio[3] = currentLogLikelihood;
logProbabilityRatio[4] = proposedLogLikelihood;
}
void Host::MutateGenesForMutualInvasion(int mutationType, KIRGene& kir_hap2, Map& kirMap, GenePool& mhcPool, double simulationTime, double time_invasion, int gene_type)
{
if(mutationType == 1)//pick another molecule as mutation
{
KIRGene newGene(RandomNumber(2,16));
/*if(!kirMap.IsGeneInMap(newGene))
{
kirMap.FillMap(mhcPool, newGene);
//cout <<simulationTime << "|" <<time_invasion <<endl;
if(simulationTime < time_invasion)//only after the invasion time, the receptor type should be allowed to mutate
newGene.SetGeneType(gene_type);
kir_hap2.Copy(newGene);
}//*/
int M_id = 0;
int mhcPoolSize = mhcPool.GetPoolSize();
//calculate the value of M_id to determine whether the gene is pseudogene or not
for(unsigned int i = 0; i < mhcPoolSize; i++)
{
Gene mhcGene;
mhcGene.SetGeneID(mhcPool.GetGenes().at(i));
int L = newGene.BindMolecule(mhcGene);
if(L >= newGene.GetGeneSpecificity())
M_id += (1<<i);
}
//set the Gene pseudo
newGene.SetPseudogene(M_id);
if(gene_type !=2)////force to have only one type of receptors, if the user wants it!
newGene.SetGeneType(gene_type);
kir_hap2.Copy(newGene);
return;
}
if(mutationType == 2)//point mutation + L
{
if(RandomNumberDouble()<0.8)
{
kir_hap2.PointMutation();
//kirMap.FillMap(mhcPool, kir_hap2);
int M_id = 0;
int mhcPoolSize = mhcPool.GetPoolSize();
//calculate the value of M_id to determine whether the gene is pseudogene or not
for(unsigned int i = 0; i < mhcPoolSize; i++)
{
Gene mhcGene;
mhcGene.SetGeneID(mhcPool.GetGenes().at(i));
int L = kir_hap2.BindMolecule(mhcGene);
if(L >= kir_hap2.GetGeneSpecificity())
M_id+= (1<<i);
}
//set the Gene pseudo
kir_hap2.SetPseudogene(M_id);
}
if(RandomNumberDouble()<0.2)
{
kir_hap2.MutateSpecificity();
//kirMap.FillMap(mhcPool, kir_hap2);
int M_id = 0;
int mhcPoolSize = mhcPool.GetPoolSize();
//calculate the value of M_id to determine whether the gene is pseudogene or not
for(unsigned int i = 0; i < mhcPoolSize; i++)
{
Gene mhcGene;
mhcGene.SetGeneID(mhcPool.GetGenes().at(i));
int L = kir_hap2.BindMolecule(mhcGene);
if(L >= kir_hap2.GetGeneSpecificity())
M_id+= (1<<i);
}
//set the Gene pseudo
kir_hap2.SetPseudogene(M_id);
}
if(RandomNumberDouble()<0.2)
{
if(simulationTime >= time_invasion) //only after the invasion time, the receptor type should be allowed to mutate
kir_hap2.MutateReceptorType();
}
return;
}
}
void Host :: MutateGenes(int mutationType, KIRGene& kir_hap2, Map& kirMap, GenePool& mhcPool, int gene_type)
{
if(mutationType == 1)//pick another molecules as mutation
{
KIRGene newGene(RandomNumber(2,16));
/*if(!kirMap.IsGeneInMap(newGene))
{
kirMap.FillMap(mhcPool, newGene);
if(gene_type !=2)////force to have only one type of receptors, if the user wants it!
newGene.SetGeneType(gene_type);
kir_hap2.Copy(newGene);
}//*/
int M_id = 0;
int mhcPoolSize = mhcPool.GetPoolSize();
//calculate the value of M_id to determine whether the gene is pseudogene or not
for(unsigned int i = 0; i < mhcPoolSize; i++)
{
Gene mhcGene;
mhcGene.SetGeneID(mhcPool.GetGenes().at(i));
int L = newGene.BindMolecule(mhcGene);
if(L >= newGene.GetGeneSpecificity())
M_id += (1<<i);
}
newGene.SetPseudogene(M_id);
if(gene_type !=2)////force to have only one type of receptors, if the user wants it!
newGene.SetGeneType(gene_type);
kir_hap2.Copy(newGene);
return;
}
if(mutationType == 2)//point mutation + L
{
if(RandomNumberDouble()<0.8) //pointmutation
{
kir_hap2.PointMutation();
//kirMap.FillMap(mhcPool, kir_hap2);
int M_id = 0;
int mhcPoolSize = mhcPool.GetPoolSize();
//calculate the value of M_id to determine whether the gene is pseudogene or not
for(unsigned int i = 0; i < mhcPoolSize; i++)
{
Gene mhcGene;
mhcGene.SetGeneID(mhcPool.GetGenes().at(i));
int L = kir_hap2.BindMolecule(mhcGene);
if(L >= kir_hap2.GetGeneSpecificity())
M_id += (1<<i);
}
kir_hap2.SetPseudogene(M_id);
}
if(RandomNumberDouble()<0.8) //mutate L
{
kir_hap2.MutateSpecificity();
//kirMap.FillMap(mhcPool, kir_hap2);
int M_id = 0;
int mhcPoolSize = mhcPool.GetPoolSize();
//calculate the value of M_id to determine whether the gene is pseudogene or not
for(unsigned int i = 0; i < mhcPoolSize; i++)
{
Gene mhcGene;
mhcGene.SetGeneID(mhcPool.GetGenes().at(i));
int L = kir_hap2.BindMolecule(mhcGene);
if(L >= kir_hap2.GetGeneSpecificity())
M_id += (1<<i);
}
kir_hap2.SetPseudogene(M_id);
}
if(RandomNumberDouble()<0.8)//mutate type
{
kir_hap2.MutateReceptorType();
}
return;
}
}
/*FUNCTIONS OF CLASS HOST
*Constructs a host for the initialization of the population: it fills the MHC genes with a randomly picked allele from the population
* and creates KIRs that match their own MHC according to the specificity*/
Host::Host(int loci_kir, int loci_mhc, double _mutationRate, bool _tuning, int numberOfExtraKirs,Map& kirMap, MHCGenePool& mhcPool, bool hla) {
InitializeHostParameters(_mutationRate,_tuning, loci_kir, loci_mhc);
//fill the mhc Genes
for(int i = 0; i <lociMHC*TWO; i++)
{
Gene firstGene;
int mhc1 = mhcPool.RandomlyPickGene(hla);
firstGene.SetGeneID(mhc1);
mhcGenes.push_back(firstGene);
}
/*
Gene secondGene;
secondGene.SetGeneID(mhc2);
mhcGenes.push_back(secondGene);*/
//create random KIRs with random specificity for ONE haplotype
// (at the beginning of the simulation, the size of the map should equal the LOCI_NUMBER)
map< pair<int,int>, pair <int, int> > ::iterator it;
for(it = kirMap.GetMap().begin(); it != kirMap.GetMap().end(); it ++)
{
int id = it->first.first;
int geneType = it->first.second;
int L = it->second.first;
int pseudo = it->second.second;
KIRGene kir;
kir.SetGeneSpecificity(L);
kir.SetGeneID(id);
kir.SetPseudogene(pseudo);
kir.SetGeneType(geneType);
kir.SetGeneFunctionality(false);
kir.SetGeneExpression(false);
kirGenes.push_back(kir);
//cout << "printing genes in host first constructor" <<endl;
//kir.PrintGenes();
}
int size = kirGenes.size();
//make sure that the first haplotype has number lociKIR (regardless of the Map size!)
while(size < lociKIR)
{
KIRGene bla = kirGenes.at(size-1);
kirGenes.push_back(bla);
size ++;
}
//copy the first kirs into the other haplotype (all individuals are homozygous!)
for(int i=0; i<lociKIR; i++)
{
KIRGene kir = kirGenes.at(i);
kirGenes.push_back(kir);
}
if(tuning == true)
EducateKIRs();
ExpressKIRs(numberOfExtraKirs);
//CountFunctionalKIRs();
age = RandomNumber(1,70); //population initialized with a random age between 1 and 70
//cout <<inhibitoryKIRs << "|" <<activatingKIRs <<"|"<<CountExpressedKIRs() <<endl;
}
int main(int argc, char * argv[])
{
int c;
int option_index = 0;
string truth_file="";
string result_file="";
string gene_file="";
string output_file="";
string rule_file="";
int base_resolution=1;
int max_diff=20;
string pseudo_counts="0,0,0,0,0,0";
int print_num=0;
static struct option long_options[] = {
{"truth-file", required_argument, 0, 't' },
{"result-file", required_argument, 0, 'r' },
{"gene-annotation-file", required_argument, 0, 'g' },
{"output-file", required_argument, 0, 'o' },
{"subsetting-rule-file", required_argument, 0, 's' },
{"base-resolution", required_argument, 0, 'b' },
{"max-diff", required_argument, 0, 'm' },
{"pseudo-counts", required_argument, 0, 'p' },
{"use-number", no_argument, 0, 'u' },
{"help", no_argument, 0, 'h' },
{0, 0, 0, 0}
};
while(1)
{
c = getopt_long(argc, argv, "t:r:g:o:s:b:m:p:uh",
long_options, &option_index);
if (c==-1)
{
break;
}
switch(c)
{
case 'h':
usage();
exit(0);
case 't':
truth_file=optarg;
break;
case 'r':
result_file=optarg;
break;
case 'g':
gene_file=optarg;
break;
case 'o':
output_file=optarg;
break;
case 's':
rule_file=optarg;
break;
case 'b':
base_resolution=atoi(optarg);
break;
case 'm':
max_diff=atoi(optarg);
break;
case 'p':
pseudo_counts=optarg;
break;
case 'u':
print_num=1;
break;
default:
break;
}
}
if(truth_file.compare("")==0 || result_file.compare("")==0 || gene_file.compare("")==0 || output_file.compare("")==0|| rule_file.compare("")==0)
{
usage();
exit(0);
}
pseudo_counts_t pct;
get_pseudo_counts(pseudo_counts, pct);
cerr<<"loading gene annotation file..."<<endl;
Gene g;
g.loadGenesFromFile((char*)gene_file.c_str());
g.setGene();
cerr<<"loading result file..."<<endl;
Bedpe res;
res.loadFromFile((char *)result_file.c_str());
cerr<<"removing duplicate results..."<<endl;
res.uniq();
cerr<<"loading truth file..."<<endl;
Bedpe truth;
truth.loadFromFile((char*)truth_file.c_str());
vector<evaluate_t> evaluates;
cerr<<"comparing by subsetting rules..."<<endl;
ExecuteByRule exe;
exe.execute(res, truth, (char*)output_file.c_str(), (char*)rule_file.c_str(), evaluates, g, base_resolution, max_diff, pct, print_num);
cerr<<"printing evaluation results..."<<endl;
Printer per;
per.print(evaluates, (char*)output_file.c_str(), gene_file, base_resolution, max_diff, pseudo_counts, version);
return 0;
}
bool operator==(const Gene& g) const { return entrez_ID == g.getEID(); }
void FONSEModel::simulateGenome(Genome & genome)
{
unsigned codonIndex;
std::string curAA;
std::string tmpDesc = "Simulated Gene";
for (unsigned geneIndex = 0; geneIndex < genome.getGenomeSize(); geneIndex++) //loop over all genes in the genome
{
if (geneIndex % 100 == 0) my_print("Simulating Gene %\n", geneIndex);
Gene gene = genome.getGene(geneIndex);
SequenceSummary sequenceSummary = gene.geneData;
std::string tmpSeq = "ATG"; //Always will have the start amino acid
unsigned mixtureElement = getMixtureAssignment(geneIndex);
unsigned mutationCategory = getMutationCategory(mixtureElement);
unsigned selectionCategory = getSelectionCategory(mixtureElement);
unsigned synthesisRateCategory = getSynthesisRateCategory(mixtureElement);
double phi = getSynthesisRate(geneIndex, synthesisRateCategory, false);
std::string geneSeq = gene.getSequence();
for (unsigned position = 1; position < (geneSeq.size() / 3); position++)
{
std::string codon = geneSeq.substr((position * 3), 3);
curAA = SequenceSummary::codonToAA(codon);
//TODO: Throw an error here instead
if (curAA == "X") {
if (position < (geneSeq.size() / 3) - 1) my_print("Warning: Internal stop codon found in gene % at position %. Ignoring and moving on.\n", gene.getId(), position);
continue;
}
unsigned numCodons = SequenceSummary::GetNumCodonsForAA(curAA);
double* codonProb = new double[numCodons](); //size the arrays to the proper size based on # of codons.
double* mutation = new double[numCodons - 1]();
double* selection = new double[numCodons - 1]();
if (curAA == "M" || curAA == "W")
{
codonProb[0] = 1;
}
else
{
getParameterForCategory(mutationCategory, FONSEParameter::dM, curAA, false, mutation);
getParameterForCategory(selectionCategory, FONSEParameter::dOmega, curAA, false, selection);
calculateCodonProbabilityVector(numCodons, position, mutation, selection, phi, codonProb);
}
codonIndex = Parameter::randMultinom(codonProb, numCodons);
unsigned aaStart, aaEnd;
SequenceSummary::AAToCodonRange(curAA, aaStart, aaEnd, false); //need the first spot in the array where the codons for curAA are
codon = sequenceSummary.indexToCodon(aaStart + codonIndex);//get the correct codon based off codonIndex
tmpSeq += codon;
}
std::string codon = sequenceSummary.indexToCodon((unsigned)Parameter::randUnif(61.0, 64.0)); //randomly choose a stop codon, from range 61-63
tmpSeq += codon;
Gene simulatedGene(tmpSeq, tmpDesc, gene.getId());
genome.addGene(simulatedGene, true);
}
}