MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
//each process gets where it should start and stop in the file
- start = int (sqrt(float(pid)/float(processors)) * numSeqs);
- end = int (sqrt(float(pid+1)/float(processors)) * numSeqs);
+ if (output != "square") {
+ start = int (sqrt(float(pid)/float(processors)) * numSeqs);
+ end = int (sqrt(float(pid+1)/float(processors)) * numSeqs);
+ }else{
+ start = int ((float(pid)/float(processors)) * numSeqs);
+ end = int ((float(pid+1)/float(processors)) * numSeqs);
+ }
- if (output != "lt") {
+ if (output == "column") {
MPI_File outMPI;
int amode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
//do your part
string outputMyPart;
- driverMPI(start, end, outMPI, cutoff);
+
+ driverMPI(start, end, outMPI, cutoff);
if (m->control_pressed) { MPI_File_close(&outMPI); delete distCalculator; return 0; }
}
}else { //you are a child process
//do your part
- driverMPI(start, end, outMPI, cutoff);
+ driverMPI(start, end, outMPI, cutoff);
if (m->control_pressed) { MPI_File_close(&outMPI); delete distCalculator; return 0; }
//do your part
string outputMyPart;
- long mySize;
- driverMPI(start, end, outputFile, mySize);
+ unsigned long int mySize;
+
+ if (output != "square"){ driverMPI(start, end, outputFile, mySize); }
+ else { driverMPI(start, end, outputFile, mySize, output); }
if (m->control_pressed) { delete distCalculator; return 0; }
//wait on chidren
for(int b = 1; b < processors; b++) {
- long fileSize;
+ unsigned long int fileSize;
if (m->control_pressed) { MPI_File_close(&outMPI); delete distCalculator; return 0; }
MPI_File_close(&outMPI);
}else { //you are a child process
//do your part
- long size;
- driverMPI(start, end, (outputFile + toString(pid) + ".temp"), size);
+ unsigned long int size;
+ if (output != "square"){ driverMPI(start, end, (outputFile + toString(pid) + ".temp"), size); }
+ else { driverMPI(start, end, (outputFile + toString(pid) + ".temp"), size, output); }
if (m->control_pressed) { delete distCalculator; return 0; }
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
//if you don't need to fork anything
if(processors == 1){
- driver(0, numSeqs, outputFile, cutoff);
+ if (output != "square") { driver(0, numSeqs, outputFile, cutoff); }
+ else { driver(0, numSeqs, outputFile, "square"); }
}else{ //you have multiple processors
for (int i = 0; i < processors; i++) {
lines.push_back(new linePair());
- lines[i]->start = int (sqrt(float(i)/float(processors)) * numSeqs);
- lines[i]->end = int (sqrt(float(i+1)/float(processors)) * numSeqs);
+ if (output != "square") {
+ lines[i]->start = int (sqrt(float(i)/float(processors)) * numSeqs);
+ lines[i]->end = int (sqrt(float(i+1)/float(processors)) * numSeqs);
+ }else{
+ lines[i]->start = int ((float(i)/float(processors)) * numSeqs);
+ lines[i]->end = int ((float(i+1)/float(processors)) * numSeqs);
+ }
}
createProcesses(outputFile);
}
}
#else
- ifstream inFASTA;
- driver(0, numSeqs, outputFile, cutoff);
+ //ifstream inFASTA;
+ if (output != "square") { driver(0, numSeqs, outputFile, cutoff); }
+ else { driver(0, numSeqs, outputFile, "square"); }
#endif
#endif
if (pid == 0) { //only one process should output to screen
#endif
- if (output == "square") { convertMatrix(outputFile); }
+ //if (output == "square") { convertMatrix(outputFile); }
ifstream fileHandle;
fileHandle.open(outputFile.c_str());
processIDS[lines[process]->end] = pid; //create map from line number to pid so you can append files in correct order later
process++;
}else if (pid == 0){
- driver(lines[process]->start, lines[process]->end, filename + toString(getpid()) + ".temp", cutoff);
+ if (output != "square") { driver(lines[process]->start, lines[process]->end, filename + toString(getpid()) + ".temp", cutoff); }
+ else { driver(lines[process]->start, lines[process]->end, filename + toString(getpid()) + ".temp", "square"); }
exit(0);
}else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
}
if (output == "column") { outFile << alignDB.get(i).getName() << ' ' << alignDB.get(j).getName() << ' ' << dist << endl; }
}
if (output == "lt") { outFile << dist << '\t'; }
-
- if (output == "square") { //make a square column you can convert to square phylip
- outFile << alignDB.get(i).getName() << '\t' << alignDB.get(j).getName() << '\t' << dist << endl;
- outFile << alignDB.get(j).getName() << '\t' << alignDB.get(i).getName() << '\t' << dist << endl;
- }
-
}
if (output == "lt") { outFile << endl; }
exit(1);
}
}
+/**************************************************************************************************/
+/////// need to fix to work with calcs and sequencedb
+int DistanceCommand::driver(int startLine, int endLine, string dFileName, string square){
+ try {
+
+ int startTime = time(NULL);
+
+ //column file
+ ofstream outFile(dFileName.c_str(), ios::trunc);
+ outFile.setf(ios::fixed, ios::showpoint);
+ outFile << setprecision(4);
+
+ if(startLine == 0){ outFile << alignDB.getNumSeqs() << endl; }
+
+ for(int i=startLine;i<endLine;i++){
+
+ string name = alignDB.get(i).getName();
+ //pad with spaces to make compatible
+ if (name.length() < 10) { while (name.length() < 10) { name += " "; } }
+
+ outFile << name << '\t';
+
+ for(int j=0;j<alignDB.getNumSeqs();j++){
+
+ if (m->control_pressed) { outFile.close(); return 0; }
+
+ distCalculator->calcDist(alignDB.get(i), alignDB.get(j));
+ double dist = distCalculator->getDist();
+
+ outFile << dist << '\t';
+ }
+
+ outFile << endl;
+
+ if(i % 100 == 0){
+ m->mothurOut(toString(i) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
+ }
+
+ }
+ m->mothurOut(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
+
+ outFile.close();
+
+ return 1;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "DistanceCommand", "driver");
+ exit(1);
+ }
+}
#ifdef USE_MPI
/**************************************************************************************************/
/////// need to fix to work with calcs and sequencedb
double dist = distCalculator->getDist();
if(dist <= cutoff){
- if (output == "column") { outputString += (alignDB.get(i).getName() + ' ' + alignDB.get(j).getName() + ' ' + toString(dist) + '\n'); }
- }
-
- if (output == "square") { //make a square column you can convert to square phylip
- outputString += (alignDB.get(i).getName() + ' ' + alignDB.get(j).getName() + ' ' + toString(dist) + '\n');
- outputString += (alignDB.get(j).getName() + ' ' + alignDB.get(i).getName() + ' ' + toString(dist) + '\n');
+ outputString += (alignDB.get(i).getName() + ' ' + alignDB.get(j).getName() + ' ' + toString(dist) + '\n');
}
}
}
/**************************************************************************************************/
/////// need to fix to work with calcs and sequencedb
-int DistanceCommand::driverMPI(int startLine, int endLine, string file, long& size){
+int DistanceCommand::driverMPI(int startLine, int endLine, string file, unsigned long int& size){
try {
MPI_Status status;
string outputString = "";
size = 0;
- if((output == "lt") && startLine == 0){ outputString += toString(alignDB.getNumSeqs()) + "\n"; }
+ if(startLine == 0){ outputString += toString(alignDB.getNumSeqs()) + "\n"; }
for(int i=startLine;i<endLine;i++){
- if(output == "lt") {
- string name = alignDB.get(i).getName();
- if (name.length() < 10) { //pad with spaces to make compatible
- while (name.length() < 10) { name += " "; }
- }
- outputString += name + "\t";
+
+ string name = alignDB.get(i).getName();
+ if (name.length() < 10) { //pad with spaces to make compatible
+ while (name.length() < 10) { name += " "; }
}
+ outputString += name + "\t";
+
for(int j=0;j<i;j++){
if (m->control_pressed) { return 0; }
distCalculator->calcDist(alignDB.get(i), alignDB.get(j));
double dist = distCalculator->getDist();
- if (output == "lt") { outputString += toString(dist) + "\t"; }
+ outputString += toString(dist) + "\t";
}
- if (output == "lt") { outputString += "\n"; }
+ outputString += "\n";
if(i % 100 == 0){
exit(1);
}
}
-#endif
/**************************************************************************************************/
+/////// need to fix to work with calcs and sequencedb
+int DistanceCommand::driverMPI(int startLine, int endLine, string file, unsigned long int& size, string square){
+ try {
+ MPI_Status status;
+
+ MPI_File outMPI;
+ int amode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
+
+ //char* filename = new char[file.length()];
+ //memcpy(filename, file.c_str(), file.length());
+
+ char filename[1024];
+ strcpy(filename, file.c_str());
+
+ MPI_File_open(MPI_COMM_SELF, filename, amode, MPI_INFO_NULL, &outMPI);
+ //delete filename;
+
+ int startTime = time(NULL);
+
+ string outputString = "";
+ size = 0;
+
+ if(startLine == 0){ outputString += toString(alignDB.getNumSeqs()) + "\n"; }
+
+ for(int i=startLine;i<endLine;i++){
+
+ string name = alignDB.get(i).getName();
+ if (name.length() < 10) { //pad with spaces to make compatible
+ while (name.length() < 10) { name += " "; }
+ }
+ outputString += name + "\t";
+
+ for(int j=0;j<alignDB.getNumSeqs();j++){
+
+ if (m->control_pressed) { return 0; }
+
+ distCalculator->calcDist(alignDB.get(i), alignDB.get(j));
+ double dist = distCalculator->getDist();
+
+ outputString += toString(dist) + "\t";
+ }
+
+ outputString += "\n";
+
+
+ if(i % 100 == 0){
+ //m->mothurOut(toString(i) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
+ cout << i << '\t' << (time(NULL) - startTime) << endl;
+ }
+
+
+ //send results to parent
+ int length = outputString.length();
+ char* buf = new char[length];
+ memcpy(buf, outputString.c_str(), length);
+
+ MPI_File_write(outMPI, buf, length, MPI_CHAR, &status);
+ size += outputString.length();
+ outputString = "";
+ delete buf;
+ }
+
+ //m->mothurOut(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
+ cout << (endLine-1) << '\t' << (time(NULL) - startTime) << endl;
+ MPI_File_close(&outMPI);
+
+ return 1;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "DistanceCommand", "driverMPI");
+ exit(1);
+ }
+}
+#endif
+/**************************************************************************************************
int DistanceCommand::convertMatrix(string outputFile) {
try{
exit(1);
}
}
-/**************************************************************************************************/
+/**************************************************************************************************
int DistanceCommand::convertToLowerTriangle(string outputFile) {
try{
exit(1);
}
}
-
-/**************************************************************************************************
-void DistanceCommand::m->appendFiles(string temp, string filename) {
- try{
- ofstream output;
- ifstream input;
-
- //open output file in append mode
- m->openOutputFileAppend(filename, output);
- m->openInputFile(temp, input);
-
- while(char c = input.get()){
- if(input.eof()) { break; }
- else { output << c; }
- }
-
- input.close();
- output.close();
- }
- catch(exception& e) {
- m->errorOut(e, "DistanceCommand", "m->appendFiles");
- exit(1);
- }
-}
/**************************************************************************************************/
+
+
//void m->appendFiles(string, string);
void createProcesses(string);
int driver(/*Dist*, SequenceDB, */int, int, string, float);
+ int driver(int, int, string, string);
#ifdef USE_MPI
int driverMPI(int, int, MPI_File&, float);
- int driverMPI(int, int, string, long&);
+ int driverMPI(int, int, string, unsigned long int&);
+ int driverMPI(int, int, string, unsigned long int&, string);
#endif
- int convertMatrix(string);
+ //int convertMatrix(string);
bool sanityCheck();
- int convertToLowerTriangle(string);
+ //int convertToLowerTriangle(string);
};
UWScoreSig.resize(numComp);
userData = unweighted->getValues(T[i], processors, outputDir); //userData[0] = unweightedscore
-
+
if (m->control_pressed) { if (random) { delete output; } outSum.close(); for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); }return 0; }
//output scores for each combination
//add users score to validscores
validScores[userData[k]] = userData[k];
}
-
+
//get unweighted scores for random trees - if random is false iters = 0
for (int j = 0; j < iters; j++) {
+
//we need a different getValues because when we swap the labels we only want to swap those in each pairwise comparison
- randomData = unweighted->getValues(T[i], "", "");
+ randomData = unweighted->getValues(T[i], "", "", processors, outputDir);
- if (m->control_pressed) {
- if (random) { delete output; }
- outSum.close();
- for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); }
- return 0;
- }
+ if (m->control_pressed) { if (random) { delete output; } outSum.close(); for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
for(int k = 0; k < numComp; k++) {
//add trees unweighted score to map of scores
//add randoms score to validscores
validScores[randomData[k]] = randomData[k];
}
+
+ //report progress
+ m->mothurOut("Iter: " + toString(j+1)); m->mothurOutEndLine();
}
for(int a = 0; a < numComp; a++) {
}
-
- if (m->control_pressed) {
- if (random) { delete output; }
- outSum.close();
- for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); }
- return 0;
- }
+ if (m->control_pressed) { if (random) { delete output; } outSum.close(); for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
//print output files
printUWSummaryFile(i);
if (UWScoreSig[a][0] > (1/(float)iters)) {
outSum << setprecision(6) << groupComb[a] << '\t' << utreeScores[a][0] << '\t' << setprecision(itersString.length()) << UWScoreSig[a][0] << endl;
cout << setprecision(6) << groupComb[a] << '\t' << utreeScores[a][0] << '\t' << setprecision(itersString.length()) << UWScoreSig[a][0] << endl;
- m->mothurOutJustToLog(groupComb[a] + "\t" + toString(utreeScores[a][0]) + "\t" + toString(UWScoreSig[a][0])); m->mothurOutEndLine();
+ m->mothurOutJustToLog(groupComb[a] + "\t" + toString(utreeScores[a][0]) + "\t" + toString(UWScoreSig[a][0])+ "\n");
}else {
outSum << setprecision(6) << groupComb[a] << '\t' << utreeScores[a][0] << '\t' << setprecision(itersString.length()) << "<" << (1/float(iters)) << endl;
cout << setprecision(6) << groupComb[a] << '\t' << utreeScores[a][0] << '\t' << setprecision(itersString.length()) << "<" << (1/float(iters)) << endl;
- m->mothurOutJustToLog(groupComb[a] + "\t" + toString(utreeScores[a][0]) + "\t<" + toString((1/float(iters)))); m->mothurOutEndLine();
+ m->mothurOutJustToLog(groupComb[a] + "\t" + toString(utreeScores[a][0]) + "\t<" + toString((1/float(iters))) + "\n");
}
}else{
outSum << setprecision(6) << groupComb[a] << '\t' << utreeScores[a][0] << '\t' << "0.00" << endl;
cout << setprecision(6) << groupComb[a] << '\t' << utreeScores[a][0] << '\t' << "0.00" << endl;
- m->mothurOutJustToLog(groupComb[a] + "\t" + toString(utreeScores[a][0]) + "\t0.00"); m->mothurOutEndLine();
+ m->mothurOutJustToLog(groupComb[a] + "\t" + toString(utreeScores[a][0]) + "\t0.00\n");
}
}
userData.resize(numComp,0); //data[0] = weightedscore AB, data[1] = weightedscore AC...
randomData.resize(numComp,0); //data[0] = weightedscore AB, data[1] = weightedscore AC...
- //create new tree with same num nodes and leaves as users
- randT = new Tree();
-
//get weighted scores for users trees
for (int i = 0; i < T.size(); i++) {
- if (m->control_pressed) { delete randT; outSum.close(); for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+ if (m->control_pressed) { outSum.close(); for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
counter = 0;
rScores.resize(numComp); //data[0] = weightedscore AB, data[1] = weightedscore AC...
userData = weighted->getValues(T[i], processors, outputDir); //userData[0] = weightedscore
- if (m->control_pressed) {
- delete randT;
- if (random) { delete output; }
- outSum.close();
- for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); }
- return 0;
- }
-
+ if (m->control_pressed) { if (random) { delete output; } outSum.close(); for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
//save users score
for (int s=0; s<numComp; s++) {
namesOfGroupCombos.push_back(groups);
}
}
-
+
+ lines.clear();
+
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
if(processors != 1){
int numPairs = namesOfGroupCombos.size();
if(i == processors - 1){
numPairsPerProcessor = numPairs - i * numPairsPerProcessor;
}
- lines.push_back(new linePair(startPos, numPairsPerProcessor));
+ lines.push_back(linePair(startPos, numPairsPerProcessor));
}
}
#endif
//get scores for random trees
for (int j = 0; j < iters; j++) {
-
+
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
if(processors == 1){
- driver(T[i], randT, namesOfGroupCombos, 0, namesOfGroupCombos.size(), sums, rScores);
+ driver(T[i], namesOfGroupCombos, 0, namesOfGroupCombos.size(), sums, rScores);
}else{
- createProcesses(T[i], randT, namesOfGroupCombos, sums, rScores);
+ createProcesses(T[i], namesOfGroupCombos, sums, rScores);
}
#else
- driver(T[i], randT, namesOfGroupCombos, 0, namesOfGroupCombos.size(), sums, rScores);
+ driver(T[i], namesOfGroupCombos, 0, namesOfGroupCombos.size(), sums, rScores);
#endif
if (m->control_pressed) { delete output; outSum.close(); for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
//report progress
m->mothurOut("Iter: " + toString(j+1)); m->mothurOutEndLine();
}
-
- for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear();
-
+ lines.clear();
+
//find the signifigance of the score for summary file
for (int f = 0; f < numComp; f++) {
//sort random scores
}
- if (m->control_pressed) { delete randT; outSum.close(); for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+ if (m->control_pressed) { outSum.close(); for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
printWSummaryFile();
//clear out users groups
globaldata->Groups.clear();
- delete randT;
if (m->control_pressed) {
for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); }
}
/**************************************************************************************************/
-int UnifracWeightedCommand::createProcesses(Tree* t, Tree* randT, vector< vector<string> > namesOfGroupCombos, vector<double>& sums, vector< vector<double> >& scores) {
+int UnifracWeightedCommand::createProcesses(Tree* t, vector< vector<string> > namesOfGroupCombos, vector<double>& sums, vector< vector<double> >& scores) {
try {
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
int process = 1;
processIDS.push_back(pid); //create map from line number to pid so you can append files in correct order later
process++;
}else if (pid == 0){
- driver(t, randT, namesOfGroupCombos, lines[process]->start, lines[process]->num, sums, scores);
+ driver(t, namesOfGroupCombos, lines[process].start, lines[process].num, sums, scores);
//pass numSeqs to parent
ofstream out;
string tempFile = outputDir + toString(getpid()) + ".weightedcommand.results.temp";
m->openOutputFile(tempFile, out);
- for (int i = lines[process]->start; i < (lines[process]->start + lines[process]->num); i++) { out << scores[i][(scores[i].size()-1)] << '\t'; } out << endl;
+ for (int i = lines[process].start; i < (lines[process].start + lines[process].num); i++) { out << scores[i][(scores[i].size()-1)] << '\t'; } out << endl;
out.close();
exit(0);
}else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
}
- driver(t, randT, namesOfGroupCombos, lines[0]->start, lines[0]->num, sums, scores);
+ driver(t, namesOfGroupCombos, lines[0].start, lines[0].num, sums, scores);
//force parent to wait until all the processes are done
for (int i=0;i<(processors-1);i++) {
int temp = processIDS[i];
wait(&temp);
}
-
+
//get data created by processes
for (int i=0;i<(processors-1);i++) {
+
ifstream in;
string s = outputDir + toString(processIDS[i]) + ".weightedcommand.results.temp";
m->openInputFile(s, in);
double tempScore;
- for (int i = lines[process]->start; i < (lines[process]->start + lines[process]->num); i++) { in >> tempScore; scores[i].push_back(tempScore); }
+ for (int j = lines[(i+1)].start; j < (lines[(i+1)].start + lines[(i+1)].num); j++) { in >> tempScore; scores[j].push_back(tempScore); }
in.close();
remove(s.c_str());
}
}
/**************************************************************************************************/
-int UnifracWeightedCommand::driver(Tree* t, Tree* randT, vector< vector<string> > namesOfGroupCombos, int start, int num, vector<double>& sums, vector< vector<double> >& scores) {
+int UnifracWeightedCommand::driver(Tree* t, vector< vector<string> > namesOfGroupCombos, int start, int num, vector<double>& sums, vector< vector<double> >& scores) {
try {
-
+ Tree* randT = new Tree();
+
for (int h = start; h < (start+num); h++) {
- cout << "doing " << h << endl;
+
if (m->control_pressed) { return 0; }
//initialize weighted score
if (m->control_pressed) { delete randT; return 0; }
-
//get wscore of random tree
EstOutput randomData = weighted->getValues(randT, groupA, groupB, sums);
-
+
if (m->control_pressed) { delete randT; return 0; }
//save scores
scores[h].push_back(randomData[0]);
}
-
+
+ delete randT;
+
return 0;
}
if (WScoreSig[count] > (1/(float)iters)) {
outSum << setprecision(6) << i+1 << '\t' << groupComb[j] << '\t' << utreeScores[count] << '\t' << setprecision(itersString.length()) << WScoreSig[count] << endl;
cout << setprecision(6) << i+1 << '\t' << groupComb[j] << '\t' << utreeScores[count] << '\t' << setprecision(itersString.length()) << WScoreSig[count] << endl;
- m->mothurOutJustToLog(toString(i+1) +"\t" + groupComb[j] +"\t" + toString(utreeScores[count]) +"\t" + toString(WScoreSig[count])); m->mothurOutEndLine();
+ m->mothurOutJustToLog(toString(i+1) +"\t" + groupComb[j] +"\t" + toString(utreeScores[count]) +"\t" + toString(WScoreSig[count]) + "\n");
}else{
outSum << setprecision(6) << i+1 << '\t' << groupComb[j] << '\t' << utreeScores[count] << '\t' << setprecision(itersString.length()) << "<" << (1/float(iters)) << endl;
cout << setprecision(6) << i+1 << '\t' << groupComb[j] << '\t' << utreeScores[count] << '\t' << setprecision(itersString.length()) << "<" << (1/float(iters)) << endl;
- m->mothurOutJustToLog(toString(i+1) +"\t" + groupComb[j] +"\t" + toString(utreeScores[count]) +"\t<" + toString((1/float(iters)))); m->mothurOutEndLine();
+ m->mothurOutJustToLog(toString(i+1) +"\t" + groupComb[j] +"\t" + toString(utreeScores[count]) +"\t<" + toString((1/float(iters))) + "\n");
}
}else{
outSum << setprecision(6) << i+1 << '\t' << groupComb[j] << '\t' << utreeScores[count] << '\t' << "0.00" << endl;
cout << setprecision(6) << i+1 << '\t' << groupComb[j] << '\t' << utreeScores[count] << '\t' << "0.00" << endl;
- m->mothurOutJustToLog(toString(i+1) +"\t" + groupComb[j] +"\t" + toString(utreeScores[count]) +"\t0.00"); m->mothurOutEndLine();
+ m->mothurOutJustToLog(toString(i+1) +"\t" + groupComb[j] +"\t" + toString(utreeScores[count]) +"\t0.00\n");
}
count++;
}
int num;
linePair(int i, int j) : start(i), num(j) {}
};
- vector<linePair*> lines;
+ vector<linePair> lines;
GlobalData* globaldata;
SharedUtil* util;
vector<double> utreeScores; //user tree unweighted scores
vector<double> WScoreSig; //tree weighted score signifigance when compared to random trees - percentage of random trees with that score or lower.
vector<string> groupComb; // AB. AC, BC...
- Tree* randT; //random tree
TreeMap* tmap;
Weighted* weighted;
string sumFile, outputDir;
//void removeValidScoresDuplicates();
int findIndex(float, int);
void calculateFreqsCumuls();
- int createProcesses(Tree*, Tree*, vector< vector<string> >, vector<double>&, vector< vector<double> >&);
- int driver(Tree*, Tree*, vector< vector<string> >, int, int, vector<double>&, vector< vector<double> >&);
+ int createProcesses(Tree*, vector< vector<string> >, vector<double>&, vector< vector<double> >&);
+ int driver(Tree*, vector< vector<string> >, int, int, vector<double>&, vector< vector<double> >&);
};
for (int i = 0; i < processors; i++) {
int startPos = i * numPairsPerProcessor;
+
if(i == processors - 1){
numPairsPerProcessor = numPairs - i * numPairsPerProcessor;
}
- lines.push_back(new linePair(startPos, numPairsPerProcessor));
+
+ lines.push_back(linePair(startPos, numPairsPerProcessor));
}
data = createProcesses(t, namesOfGroupCombos);
-
- for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear();
+ lines.clear();
}
#else
data = driver(t, namesOfGroupCombos, 0, namesOfGroupCombos.size());
process++;
}else if (pid == 0){
EstOutput myresults;
- myresults = driver(t, namesOfGroupCombos, lines[process]->start, lines[process]->num);
+ myresults = driver(t, namesOfGroupCombos, lines[process].start, lines[process].num);
if (m->control_pressed) { exit(0); }
}else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
}
- results = driver(t, namesOfGroupCombos, lines[0]->start, lines[0]->num);
+ results = driver(t, namesOfGroupCombos, lines[0].start, lines[0].num);
//force parent to wait until all the processes are done
for (int i=0;i<(processors-1);i++) {
int count = 0;
int total = num;
int twentyPercent = (total * 0.20);
-
+ if (twentyPercent == 0) { twentyPercent = 1; }
+
for (int h = start; h < (start+num); h++) {
if (m->control_pressed) { return results; }
totalBL += abs(t->tree[i].getBranchLength());
}
}
-
+
UW = (UniqueBL / totalBL);
if (isnan(UW) || isinf(UW)) { UW = 0; }
count++;
//report progress
- if((count) % twentyPercent == 0){ m->mothurOut("Percentage complete: " + toString(int((count / (float)total) * 100.0))); m->mothurOutEndLine(); }
+ if((count % twentyPercent) == 0) { float tempOut = (count / (float)total); if (isnan(tempOut) || isinf(tempOut)) { tempOut = 0.0; } m->mothurOut("Percentage complete: " + toString((int(tempOut) * 100.0))); m->mothurOutEndLine(); }
}
- m->mothurOut("Percentage complete: 100"); m->mothurOutEndLine();
+ //report progress
+ if((count % twentyPercent) != 0) { float tempOut = (count / (float)total); if (isnan(tempOut) || isinf(tempOut)) { tempOut = 0.0; } m->mothurOut("Percentage complete: " + toString((int(tempOut) * 100.0))); m->mothurOutEndLine(); }
return results;
}
}
/**************************************************************************************************/
-EstOutput Unweighted::getValues(Tree* t, string groupA, string groupB) {
+EstOutput Unweighted::getValues(Tree* t, string groupA, string groupB, int p, string o) {
try {
- globaldata = GlobalData::getInstance();
+ globaldata = GlobalData::getInstance();
+ processors = p;
+ outputDir = o;
+
- vector<string> groups;
- double UniqueBL; //a branch length is unique if it's chidren are from the same group
- double totalBL; //all branch lengths
- double UW; //Unweighted Value = UniqueBL / totalBL;
- copyTree = new Tree;
-
//if the users enters no groups then give them the score of all groups
int numGroups = globaldata->Groups.size();
-
+
//calculate number of comparsions
int numComp = 0;
+ vector< vector<string> > namesOfGroupCombos;
for (int r=0; r<numGroups; r++) {
for (int l = r+1; l < numGroups; l++) {
numComp++;
- }
- }
-
- //numComp+1 for AB, AC, BC, ABC
- data.resize(numComp+1,0);
-
- int count = 0;
- for (int a=0; a<numGroups; a++) {
- for (int l = a+1; l < numGroups; l++) {
- UniqueBL=0.0000; //a branch length is unique if it's chidren are from the same group
- totalBL = 0.00; //all branch lengths
- UW = 0.00; //Unweighted Value = UniqueBL / totalBL;
-
- //copy random tree passed in
- copyTree->getCopy(t);
-
- //groups in this combo
- groups.push_back(globaldata->Groups[a]); groups.push_back(globaldata->Groups[l]);
-
- //swap labels in the groups you want to compare
- copyTree->assembleRandomUnifracTree(groups[0], groups[1]);
-
- if (m->control_pressed) { delete copyTree; return data; }
-
- for(int i=0;i<copyTree->getNumNodes();i++){
-
- if (m->control_pressed) { return data; }
-
- //pcountSize = 0, they are from a branch that is entirely from a group the user doesn't want
- //pcountSize = 2, not unique to one group
- //pcountSize = 1, unique to one group
-
- int pcountSize = 0;
- for (int j = 0; j < groups.size(); j++) {
- map<string, int>::iterator itGroup = copyTree->tree[i].pcount.find(groups[j]);
- if (itGroup != copyTree->tree[i].pcount.end()) { pcountSize++; }
- }
-
- if (pcountSize == 0) { }
- else if ((copyTree->tree[i].getBranchLength() != -1) && (pcountSize == 1)) { UniqueBL += abs(copyTree->tree[i].getBranchLength()); }
-
- if ((copyTree->tree[i].getBranchLength() != -1) && (pcountSize != 0)) {
- totalBL += abs(copyTree->tree[i].getBranchLength());
- }
- }
-
-
- UW = (UniqueBL / totalBL);
-
- if (isnan(UW) || isinf(UW)) { UW = 0; }
-
- data[count] = UW;
- count++;
- groups.clear();
+ vector<string> groups; groups.push_back(globaldata->Groups[r]); groups.push_back(globaldata->Groups[l]);
+ namesOfGroupCombos.push_back(groups);
}
}
-
if (numComp != 1) {
+ vector<string> groups;
if (numGroups == 0) {
//get score for all users groups
for (int i = 0; i < tmap->namesOfGroups.size(); i++) {
groups.push_back(tmap->namesOfGroups[i]);
}
}
+ namesOfGroupCombos.push_back(groups);
}else {
for (int i = 0; i < globaldata->Groups.size(); i++) {
groups.push_back(globaldata->Groups[i]);
}
+ namesOfGroupCombos.push_back(groups);
}
+ }
+
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ if(processors == 1){
+ data = driver(t, namesOfGroupCombos, 0, namesOfGroupCombos.size(), true);
+ }else{
+ int numPairs = namesOfGroupCombos.size();
+
+ int numPairsPerProcessor = numPairs / processors;
+
+ for (int i = 0; i < processors; i++) {
+ int startPos = i * numPairsPerProcessor;
+ if(i == processors - 1){
+ numPairsPerProcessor = numPairs - i * numPairsPerProcessor;
+ }
+ lines.push_back(linePair(startPos, numPairsPerProcessor));
+ }
+
+ data = createProcesses(t, namesOfGroupCombos, true);
+
+ lines.clear();
+ }
+ #else
+ data = driver(t, namesOfGroupCombos, 0, namesOfGroupCombos.size(), true);
+ #endif
+
+ return data;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Unweighted", "getValues");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+
+EstOutput Unweighted::createProcesses(Tree* t, vector< vector<string> > namesOfGroupCombos, bool usingGroups) {
+ try {
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ int process = 1;
+ int num = 0;
+ vector<int> processIDS;
- UniqueBL=0.0000; //a branch length is unique if it's chidren are from the same group
- totalBL = 0.00; //all branch lengths
- UW = 0.00; //Unweighted Value = UniqueBL / totalBL;
+ EstOutput results;
+
+ //loop through and create all the processes you want
+ while (process != processors) {
+ int pid = fork();
+
+ if (pid > 0) {
+ processIDS.push_back(pid); //create map from line number to pid so you can append files in correct order later
+ process++;
+ }else if (pid == 0){
+ EstOutput myresults;
+ myresults = driver(t, namesOfGroupCombos, lines[process].start, lines[process].num, usingGroups);
+
+ if (m->control_pressed) { exit(0); }
+
+ //pass numSeqs to parent
+ ofstream out;
+ string tempFile = outputDir + toString(getpid()) + ".unweighted.results.temp";
+ m->openOutputFile(tempFile, out);
+ out << myresults.size() << endl;
+ for (int i = 0; i < myresults.size(); i++) { out << myresults[i] << '\t'; } out << endl;
+ out.close();
+
+ exit(0);
+ }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
+ }
+
+ results = driver(t, namesOfGroupCombos, lines[0].start, lines[0].num, usingGroups);
+
+ //force parent to wait until all the processes are done
+ for (int i=0;i<(processors-1);i++) {
+ int temp = processIDS[i];
+ wait(&temp);
+ }
+
+ if (m->control_pressed) { return results; }
+
+ //get data created by processes
+ for (int i=0;i<(processors-1);i++) {
+ ifstream in;
+ string s = outputDir + toString(processIDS[i]) + ".unweighted.results.temp";
+ m->openInputFile(s, in);
+
+ //get quantiles
+ if (!in.eof()) {
+ int num;
+ in >> num; m->gobble(in);
+
+ if (m->control_pressed) { break; }
+
+ double w;
+ for (int j = 0; j < num; j++) {
+ in >> w;
+ results.push_back(w);
+ }
+ m->gobble(in);
+ }
+ in.close();
+ remove(s.c_str());
+ }
+
+ return results;
+#endif
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Unweighted", "createProcesses");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+EstOutput Unweighted::driver(Tree* t, vector< vector<string> > namesOfGroupCombos, int start, int num, bool usingGroups) {
+ try {
+
+ EstOutput results; results.resize(num);
+
+ int count = 0;
+ int total = num;
+ int twentyPercent = (total * 0.20);
+
+ Tree* copyTree = new Tree;
+
+ for (int h = start; h < (start+num); h++) {
+
+ if (m->control_pressed) { return results; }
//copy random tree passed in
copyTree->getCopy(t);
- //swap labels in all the groups you want to compare
- copyTree->assembleRandomUnifracTree(groups);
+ //swap labels in the groups you want to compare
+ copyTree->assembleRandomUnifracTree(namesOfGroupCombos[h]);
- if (m->control_pressed) { delete copyTree; return data; }
-
- for(int i=0;i<copyTree->getNumNodes();i++){
+ double UniqueBL=0.0000; //a branch length is unique if it's chidren are from the same group
+ double totalBL = 0.00; //all branch lengths
+ double UW = 0.00; //Unweighted Value = UniqueBL / totalBL;
+
+ for(int i=0;i<t->getNumNodes();i++){
if (m->control_pressed) { return data; }
//pcountSize = 1, unique to one group
int pcountSize = 0;
- for (int j = 0; j < groups.size(); j++) {
- map<string, int>::iterator itGroup = copyTree->tree[i].pcount.find(groups[j]);
- if (itGroup != copyTree->tree[i].pcount.end()) { pcountSize++; if (pcountSize > 1) { break; } }
+ for (int j = 0; j < namesOfGroupCombos[h].size(); j++) {
+ map<string, int>::iterator itGroup = t->tree[i].pcount.find(namesOfGroupCombos[h][j]);
+ if (itGroup != t->tree[i].pcount.end()) { pcountSize++; if (pcountSize > 1) { break; } }
}
if (pcountSize == 0) { }
- else if ((copyTree->tree[i].getBranchLength() != -1) && (pcountSize == 1)) { UniqueBL += abs(copyTree->tree[i].getBranchLength()); }
+ else if ((t->tree[i].getBranchLength() != -1) && (pcountSize == 1)) { UniqueBL += abs(t->tree[i].getBranchLength()); }
- if ((copyTree->tree[i].getBranchLength() != -1) && (pcountSize != 0)) {
- totalBL += abs(copyTree->tree[i].getBranchLength());
+ if ((t->tree[i].getBranchLength() != -1) && (pcountSize != 0)) {
+ totalBL += abs(t->tree[i].getBranchLength());
}
}
if (isnan(UW) || isinf(UW)) { UW = 0; }
- data[count] = UW;
+ results[count] = UW;
+ count++;
+
}
delete copyTree;
- return data;
-
+ return results;
}
catch(exception& e) {
- m->errorOut(e, "Unweighted", "getValues");
+ m->errorOut(e, "Unweighted", "driver");
exit(1);
}
}
-
/**************************************************************************************************/
Unweighted(TreeMap* t) : tmap(t) {};
~Unweighted() {};
EstOutput getValues(Tree*, int, string);
- EstOutput getValues(Tree*, string, string);
+ EstOutput getValues(Tree*, string, string, int, string);
private:
struct linePair {
int num;
linePair(int i, int j) : start(i), num(j) {}
};
- vector<linePair*> lines;
+ vector<linePair> lines;
GlobalData* globaldata;
- Tree* copyTree;
EstOutput data;
TreeMap* tmap;
int processors;
EstOutput driver(Tree*, vector< vector<string> >, int, int);
EstOutput createProcesses(Tree*, vector< vector<string> >);
+ EstOutput driver(Tree*, vector< vector<string> >, int, int, bool);
+ EstOutput createProcesses(Tree*, vector< vector<string> >, bool);
};
if(i == processors - 1){
numPairsPerProcessor = numPairs - i * numPairsPerProcessor;
}
- lines.push_back(new linePair(startPos, numPairsPerProcessor));
+ lines.push_back(linePair(startPos, numPairsPerProcessor));
}
data = createProcesses(t, namesOfGroupCombos, sums);
- for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear();
+ lines.clear();
}
#else
data = driver(t, namesOfGroupCombos, 0, namesOfGroupCombos.size(), sums);
}else if (pid == 0){
EstOutput Myresults;
- Myresults = driver(t, namesOfGroupCombos, lines[process]->start, lines[process]->num, sums);
+ Myresults = driver(t, namesOfGroupCombos, lines[process].start, lines[process].num, sums);
m->mothurOut("Merging results."); m->mothurOutEndLine();
}else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
}
- results = driver(t, namesOfGroupCombos, lines[0]->start, lines[0]->num, sums);
+ results = driver(t, namesOfGroupCombos, lines[0].start, lines[0].num, sums);
//force parent to wait until all the processes are done
for (int i=0;i<(processors-1);i++) {
//calculate u for the group comb
int total = t->getNumNodes();
int twentyPercent = (total * 0.20);
+
for(int i=0;i<t->getNumNodes();i++){
for (int h = start; h < (start+num); h++) {
int num;
linePair(int i, int j) : start(i), num(j) {}
};
- vector<linePair*> lines;
+ vector<linePair> lines;
GlobalData* globaldata;
EstOutput data;
projects / mothur.git / commitdiff