#include "boneh.h"
#include "solow.h"
#include "shen.h"
+#include "subsample.h"
//**********************************************************************************************************************
vector<string> SummaryCommand::setParameters(){
CommandParameter prabund("rabund", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(prabund);
CommandParameter psabund("sabund", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(psabund);
CommandParameter pshared("shared", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(pshared);
+ CommandParameter psubsample("subsample", "String", "", "", "", "", "",false,false); parameters.push_back(psubsample);
+ CommandParameter piters("iters", "Number", "", "1000", "", "", "",false,false); parameters.push_back(piters);
CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
CommandParameter pcalc("calc", "Multiple", "sobs-chao-nseqs-coverage-ace-jack-shannon-shannoneven-npshannon-heip-smithwilson-simpson-simpsoneven-invsimpson-bootstrap-geometric-qstat-logseries-bergerparker-bstick-goodscoverage-efron-boneh-solow-shen", "sobs-chao-ace-jack-shannon-npshannon-simpson", "", "", "",true,false); parameters.push_back(pcalc);
CommandParameter pabund("abund", "Number", "", "10", "", "", "",false,false); parameters.push_back(pabund);
try {
string helpString = "";
ValidCalculators validCalculator;
- helpString += "The summary.single command parameters are list, sabund, rabund, shared, label, calc, abund and groupmode. list, sabund, rabund or shared is required unless you have a valid current file.\n";
+ helpString += "The summary.single command parameters are list, sabund, rabund, shared, subsample, iters, label, calc, abund and groupmode. list, sabund, rabund or shared is required unless you have a valid current file.\n";
helpString += "The summary.single command should be in the following format: \n";
helpString += "summary.single(label=yourLabel, calc=yourEstimators).\n";
helpString += "Example summary.single(label=unique-.01-.03, calc=sobs-chao-ace-jack-bootstrap-shannon-npshannon-simpson).\n";
helpString += validCalculator.printCalc("summary");
+ helpString += "The subsample parameter allows you to enter the size of the sample or you can set subsample=T and mothur will use the size of your smallest group in the case of a shared file. With a list, sabund or rabund file you must provide a subsample size.\n";
+ helpString += "The iters parameter allows you to choose the number of times you would like to run the subsample.\n";
helpString += "The default value calc is sobs-chao-ace-jack-shannon-npshannon-simpson\n";
helpString += "If you are running summary.single with a shared file and would like your summary results collated in one file, set groupmode=t. (Default=true).\n";
helpString += "The label parameter is used to analyze specific labels in your input.\n";
temp = validParameter.validFile(parameters, "groupmode", false); if (temp == "not found") { temp = "T"; }
groupMode = m->isTrue(temp);
-
+ temp = validParameter.validFile(parameters, "iters", false); if (temp == "not found") { temp = "1000"; }
+ m->mothurConvert(temp, iters);
+
+ temp = validParameter.validFile(parameters, "subsample", false); if (temp == "not found") { temp = "F"; }
+ if (m->isNumeric1(temp)) { m->mothurConvert(temp, subsampleSize); subsample = true; }
+ else {
+ if (m->isTrue(temp)) { subsample = true; subsampleSize = -1; } //we will set it to smallest group later
+ else { subsample = false; subsampleSize = -1; }
+ }
+
+ if (subsample == false) { iters = 1; }
+ else {
+ //if you did not set a samplesize and are not using a sharedfile
+ if ((subsampleSize == -1) && (format != "sharedfile")) { m->mothurOut("[ERROR]: If you want to subsample with a list, rabund or sabund file, you must provide the sample size. You can do this by setting subsample=yourSampleSize.\n"); abort=true; }
+ }
+
}
}
catch(exception& e) {
int numLines = 0;
int numCols = 0;
-
+ map<string, string> groupIndex;
+
for (int p = 0; p < inputFileNames.size(); p++) {
numLines = 0;
numCols = 0;
string fileNameRoot = outputDir + m->getRootName(m->getSimpleName(inputFileNames[p])) + "summary";
+ string fileNameAve = outputDir + m->getRootName(m->getSimpleName(inputFileNames[p])) + "ave";
+ string fileNameSTD = outputDir + m->getRootName(m->getSimpleName(inputFileNames[p])) + "std";
outputNames.push_back(fileNameRoot); outputTypes["summary"].push_back(fileNameRoot);
+
+
if (inputFileNames.size() > 1) {
m->mothurOutEndLine(); m->mothurOut("Processing group " + groups[p]); m->mothurOutEndLine(); m->mothurOutEndLine();
+ groupIndex[fileNameRoot] = groups[p];
}
sumCalculators.clear();
ofstream outputFileHandle;
m->openOutputFile(fileNameRoot, outputFileHandle);
outputFileHandle << "label";
+
+ ofstream outAve, outSTD;
+ if (subsample) {
+ m->openOutputFile(fileNameAve, outAve);
+ m->openOutputFile(fileNameSTD, outSTD);
+ outputNames.push_back(fileNameAve); outputTypes["ave"].push_back(fileNameAve);
+ outputNames.push_back(fileNameSTD); outputTypes["std"].push_back(fileNameSTD);
+ outAve << "label"; outSTD << "label";
+ outAve.setf(ios::fixed, ios::floatfield); outAve.setf(ios::showpoint);
+ outSTD.setf(ios::fixed, ios::floatfield); outSTD.setf(ios::showpoint);
+ if (inputFileNames.size() > 1) {
+ groupIndex[fileNameAve] = groups[p];
+ groupIndex[fileNameSTD] = groups[p];
+ }
+ }
input = new InputData(inputFileNames[p], format);
sabund = input->getSAbundVector();
for(int i=0;i<sumCalculators.size();i++){
if(sumCalculators[i]->getCols() == 1){
outputFileHandle << '\t' << sumCalculators[i]->getName();
+ if (subsample) { outAve << '\t' << sumCalculators[i]->getName(); outSTD << '\t' << sumCalculators[i]->getName(); }
numCols++;
}
else{
outputFileHandle << '\t' << sumCalculators[i]->getName() << "\t" << sumCalculators[i]->getName() << "_lci\t" << sumCalculators[i]->getName() << "_hci";
+ if (subsample) { outAve << '\t' << sumCalculators[i]->getName() << "\t" << sumCalculators[i]->getName() << "_lci\t" << sumCalculators[i]->getName() << "_hci"; outSTD << '\t' << sumCalculators[i]->getName() << "\t" << sumCalculators[i]->getName() << "_lci\t" << sumCalculators[i]->getName() << "_hci"; }
numCols += 3;
}
}
outputFileHandle << endl;
+ if (subsample) { outSTD << endl; outAve << endl; }
//if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
set<string> processedLabels;
set<string> userLabels = labels;
- if (m->control_pressed) { outputFileHandle.close(); for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } for(int i=0;i<sumCalculators.size();i++){ delete sumCalculators[i]; } delete sabund; delete input; return 0; }
+
+
+ if (m->control_pressed) { outputFileHandle.close(); outAve.close(); outSTD.close(); for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } for(int i=0;i<sumCalculators.size();i++){ delete sumCalculators[i]; } delete sabund; delete input; return 0; }
while((sabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
- if (m->control_pressed) { outputFileHandle.close(); for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } for(int i=0;i<sumCalculators.size();i++){ delete sumCalculators[i]; } delete sabund; delete input; return 0; }
+ if (m->control_pressed) { outputFileHandle.close(); outAve.close(); outSTD.close(); for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } for(int i=0;i<sumCalculators.size();i++){ delete sumCalculators[i]; } delete sabund; delete input; return 0; }
if(allLines == 1 || labels.count(sabund->getLabel()) == 1){
processedLabels.insert(sabund->getLabel());
userLabels.erase(sabund->getLabel());
- outputFileHandle << sabund->getLabel();
- for(int i=0;i<sumCalculators.size();i++){
- vector<double> data = sumCalculators[i]->getValues(sabund);
-
- if (m->control_pressed) { outputFileHandle.close(); for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } for(int i=0;i<sumCalculators.size();i++){ delete sumCalculators[i]; } delete sabund; delete input; return 0; }
-
- outputFileHandle << '\t';
- sumCalculators[i]->print(outputFileHandle);
- }
- outputFileHandle << endl;
+ process(sabund, outputFileHandle, outAve, outSTD);
+
+ if (m->control_pressed) { outputFileHandle.close(); outAve.close(); outSTD.close(); for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } for(int i=0;i<sumCalculators.size();i++){ delete sumCalculators[i]; } delete sabund; delete input; return 0; }
numLines++;
}
processedLabels.insert(sabund->getLabel());
userLabels.erase(sabund->getLabel());
- outputFileHandle << sabund->getLabel();
- for(int i=0;i<sumCalculators.size();i++){
- vector<double> data = sumCalculators[i]->getValues(sabund);
-
- if (m->control_pressed) { outputFileHandle.close(); for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } for(int i=0;i<sumCalculators.size();i++){ delete sumCalculators[i]; } delete sabund; delete input; return 0; }
-
- outputFileHandle << '\t';
- sumCalculators[i]->print(outputFileHandle);
- }
- outputFileHandle << endl;
+ process(sabund, outputFileHandle, outAve, outSTD);
+
+ if (m->control_pressed) { outputFileHandle.close(); outAve.close(); outSTD.close(); for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } for(int i=0;i<sumCalculators.size();i++){ delete sumCalculators[i]; } delete sabund; delete input; return 0; }
numLines++;
//restore real lastlabel to save below
sabund = input->getSAbundVector();
}
- if (m->control_pressed) { outputFileHandle.close(); for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } for(int i=0;i<sumCalculators.size();i++){ delete sumCalculators[i]; } delete input; return 0; }
+ if (m->control_pressed) { outputFileHandle.close(); outAve.close(); outSTD.close(); for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } for(int i=0;i<sumCalculators.size();i++){ delete sumCalculators[i]; } delete input; return 0; }
//output error messages about any remaining user labels
set<string>::iterator it;
sabund = input->getSAbundVector(lastLabel);
m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
- outputFileHandle << sabund->getLabel();
- for(int i=0;i<sumCalculators.size();i++){
- vector<double> data = sumCalculators[i]->getValues(sabund);
-
- if (m->control_pressed) { outputFileHandle.close(); for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } for(int i=0;i<sumCalculators.size();i++){ delete sumCalculators[i]; } delete sabund; delete input; return 0; }
-
- outputFileHandle << '\t';
- sumCalculators[i]->print(outputFileHandle);
- }
- outputFileHandle << endl;
+ process(sabund, outputFileHandle, outAve, outSTD);
+
+ if (m->control_pressed) { outputFileHandle.close(); outAve.close(); outSTD.close(); for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } for(int i=0;i<sumCalculators.size();i++){ delete sumCalculators[i]; } delete sabund; delete input; return 0; }
numLines++;
delete sabund;
}
outputFileHandle.close();
+ if (subsample) { outAve.close(); outSTD.close(); }
if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } for(int i=0;i<sumCalculators.size();i++){ delete sumCalculators[i]; } delete input; return 0; }
if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
//create summary file containing all the groups data for each label - this function just combines the info from the files already created.
- if ((sharedfile != "") && (groupMode)) { outputNames.push_back(createGroupSummaryFile(numLines, numCols, outputNames)); }
+ if ((sharedfile != "") && (groupMode)) { vector<string> comboNames = createGroupSummaryFile(numLines, numCols, outputNames, groupIndex); for (int i = 0; i < comboNames.size(); i++) { outputNames.push_back(comboNames[i]); } }
if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
}
}
//**********************************************************************************************************************
+int SummaryCommand::process(SAbundVector*& sabund, ofstream& outputFileHandle, ofstream& outAve, ofstream& outStd) {
+ try {
+
+ //calculator -> data -> values
+ vector< vector< vector<double> > > results; results.resize(sumCalculators.size());
+
+ outputFileHandle << sabund->getLabel();
+
+ SubSample sample;
+ for (int thisIter = 0; thisIter < iters+1; thisIter++) {
+
+ SAbundVector* thisIterSabund = sabund;
+
+ //we want the summary results for the whole dataset, then the subsampling
+ if ((thisIter > 0) && subsample) { //subsample sabund and run it
+ //copy sabund since getSample destroys it
+ RAbundVector rabund = sabund->getRAbundVector();
+ SAbundVector* newSabund = new SAbundVector();
+ *newSabund = rabund.getSAbundVector();
+
+ sample.getSample(newSabund, subsampleSize);
+ thisIterSabund = newSabund;
+ }
+
+ for(int i=0;i<sumCalculators.size();i++){
+ vector<double> data = sumCalculators[i]->getValues(thisIterSabund);
+
+ if (m->control_pressed) { return 0; }
+
+ if (thisIter == 0) {
+ outputFileHandle << '\t';
+ sumCalculators[i]->print(outputFileHandle);
+ }else {
+ //some of the calc have hci and lci need to make room for that
+ if (results[i].size() == 0) { results[i].resize(data.size()); }
+ //save results for ave and std.
+ for (int j = 0; j < data.size(); j++) {
+ if (m->control_pressed) { return 0; }
+ results[i][j].push_back(data[j]);
+ }
+ }
+ }
+
+ //cleanup memory
+ if ((thisIter > 0) && subsample) { delete thisIterSabund; }
+ }
+ outputFileHandle << endl;
+
+ if (subsample) {
+ outAve << sabund->getLabel() << '\t'; outStd << sabund->getLabel() << '\t';
+ //find ave and std for this label and output
+ //will need to modify the createGroupSummary to combine results and not mess with the .summary file.
+
+ //calcs -> values
+ vector< vector<double> > calcAverages; calcAverages.resize(sumCalculators.size());
+ for (int i = 0; i < calcAverages.size(); i++) { calcAverages[i].resize(results[i].size(), 0); }
+
+ for (int thisIter = 0; thisIter < iters; thisIter++) { //sum all groups dists for each calculator
+ for (int i = 0; i < calcAverages.size(); i++) { //initialize sums to zero.
+ for (int j = 0; j < calcAverages[i].size(); j++) {
+ calcAverages[i][j] += results[i][j][thisIter];
+ }
+ }
+ }
+
+ for (int i = 0; i < calcAverages.size(); i++) { //finds average.
+ for (int j = 0; j < calcAverages[i].size(); j++) {
+ calcAverages[i][j] /= (float) iters;
+ outAve << calcAverages[i][j] << '\t';
+ }
+ }
+
+ //find standard deviation
+ vector< vector<double> > stdDev; stdDev.resize(sumCalculators.size());
+ for (int i = 0; i < stdDev.size(); i++) { stdDev[i].resize(results[i].size(), 0); }
+
+ for (int thisIter = 0; thisIter < iters; thisIter++) { //compute the difference of each dist from the mean, and square the result of each
+ for (int i = 0; i < stdDev.size(); i++) {
+ for (int j = 0; j < stdDev[i].size(); j++) {
+ stdDev[i][j] += ((results[i][j][thisIter] - calcAverages[i][j]) * (results[i][j][thisIter] - calcAverages[i][j]));
+ }
+ }
+ }
+
+ for (int i = 0; i < stdDev.size(); i++) { //finds average.
+ for (int j = 0; j < stdDev[i].size(); j++) {
+ stdDev[i][j] /= (float) iters;
+ stdDev[i][j] = sqrt(stdDev[i][j]);
+ outStd << stdDev[i][j] << '\t';
+ }
+ }
+ outAve << endl; outStd << endl;
+ }
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SummaryCommand", "process");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
vector<string> SummaryCommand::parseSharedFile(string filename) {
try {
vector<string> filenames;
string sharedFileRoot = m->getRootName(filename);
- //clears file before we start to write to it below
+ /******************************************************/
+ if (subsample) {
+ if (subsampleSize == -1) { //user has not set size, set size = smallest samples size
+ subsampleSize = lookup[0]->getNumSeqs();
+ for (int i = 1; i < lookup.size(); i++) {
+ int thisSize = lookup[i]->getNumSeqs();
+
+ if (thisSize < subsampleSize) { subsampleSize = thisSize; }
+ }
+ }else {
+ m->clearGroups();
+ vector<string> Groups;
+ vector<SharedRAbundVector*> temp;
+ for (int i = 0; i < lookup.size(); i++) {
+ if (lookup[i]->getNumSeqs() < subsampleSize) {
+ m->mothurOut(lookup[i]->getGroup() + " contains " + toString(lookup[i]->getNumSeqs()) + ". Eliminating."); m->mothurOutEndLine();
+ delete lookup[i];
+ }else {
+ Groups.push_back(lookup[i]->getGroup());
+ temp.push_back(lookup[i]);
+ }
+ }
+ lookup = temp;
+ m->setGroups(Groups);
+ }
+
+ if (lookup.size() < 1) { m->mothurOut("You have not provided enough valid groups. I cannot run the command."); m->mothurOutEndLine(); m->control_pressed = true; delete input; return filenames; }
+ }
+
+
+ /******************************************************/
+
+ //clears file before we start to write to it below
for (int i=0; i<lookup.size(); i++) {
m->mothurRemove((sharedFileRoot + lookup[i]->getGroup() + ".rabund"));
filenames.push_back((sharedFileRoot + lookup[i]->getGroup() + ".rabund"));
}
-
+
ofstream* temp;
for (int i=0; i<lookup.size(); i++) {
temp = new ofstream;
}
}
//**********************************************************************************************************************
-string SummaryCommand::createGroupSummaryFile(int numLines, int numCols, vector<string>& outputNames) {
+vector<string> SummaryCommand::createGroupSummaryFile(int numLines, int numCols, vector<string>& outputNames, map<string, string> groupIndex) {
try {
-
- ofstream out;
- string combineFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + "groups.summary";
-
- //open combined file
- m->openOutputFile(combineFileName, out);
-
+
//open each groups summary file
+ vector<string> newComboNames;
string newLabel = "";
- map<string, vector<string> > files;
+ map<string, map<string, vector<string> > > files;
for (int i=0; i<outputNames.size(); i++) {
+ string extension = m->getExtension(outputNames[i]);
+ string combineFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + "groups" + extension;
+ m->mothurRemove(combineFileName); //remove old file
+
vector<string> thisFilesLines;
-
+
ifstream temp;
m->openInputFile(outputNames[i], temp);
temp >> tempLabel;
//save for later
- if (j == 1) { thisLine += groups[i] + "\t" + tempLabel + "\t"; }
+ if (j == 1) { thisLine += groupIndex[outputNames[i]] + "\t" + tempLabel + "\t"; }
else{ thisLine += tempLabel + "\t"; }
}
m->gobble(temp);
}
-
- files[outputNames[i]] = thisFilesLines;
+
+ map<string, map<string, vector<string> > >::iterator itFiles = files.find(extension);
+ if (itFiles != files.end()) { //add new files info to existing type
+ files[extension][outputNames[i]] = thisFilesLines;
+ }else {
+ map<string, vector<string> > thisFile;
+ thisFile[outputNames[i]] = thisFilesLines;
+ files[extension] = thisFile;
+ }
temp.close();
m->mothurRemove(outputNames[i]);
}
- //output label line to new file
- out << newLabel << endl;
-
- //for each label
- for (int k = 0; k < numLines; k++) {
-
- //grab summary data for each group
- for (int i=0; i<outputNames.size(); i++) {
- out << files[outputNames[i]][k];
- }
- }
-
- outputNames.clear();
-
- out.close();
+
+ for (map<string, map<string, vector<string> > >::iterator itFiles = files.begin(); itFiles != files.end(); itFiles++) {
+
+ if (m->control_pressed) { break; }
+
+ string extension = itFiles->first;
+ map<string, vector<string> > thisType = itFiles->second;
+ string combineFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + "groups" + extension;
+ newComboNames.push_back(combineFileName);
+ //open combined file
+ ofstream out;
+ m->openOutputFile(combineFileName, out);
+
+ //output label line to new file
+ out << newLabel << endl;
+
+ //for each label
+ for (int k = 0; k < numLines; k++) {
+
+ //grab summary data for each group
+ for (map<string, vector<string> >::iterator itType = thisType.begin(); itType != thisType.end(); itType++) {
+ out << (itType->second)[k];
+ }
+ }
+
+ outputNames.clear();
+
+ out.close();
+ }
//return combine file name
- return combineFileName;
+ return newComboNames;
}
catch(exception& e) {
return 0;
}
/******************************************************/
-
+ if (subsample) {
+ if (subsampleSize == -1) { //user has not set size, set size = smallest samples size
+ subsampleSize = lookup[0]->getNumSeqs();
+ for (int i = 1; i < lookup.size(); i++) {
+ int thisSize = lookup[i]->getNumSeqs();
+
+ if (thisSize < subsampleSize) { subsampleSize = thisSize; }
+ }
+ }else {
+ m->clearGroups();
+ Groups.clear();
+ vector<SharedRAbundVector*> temp;
+ for (int i = 0; i < lookup.size(); i++) {
+ if (lookup[i]->getNumSeqs() < subsampleSize) {
+ m->mothurOut(lookup[i]->getGroup() + " contains " + toString(lookup[i]->getNumSeqs()) + ". Eliminating."); m->mothurOutEndLine();
+ delete lookup[i];
+ }else {
+ Groups.push_back(lookup[i]->getGroup());
+ temp.push_back(lookup[i]);
+ }
+ }
+ lookup = temp;
+ m->setGroups(Groups);
+ }
+
+ if (lookup.size() < 2) { m->mothurOut("You have not provided enough valid groups. I cannot run the command."); m->mothurOutEndLine(); m->control_pressed = true; delete input; return 0; }
+ }
+
/******************************************************/
//comparison breakup to be used by different processes later
- numGroups = m->getNumGroups();
+ numGroups = lookup.size();
lines.resize(processors);
for (int i = 0; i < processors; i++) {
lines[i].start = int (sqrt(float(i)/float(processors)) * numGroups);
vector< vector< vector<seqDist> > > calcDistsTotals; //each iter, one for each calc, then each groupCombos dists. this will be used to make .dist files
vector< vector<seqDist> > calcDists; calcDists.resize(sumCalculators.size());
- for (int thisIter = 0; thisIter < iters; thisIter++) {
+ for (int thisIter = 0; thisIter < iters+1; thisIter++) {
vector<SharedRAbundVector*> thisItersLookup = thisLookup;
- if (subsample) {
+ if (subsample && (thisIter != 0)) { //we want the summary results for the whole dataset, then the subsampling
SubSample sample;
vector<string> tempLabels; //dont need since we arent printing the sampled sharedRabunds
#endif
}
- calcDistsTotals.push_back(calcDists);
- if (subsample) {
+ if (subsample && (thisIter != 0)) { //we want the summary results for the whole dataset, then the subsampling
+ calcDistsTotals.push_back(calcDists);
//clean up memory
for (int i = 0; i < thisItersLookup.size(); i++) { delete thisItersLookup[i]; }
thisItersLookup.clear();
for (int i = 0; i < calcDists.size(); i++) { calcDists[i].clear(); }
+ }else {
+ if (createPhylip) {
+ for (int i = 0; i < calcDists.size(); i++) {
+ if (m->control_pressed) { break; }
+
+ //initialize matrix
+ vector< vector<double> > matrix; //square matrix to represent the distance
+ matrix.resize(thisLookup.size());
+ for (int k = 0; k < thisLookup.size(); k++) { matrix[k].resize(thisLookup.size(), 0.0); }
+
+ for (int j = 0; j < calcDists[i].size(); j++) {
+ int row = calcDists[i][j].seq1;
+ int column = calcDists[i][j].seq2;
+ double dist = calcDists[i][j].dist;
+
+ matrix[row][column] = dist;
+ matrix[column][row] = dist;
+ }
+
+ string distFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + sumCalculators[i]->getName() + "." + thisLookup[0]->getLabel() + "." + output + ".dist";
+ outputNames.push_back(distFileName); outputTypes["phylip"].push_back(distFileName);
+ ofstream outDist;
+ m->openOutputFile(distFileName, outDist);
+ outDist.setf(ios::fixed, ios::floatfield); outDist.setf(ios::showpoint);
+
+ printSims(outDist, matrix);
+
+ outDist.close();
+ }
+ }
}
}
outSTD.close();
}
- }else {
- if (createPhylip) {
- for (int i = 0; i < calcDists.size(); i++) {
- if (m->control_pressed) { break; }
-
- //initialize matrix
- vector< vector<double> > matrix; //square matrix to represent the distance
- matrix.resize(thisLookup.size());
- for (int k = 0; k < thisLookup.size(); k++) { matrix[k].resize(thisLookup.size(), 0.0); }
-
- for (int j = 0; j < calcDists[i].size(); j++) {
- int row = calcDists[i][j].seq1;
- int column = calcDists[i][j].seq2;
- double dist = calcDists[i][j].dist;
-
- matrix[row][column] = dist;
- matrix[column][row] = dist;
- }
-
- string distFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + sumCalculators[i]->getName() + "." + thisLookup[0]->getLabel() + "." + output + ".dist";
- outputNames.push_back(distFileName); outputTypes["phylip"].push_back(distFileName);
- ofstream outDist;
- m->openOutputFile(distFileName, outDist);
- outDist.setf(ios::fixed, ios::floatfield); outDist.setf(ios::showpoint);
-
- printSims(outDist, matrix);
-
- outDist.close();
- }
- }
}
-
+
return 0;
}
catch(exception& e) {
projects / mothur.git / commitdiff