outputFileHandle << "label" <<'\t' << "comparison" << '\t';
for(int i=0;i<sumCalculators.size();i++){
outputFileHandle << '\t' << sumCalculators[i]->getName();
- if (sumCalculators[i]->getCols() == 3) { outputFileHandle << "\tlci\thci"; }
+ if (sumCalculators[i]->getCols() == 3) { outputFileHandle << "\t" << sumCalculators[i]->getName() << "_lci\t" << sumCalculators[i]->getName() << "_hci"; }
}
outputFileHandle << endl;
else {
//valid paramters for this command
- string Array[] = {"groups","iters","distance","random", "outputdir","inputdir"};
+ string Array[] = {"groups","iters","distance","random", "processors","outputdir","inputdir"};
vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
OptionParser parser(option);
temp = validParameter.validFile(parameters, "random", false); if (temp == "not found") { temp = "f"; }
random = m->isTrue(temp);
+ temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = "1"; }
+ convert(temp, processors);
+
if (!random) { iters = 0; } //turn off random calcs
//if user selects distance = true and no groups it won't calc the pairwise
utreeScores.resize(numComp);
UWScoreSig.resize(numComp);
- userData = unweighted->getValues(T[i]); //userData[0] = unweightedscore
+ 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;
- }
+ 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
for(int k = 0; k < numComp; k++) {
Unweighted* unweighted;
string sumFile, allGroups;
vector<string> groupComb; // AB. AC, BC...
- int iters, numGroups, numComp, counter;
+ int iters, numGroups, numComp, counter, processors;
EstOutput userData; //unweighted score info for user tree
EstOutput randomData; //unweighted score info for random trees
vector< vector<float> > utreeScores; //scores for users trees for each comb.
int UnifracWeightedCommand::createProcesses(Tree* t, Tree* randT, vector< vector<string> > namesOfGroupCombos, vector<double>& sums, vector< vector<double> >& scores) {
try {
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
- int process = 0;
+ int process = 1;
int num = 0;
vector<int> processIDS;
//pass numSeqs to parent
ofstream out;
- string tempFile = outputDir + toString(getpid()) + ".results.temp";
+ string tempFile = outputDir + toString(getpid()) + ".weightedcommand.results.temp";
m->openOutputFile(tempFile, out);
- out << results.size() << endl;
- for (int i = lines[process]->start; i < (lines[process]->start + lines[process]->num); i++) { out << results[i] << '\t'; } out << endl;
+ for (int i = lines[process]->start; i < (lines[process]->start + lines[process]->num); i++) { out << scores[i][0] << '\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);
+
//force parent to wait until all the processes are done
- for (int i=0;i<processors;i++) {
+ 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;i++) {
+ for (int i=0;i<(processors-1);i++) {
ifstream in;
- string s = outputDir + toString(processIDS[i]) + ".results.temp";
+ string s = outputDir + toString(processIDS[i]) + ".weightedcommand.results.temp";
m->openInputFile(s, in);
- vector<double> r;
-
- //get quantiles
- while (!in.eof()) {
- int num;
- in >> num;
-
- m->gobble(in);
-
- double w;
- for (int j = 0; j < num; j++) {
- in >> w;
- r.push_back(w);
- }
- m->gobble(in);
- }
+ for (int i = lines[process]->start; i < (lines[process]->start + lines[process]->num); i++) { in >> scores[i][0]; }
in.close();
remove(s.c_str());
-
- //save quan in quantiles
- for (int j = 0; j < r.size(); j++) {
- //put all values of r into results
- results.push_back(r[j]);
- }
}
m->mothurOut("DONE."); m->mothurOutEndLine(); m->mothurOutEndLine();
int UnifracWeightedCommand::driver(Tree* t, Tree* randT, vector< vector<string> > namesOfGroupCombos, int start, int num, vector<double>& sums, vector< vector<double> >& scores) {
try {
int count = 0;
- int total = start+num;
+ int total = num;
int twentyPercent = (total * 0.20);
for (int h = start; h < (start+num); h++) {
count++;
//report progress
- if((h) % twentyPercent == 0){ m->mothurOut("Random comparison percentage complete: " + toString(int((h / (float)total) * 100.0))); m->mothurOutEndLine(); }
+ if((count) % twentyPercent == 0){ m->mothurOut("Random comparison percentage complete: " + toString(int((count / (float)total) * 100.0))); m->mothurOutEndLine(); }
}
m->mothurOut("Random comparison percentage complete: 100"); m->mothurOutEndLine();
/**************************************************************************************************/
-EstOutput Unweighted::getValues(Tree* t) {
+EstOutput Unweighted::getValues(Tree* t, int p, string o) {
try {
globaldata = GlobalData::getInstance();
-
- 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;
-
+ processors = p;
+ outputDir = o;
+
//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++;
+ vector<string> groups; groups.push_back(globaldata->Groups[r]); groups.push_back(globaldata->Groups[l]);
+ namesOfGroupCombos.push_back(groups);
}
}
-
- //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;
- //copyIpcount.clear();
-
- //groups in this combo
- groups.push_back(globaldata->Groups[a]); groups.push_back(globaldata->Groups[l]);
-
- for(int i=0;i<t->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 = t->tree[i].pcount.find(groups[j]);
- if (itGroup != t->tree[i].pcount.end()) { pcountSize++; }
- }
-
- if (pcountSize == 0) { }
- else if ((t->tree[i].getBranchLength() != -1) && (pcountSize == 1)) { UniqueBL += abs(t->tree[i].getBranchLength()); }
-
- if ((t->tree[i].getBranchLength() != -1) && (pcountSize != 0)) {
- totalBL += abs(t->tree[i].getBranchLength());
- }
- }
-
- UW = (UniqueBL / totalBL);
-
- if (isnan(UW) || isinf(UW)) { UW = 0; }
-
- data[count] = UW;
- count++;
- groups.clear();
- }
- }
-
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());
+ }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(new linePair(startPos, numPairsPerProcessor));
+ }
+
+ data = createProcesses(t, namesOfGroupCombos);
+
+ for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear();
}
+ #else
+ data = driver(t, namesOfGroupCombos, 0, namesOfGroupCombos.size());
+ #endif
- 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;
+ return data;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Unweighted", "getValues");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+
+EstOutput Unweighted::createProcesses(Tree* t, vector< vector<string> > namesOfGroupCombos) {
+ try {
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ int process = 1;
+ int num = 0;
+ vector<int> processIDS;
+
+ 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);
+
+ if (m->control_pressed) { exit(0); }
+
+ m->mothurOut("Merging results."); m->mothurOutEndLine();
+
+ //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);
+
+ //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());
+ }
+
+ m->mothurOut("DONE."); m->mothurOutEndLine(); m->mothurOutEndLine();
+
+ 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) {
+ try {
+
+ EstOutput results; results.resize(num);
+
+ int count = 0;
+ int total = num;
+ int twentyPercent = (total * 0.20);
+
+ for (int h = start; h < (start+num); h++) {
+
+ if (m->control_pressed) { return results; }
+
+ 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++){
//pcountSize = 1, unique to one group
int pcountSize = 0;
- for (int j = 0; j < groups.size(); j++) {
- map<string, int>::iterator itGroup = t->tree[i].pcount.find(groups[j]);
+ 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 (isnan(UW) || isinf(UW)) { UW = 0; }
- data[count] = UW;
- }
+ results[count] = UW;
+ count++;
- return data;
-
+ //report progress
+ if((count) % twentyPercent == 0){ m->mothurOut("Percentage complete: " + toString(int((count / (float)total) * 100.0))); m->mothurOutEndLine(); }
+ }
+
+ m->mothurOut("Percentage complete: 100"); m->mothurOutEndLine();
+
+ return results;
}
catch(exception& e) {
- m->errorOut(e, "Unweighted", "getValues");
+ m->errorOut(e, "Unweighted", "driver");
exit(1);
}
}
-
/**************************************************************************************************/
EstOutput Unweighted::getValues(Tree* t, string groupA, string groupB) {
}
}
-
+/**************************************************************************************************/
public:
Unweighted(TreeMap* t) : tmap(t) {};
~Unweighted() {};
- EstOutput getValues(Tree*);
+ EstOutput getValues(Tree*, int, string);
EstOutput getValues(Tree*, string, string);
private:
+ struct linePair {
+ int start;
+ int num;
+ linePair(int i, int j) : start(i), num(j) {}
+ };
+ vector<linePair*> lines;
+
GlobalData* globaldata;
Tree* copyTree;
EstOutput data;
TreeMap* tmap;
+ int processors;
+ string outputDir;
+
+ EstOutput driver(Tree*, vector< vector<string> >, int, int);
+ EstOutput createProcesses(Tree*, vector< vector<string> >);
};
EstOutput Weighted::createProcesses(Tree* t, vector< vector<string> > namesOfGroupCombos, vector<double>& sums) {
try {
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
- int process = 0;
+ int process = 1;
int num = 0;
vector<int> processIDS;
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){
- results = driver(t, namesOfGroupCombos, lines[process]->start, lines[process]->num, sums);
+ EstOutput Myresults;
+ Myresults = driver(t, namesOfGroupCombos, lines[process]->start, lines[process]->num, sums);
if (m->control_pressed) { exit(0); }
//pass numSeqs to parent
ofstream out;
- string tempFile = outputDir + toString(getpid()) + ".results.temp";
+ string tempFile = outputDir + toString(getpid()) + ".weighted.results.temp";
m->openOutputFile(tempFile, out);
- out << results.size() << endl;
- for (int i = 0; i < results.size(); i++) { out << results[i] << '\t'; } out << endl;
+ 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, sums);
//force parent to wait until all the processes are done
- for (int i=0;i<processors;i++) {
+ 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;i++) {
+ for (int i=0;i<(processors-1);i++) {
ifstream in;
- string s = outputDir + toString(processIDS[i]) + ".results.temp";
+ string s = outputDir + toString(processIDS[i]) + ".weighted.results.temp";
m->openInputFile(s, in);
- vector<double> r;
-
//get quantiles
while (!in.eof()) {
int num;
- in >> num;
+ in >> num; m->gobble(in);
if (m->control_pressed) { break; }
-
- m->gobble(in);
double w;
for (int j = 0; j < num; j++) {
in >> w;
- r.push_back(w);
+ results.push_back(w);
}
m->gobble(in);
}
in.close();
remove(s.c_str());
-
- //save quan in quantiles
- for (int j = 0; j < r.size(); j++) {
- //put all values of r into results
- results.push_back(r[j]);
- }
}
m->mothurOut("DONE."); m->mothurOutEndLine(); m->mothurOutEndLine();
vector<double> D;
int count = 0;
- int total = start+num;
+ int total = num;
int twentyPercent = (total * 0.20);
for (int h = start; h < (start+num); h++) {
count++;
//report progress
- if((h) % twentyPercent == 0){ m->mothurOut("Percentage complete: " + toString(int((h / (float)total) * 100.0))); m->mothurOutEndLine(); }
+ if((count) % twentyPercent == 0){ m->mothurOut("Percentage complete: " + toString(int((count / (float)total) * 100.0))); m->mothurOutEndLine(); }
}
m->mothurOut("Percentage complete: 100"); m->mothurOutEndLine();
projects / mothur.git / commitdiff