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EukPhylo/PTL2/Scripts-GRID/guidance.v2.02/libs/phylogeny/computeSubstitutionCounts.cpp
Katzlab dd76ab1d12 Added PTL2 Scripts 
These are PTL2 files from Auden 2/9
2023-02-14 11:20:52 -05:00

379 lines
20 KiB
C++
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#include "computeSubstitutionCounts.h"
#include "computePosteriorExpectationOfSubstitutions.h"
#include "computePosteriorExpectationOfSubstitutions_nonReversibleSp.h"
#include "multipleStochasticProcess.h"
#include "matrixUtils.h"
#include "simulateJumps.h"
#include "simulateCodonsJumps.h"
#include "simulateJumpsAbstract.h"
#include "treeIt.h"
#include "treeUtil.h"
/********************************************************************************************
computeSubstitutionCounts
*********************************************************************************************/
computeSubstitutionCounts::computeSubstitutionCounts(const sequenceContainer& sc, const tree& tr, multipleStochasticProcess* MultSpPtr, string& outDir, VVVdouble& LpostPerSpPerCat, const int simulationsIterNum, const MDOUBLE probCutOffSum, bool isSilent):
_tr(tr),_sc(sc),_pMSp(MultSpPtr),_outDir(outDir),_LpostPerSpPerCat(LpostPerSpPerCat), _simulationsIterNum(simulationsIterNum), _probCutOffSum(probCutOffSum),_isSilent(isSilent)
{
if(!_pMSp->getSPVecSize()){
errorMsg::reportError("Trying to call computeSubstitutionCounts with an empty multipleStochasticProcess object at computeSubstitutionCounts::computeSubstitutionCounts");
}
_alphabetSize = _pMSp->getSp(0)->alphabetSize();
}
computeSubstitutionCounts& computeSubstitutionCounts::operator=(const computeSubstitutionCounts &other){
if (this != &other) { // Check for self-assignment
}
return *this;
}
/********************************************************************************************
*********************************************************************************************/
void computeSubstitutionCounts::run()
{
for(int fatherStateIndex = 0;fatherStateIndex < _alphabetSize;++fatherStateIndex){
for(int sonStateIndex = 0;sonStateIndex < _alphabetSize;++sonStateIndex){
//if(sonStateIndex == fatherStateIndex) continue;
_expMap_father2son[fatherStateIndex][sonStateIndex].resize(_sc.seqLen(),0);
_probMap_father2son[fatherStateIndex][sonStateIndex].resize(_sc.seqLen(),0);
}
}
resize_VVVV(_sc.seqLen(),_tr.getNodesNum(),_alphabetSize,_alphabetSize,_jointProb_PosNodeXY);
resize_VVVV(_sc.seqLen(),_tr.getNodesNum(),_alphabetSize,_alphabetSize,_probChanges_PosNodeXY);
resize_VVVV(_sc.seqLen(),_tr.getNodesNum(),_alphabetSize,_alphabetSize,_expChanges_PosNodeXY);
computePosteriorOfChangeGivenTerminalsPerSpPerCat(); // GLM - multiple SPs
}
/********************************************************************************************
*********************************************************************************************/
void computeSubstitutionCounts::computePosteriorOfChangeGivenTerminalsPerSpPerCat()
{
int numOfSPs = _pMSp->getSPVecSize();
// per Sp
for (int spIndex=0; spIndex < numOfSPs; ++spIndex) {
// Per RateCategory -- All the computations are done while looping over rate categories
stochasticProcess * currentSp = _pMSp->getSp(spIndex);
int numOfRateCategories = currentSp->categories();
for (int rateCategIndex=0 ; rateCategIndex < numOfRateCategories;++rateCategIndex)
{
tree copy_et = _tr;
MDOUBLE rateCategVal = currentSp->rates(rateCategIndex);
MDOUBLE minimumRateCategVal = 0.0000001;
MDOUBLE rate2multiply = max(rateCategVal,minimumRateCategVal);
if(rateCategVal < minimumRateCategVal){
LOGnOUT(4, <<" >>> NOTE: the rate category "<<rateCategVal<<" is too low for computePosteriorExpectationOfChangePerSite"<<endl); }
copy_et.multipleAllBranchesByFactor(rate2multiply);
//if(!_isSilent)
//LOGnOUT(4, <<"running "<<gainLossOptions::_numOfSimulationsForPotExp<<" simulations for rate "<<rate2multiply<<endl);
simulateJumpsAbstract* simPerRateCategory;
if(_alphabetSize == 61)
simPerRateCategory = new simulateCodonsJumps(copy_et,*currentSp,_alphabetSize);
else
simPerRateCategory = new simulateJumps(copy_et,*currentSp,_alphabetSize);
simPerRateCategory->runSimulation(_simulationsIterNum);
if(!_isSilent)
LOGnOUT(4,<<"finished simulations"<<endl);
// Per POS
for (int pos = 0; pos <_sc.seqLen(); ++pos)
{
LOG(6,<<"pos "<<pos+1<<endl);
// I) computePosteriorOfChangeGivenTerminals
VVVdouble posteriorsGivenTerminalsPerRateCategoryPerPos;
computePosteriorExpectationOfSubstitutions* cpesPerRateCategoryPerPos ;
if(currentSp->isReversible())
cpesPerRateCategoryPerPos = new computePosteriorExpectationOfSubstitutions(copy_et,_sc,currentSp); // Per POS,CAT
else
cpesPerRateCategoryPerPos = new computePosteriorExpectationOfSubstitutions_nonReversibleSp(copy_et,_sc,currentSp); // Per POS,CAT
cpesPerRateCategoryPerPos->computePosteriorOfChangeGivenTerminals(posteriorsGivenTerminalsPerRateCategoryPerPos,pos);
// II) Exp - take in account both: 1) simulations 2) posteriorsGivenTerminal
VVVdouble expChangesForBranchPerRateCategoryPerPos; // Sim+Exp
resize_VVV(_tr.getNodesNum(),_alphabetSize,_alphabetSize,expChangesForBranchPerRateCategoryPerPos);
VVdouble expVV = cpesPerRateCategoryPerPos->computeExpectationAcrossTree(*simPerRateCategory,posteriorsGivenTerminalsPerRateCategoryPerPos,
expChangesForBranchPerRateCategoryPerPos); // Per POS
for(int fatherStateIndex = 0;fatherStateIndex < _alphabetSize;++fatherStateIndex){
for(int sonStateIndex = 0;sonStateIndex < _alphabetSize;++sonStateIndex){
if(sonStateIndex == fatherStateIndex) continue;
_expMap_father2son[fatherStateIndex][sonStateIndex][pos] += expVV[fatherStateIndex][sonStateIndex]*_LpostPerSpPerCat[spIndex][rateCategIndex][pos];
}
}
// III) Sim - take in account both: 1) simulations 2) posteriorsGivenTerminal
VVVdouble probChangesForBranchPerRateCategoryPerPos; // Sim+Prob
resize_VVV(_tr.getNodesNum(),_alphabetSize,_alphabetSize,probChangesForBranchPerRateCategoryPerPos);
VVdouble probVV = cpesPerRateCategoryPerPos->computePosteriorAcrossTree(*simPerRateCategory,posteriorsGivenTerminalsPerRateCategoryPerPos,probChangesForBranchPerRateCategoryPerPos);
for(int fatherStateIndex = 0;fatherStateIndex < _alphabetSize;++fatherStateIndex){
for(int sonStateIndex = 0;sonStateIndex < _alphabetSize;++sonStateIndex){
if(sonStateIndex == fatherStateIndex) continue;
_probMap_father2son[fatherStateIndex][sonStateIndex][pos] += probVV[fatherStateIndex][sonStateIndex]*_LpostPerSpPerCat[spIndex][rateCategIndex][pos];
}
}
// Store all information PerCat,PerPOS
for(int i=0;i<_probChanges_PosNodeXY[pos].size();++i){ // nodeId
for(int j=0;j<_probChanges_PosNodeXY[pos][i].size();++j){ // fatherState
for(int k=0;k<_probChanges_PosNodeXY[pos][i][j].size();++k){ // sonState
_jointProb_PosNodeXY[pos][i][j][k] += posteriorsGivenTerminalsPerRateCategoryPerPos[i][j][k]*_LpostPerSpPerCat[spIndex][rateCategIndex][pos];
_probChanges_PosNodeXY[pos][i][j][k] += probChangesForBranchPerRateCategoryPerPos[i][j][k]*_LpostPerSpPerCat[spIndex][rateCategIndex][pos];
_expChanges_PosNodeXY[pos][i][j][k] += expChangesForBranchPerRateCategoryPerPos[i][j][k]*_LpostPerSpPerCat[spIndex][rateCategIndex][pos];
}
}
}
delete(cpesPerRateCategoryPerPos);
}
delete(simPerRateCategory);
// Per POS
}
// per rateCat
}
// Per Sp
}
/********************************************************************************************
printProbExp()
print perPos (over all branches)
use the members _expV01, _expV10 for basic
*********************************************************************************************/
void computeSubstitutionCounts::printProbExp()
{
string posteriorExpectationOfChangeString = _outDir + "//" + "posteriorExpectationOfChange.txt";
ofstream posteriorExpectationStream(posteriorExpectationOfChangeString.c_str());
string posteriorProbabilityOfChangeString = _outDir + "//" + "posteriorProbabilityOfChange.txt";
ofstream posteriorProbabilityStream(posteriorProbabilityOfChangeString.c_str());
int fatherStateIndex,sonStateIndex;
posteriorExpectationStream<<"#POS"<<"\t";
posteriorProbabilityStream<<"#POS"<<"\t";
for (fatherStateIndex = 0;fatherStateIndex < _alphabetSize;++fatherStateIndex){
for (sonStateIndex = 0;sonStateIndex < _alphabetSize;++sonStateIndex){
if(sonStateIndex == fatherStateIndex) continue;
posteriorExpectationStream<<_sc.getAlphabet()->fromInt(fatherStateIndex)<<"->"<<_sc.getAlphabet()->fromInt(sonStateIndex)<<"\t";
posteriorProbabilityStream<<_sc.getAlphabet()->fromInt(fatherStateIndex)<<"->"<<_sc.getAlphabet()->fromInt(sonStateIndex)<<"\t";
}
}
posteriorExpectationStream<<endl;
posteriorProbabilityStream<<endl;
for (int pos = 0; pos <_sc.seqLen(); ++pos){
posteriorExpectationStream<<pos+1<<"\t";
posteriorProbabilityStream<<pos+1<<"\t";
for (fatherStateIndex = 0;fatherStateIndex < _alphabetSize;++fatherStateIndex){
for (sonStateIndex = 0;sonStateIndex < _alphabetSize;++sonStateIndex){
if(sonStateIndex == fatherStateIndex) continue;//ofir, note the change in print format
posteriorExpectationStream<<_expMap_father2son[fatherStateIndex][sonStateIndex][pos]<<"\t";
posteriorProbabilityStream<<_probMap_father2son[fatherStateIndex][sonStateIndex][pos]<<"\t";
}
}
posteriorExpectationStream<<endl;
posteriorProbabilityStream<<endl;
}
posteriorExpectationStream.close();
posteriorProbabilityStream.close();
}
/********************************************************************************************
printProbabilityPerPosPerBranch 1
produce 2 print files:
1. print detailed file (out)
2. print summary over all branches (outSum)
*********************************************************************************************/
void computeSubstitutionCounts::printProbabilityPerPosPerBranch()
{
string probabilityPerPosPerBranch = _outDir + "//" + "probabilityPerPosPerBranch.txt";
ofstream probabilityPerPosPerBranchStream(probabilityPerPosPerBranch.c_str());
probabilityPerPosPerBranchStream<<"# print values over probCutOff "<<_probCutOffSum<<endl;
probabilityPerPosPerBranchStream<<"#Event"<<"\t"<<"POS"<<"\t"<<"branch"<<"\t"<<"branchLength"<<"\t"<<"distance2root"<<"\t"<<"probability"<<endl;
string countProbPerPos = _outDir + "//" + "probabilityPerPos.txt";
ofstream countProbPerPosStream(countProbPerPos.c_str());
countProbPerPosStream<<"# print values over probCutOff "<<_probCutOffSum<<endl;
countProbPerPosStream<<"#POS"<<"\t";
for(int fatherStateIndex = 0;fatherStateIndex < _alphabetSize;++fatherStateIndex){
for(int sonStateIndex = 0;sonStateIndex < _alphabetSize;++sonStateIndex){
if(sonStateIndex == fatherStateIndex) continue;
countProbPerPosStream<<"prob"<<_sc.getAlphabet()->fromInt(fatherStateIndex)<<"->"<<_sc.getAlphabet()->fromInt(sonStateIndex)<<"\t";
}
}
countProbPerPosStream<<endl;
for (int pos = 0; pos <_sc.seqLen(); ++pos){
printProbabilityPerPosPerBranch(pos, _probChanges_PosNodeXY[pos],probabilityPerPosPerBranchStream,countProbPerPosStream);
}
}
/********************************************************************************************
printGainLossProbabilityPerPosPerBranch 1.1
*********************************************************************************************/
void computeSubstitutionCounts::printProbabilityPerPosPerBranch(int pos, VVVdouble& probChanges, ostream& out, ostream& outCount)
{
VVdouble countFromFather2Son;
countFromFather2Son.resize(_alphabetSize);
int fatherStateIndex,sonStateIndex;
treeIterTopDownConst tIt(_tr);
for (tree::nodeP mynode = tIt.first(); mynode != tIt.end(); mynode = tIt.next()) {
for(fatherStateIndex = 0;fatherStateIndex < _alphabetSize;++fatherStateIndex){
countFromFather2Son[fatherStateIndex].resize(_alphabetSize,0);
for(sonStateIndex = 0;sonStateIndex < _alphabetSize;++sonStateIndex){
if(sonStateIndex == fatherStateIndex) continue;
if(probChanges[mynode->id()][fatherStateIndex][sonStateIndex] > _probCutOffSum){//NIM
out<<_sc.getAlphabet()->fromInt(fatherStateIndex)<<"->"<<_sc.getAlphabet()->fromInt(sonStateIndex)<<"\t"<<pos+1<<"\t"<<mynode->name()<<"\t"<<mynode->dis2father()<<"\t"<<getDistanceFromNode2ROOT(mynode)<<"\t"<<probChanges[mynode->id()][fatherStateIndex][sonStateIndex]<<endl;
countFromFather2Son[fatherStateIndex][sonStateIndex] += probChanges[mynode->id()][fatherStateIndex][sonStateIndex];
}
}
}
}
outCount<<pos+1<<"\t";
for(fatherStateIndex = 0;fatherStateIndex < _alphabetSize;++fatherStateIndex){
for(sonStateIndex = 0;sonStateIndex < _alphabetSize;++sonStateIndex){
if(sonStateIndex == fatherStateIndex) continue;
//if(countFromFather2Son[fatherStateIndex][sonStateIndex] == 0) continue;//NIMROD
outCount<<countFromFather2Son[fatherStateIndex][sonStateIndex]<<"\t";
}
}
outCount<<endl;
}
/********************************************************************************************
*********************************************************************************************/
void computeSubstitutionCounts::printExpectationPerBranch()
{
// ExpectationPerBranch
VVVdouble posteriorsGivenTerminalsTotal;
resize_VVV(_tr.getNodesNum(),_alphabetSize,_alphabetSize,posteriorsGivenTerminalsTotal);
for (int pos = 0; pos <_sc.seqLen(); ++pos){
for(int i=0;i<_expChanges_PosNodeXY[pos].size();++i){
for(int j=0;j<_expChanges_PosNodeXY[pos][i].size();++j){
for(int k=0;k<_expChanges_PosNodeXY[pos][i][j].size();++k){
posteriorsGivenTerminalsTotal[i][j][k] += _expChanges_PosNodeXY[pos][i][j][k];
}
}
}
}
string expectationPerBranch = _outDir + "//" + "ExpectationPerBranch.txt";
ofstream expectationPerBranchStream(expectationPerBranch.c_str());
printExpectationPerBranch(posteriorsGivenTerminalsTotal,expectationPerBranchStream);
}
/********************************************************************************************
*********************************************************************************************/
void computeSubstitutionCounts::printExpectationPerBranch(VVVdouble& expectChanges, ostream& out)
{
treeIterTopDownConst tIt(_tr);
out<<"#Event"<<"\t"<<"branch"<<"\t"<<"branchLength"<<"\t"<<"distance2root"<<"\t"<<"expectation"<<endl;
for (tree::nodeP mynode = tIt.first(); mynode != tIt.end(); mynode = tIt.next()) {
for(int fatherStateIndex = 0;fatherStateIndex < _alphabetSize;++fatherStateIndex){
for(int sonStateIndex = 0;sonStateIndex < _alphabetSize;++sonStateIndex){
if(sonStateIndex == fatherStateIndex) continue;
out<<_sc.getAlphabet()->fromInt(fatherStateIndex)<<"->"<<_sc.getAlphabet()->fromInt(sonStateIndex)<<"\t"<<
mynode->name()<<"\t"<<mynode->dis2father()<<"\t"<<getDistanceFromNode2ROOT(mynode)<<"\t"<<expectChanges[mynode->id()][fatherStateIndex][sonStateIndex]<<endl;
}
}
}
}
/********************************************************************************************
*********************************************************************************************/
void computeSubstitutionCounts::printTreesWithExpectationValuesAsBP(int from,int to)
{
// ExpectationPerPosPerBranch - Print Trees
Vstring Vnames;
fillAllNodesNames(Vnames,_tr);
createDir(_outDir, "TreesWithExpectationValuesAsBP");
for (int pos = 0; pos <_sc.seqLen(); ++pos){
string strTreeNum = _outDir + "//" + "TreesWithExpectationValuesAsBP" + "//" + "expTree" + int2string(pos+1) + ".ph";
ofstream tree_out(strTreeNum.c_str());
printTreeWithValuesAsBP(tree_out,_tr,Vnames,&_expChanges_PosNodeXY[pos],from,to);
}
}
/********************************************************************************************
*********************************************************************************************/
void computeSubstitutionCounts::printTreesWithProbabilityValuesAsBP(int from,int to)
{
// ProbabilityPerPosPerBranch - Print Trees
Vstring Vnames;
fillAllNodesNames(Vnames,_tr);
createDir(_outDir, "TreesWithProbabilityValuesAsBP");
for (int pos = 0; pos <_sc.seqLen(); ++pos){
string strTreeNum = _outDir + "//" + "TreesWithProbabilityValuesAsBP"+ "//" + "probTree" + int2string(pos+1) + ".ph";
ofstream tree_out(strTreeNum.c_str());
printTreeWithValuesAsBP(tree_out,_tr,Vnames,&_probChanges_PosNodeXY[pos],from,to);
}
}
/********************************************************************************************
printProbExpPerPosPerBranch 1
produce 2 print files:
1. print detailed file (out)
2. print summary over all branches (outSum)
*********************************************************************************************/
void computeSubstitutionCounts::printProbExpPerPosPerBranch(MDOUBLE probCutOff, MDOUBLE countsCutOff)
{
string probExpPerPosPerBranch = _outDir + "//" + "expPerPosPerBranch.txt";
ofstream probExpPerPosPerBranchStream(probExpPerPosPerBranch.c_str());
probExpPerPosPerBranchStream<<"# print values over probCutOff "<<probCutOff<<endl;
probExpPerPosPerBranchStream<<"#Event"<<"\t"<<"POS"<<"\t"<<"branch"<<"\t"<<"branchLength"<<"\t"<<"distance2root"<<"\t"<<"probability"<<"\t"<<"expectation"<<endl;
string probExpPerPos = _outDir + "//" + "probExpCountPerPos.txt";
ofstream countProbPerPosStream(probExpPerPos.c_str());
countProbPerPosStream<<"# print count over probCutOff "<<countsCutOff<<endl;
countProbPerPosStream<<"#POS"<<"\t"<<"Event"<<"\t"<<"EventProb"<<"\t"<<"EventExp"<<"\t"<<"EventCount"<<endl;
for (int pos = 0; pos <_sc.seqLen(); ++pos){
printProbExpPerPosPerBranch(pos, probCutOff,countsCutOff, _probChanges_PosNodeXY[pos],_expChanges_PosNodeXY[pos],probExpPerPosPerBranchStream,countProbPerPosStream);
}
}
/********************************************************************************************
printGainLossProbExpPerPosPerBranch 1.1
Get pos, and iterate over all branches:
1. print detailed file (out)
2. print summary over all branches (outSum)
*********************************************************************************************/
void computeSubstitutionCounts::printProbExpPerPosPerBranch(int pos, MDOUBLE probCutOff, MDOUBLE countCutOff, VVVdouble& probChanges, VVVdouble& expChanges, ostream& out, ostream& outSum)
{
VVdouble probFather2Son,expFather2Son;
VVint countFather2Son;
probFather2Son.resize(_alphabetSize);
expFather2Son.resize(_alphabetSize);
countFather2Son.resize(_alphabetSize);
int fatherStateIndex,sonStateIndex;
treeIterTopDownConst tIt(_tr);
for (tree::nodeP mynode = tIt.first(); mynode != tIt.end(); mynode = tIt.next()) {
for(fatherStateIndex = 0;fatherStateIndex < _alphabetSize;++fatherStateIndex){
probFather2Son[fatherStateIndex].resize(_alphabetSize,0);
expFather2Son[fatherStateIndex].resize(_alphabetSize,0);
countFather2Son[fatherStateIndex].resize(_alphabetSize,0);
for(sonStateIndex = 0;sonStateIndex < _alphabetSize;++sonStateIndex){
if(sonStateIndex == fatherStateIndex) continue;
out<<_sc.getAlphabet()->fromInt(fatherStateIndex)<<"->"<<_sc.getAlphabet()->fromInt(sonStateIndex)<<"\t"<<
pos+1<<"\t"<<mynode->name()<<"\t"<<mynode->dis2father()<<"\t"<<getDistanceFromNode2ROOT(mynode)<<"\t"<<probChanges[mynode->id()][fatherStateIndex][sonStateIndex]<<"\t"<<expChanges[mynode->id()][fatherStateIndex][sonStateIndex]<<endl;
probFather2Son[fatherStateIndex][sonStateIndex] += probChanges[mynode->id()][fatherStateIndex][sonStateIndex];
expFather2Son[fatherStateIndex][sonStateIndex] += expChanges[mynode->id()][fatherStateIndex][sonStateIndex];
if (probChanges[mynode->id()][fatherStateIndex][sonStateIndex] > countCutOff)
countFather2Son[fatherStateIndex][sonStateIndex] += 1;
}
}
}
for(fatherStateIndex = 0;fatherStateIndex < _alphabetSize;++fatherStateIndex){
for(sonStateIndex = 0;sonStateIndex < _alphabetSize;++sonStateIndex){
if(sonStateIndex == fatherStateIndex) continue;
outSum<<pos+1<<"\t"<<_sc.getAlphabet()->fromInt(fatherStateIndex)<<"->"<<_sc.getAlphabet()->fromInt(sonStateIndex)<<"\t"<<
probFather2Son[fatherStateIndex][sonStateIndex]<<"\t"<<expFather2Son[fatherStateIndex][sonStateIndex]<<"\t"<<countFather2Son[fatherStateIndex][sonStateIndex]<<endl;
}
}
}
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