#include "sharedsobs.h"
#include "sharednseqs.h"
#include "sharedutilities.h"
+#include "subsample.h"
//**********************************************************************************************************************
vector<string> RareFactSharedCommand::setParameters(){
try {
- CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pshared);
- CommandParameter pdesign("design", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pdesign);
- CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
- CommandParameter pfreq("freq", "Number", "", "100", "", "", "",false,false); parameters.push_back(pfreq);
- CommandParameter piters("iters", "Number", "", "1000", "", "", "",false,false); parameters.push_back(piters);
- CommandParameter pcalc("calc", "Multiple", "sharednseqs-sharedobserved", "sharedobserved", "", "", "",true,false); parameters.push_back(pcalc);
- CommandParameter pjumble("jumble", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pjumble);
- CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
- CommandParameter psets("sets", "String", "", "", "", "", "",false,false); parameters.push_back(psets);
- CommandParameter pgroupmode("groupmode", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pgroupmode);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(pshared);
+ CommandParameter pdesign("design", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pdesign);
+ CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
+ CommandParameter pfreq("freq", "Number", "", "100", "", "", "","",false,false); parameters.push_back(pfreq);
+ CommandParameter piters("iters", "Number", "", "1000", "", "", "","",false,false); parameters.push_back(piters);
+ CommandParameter pcalc("calc", "Multiple", "sharednseqs-sharedobserved", "sharedobserved", "", "", "","",true,false,true); parameters.push_back(pcalc);
+ CommandParameter psubsampleiters("subsampleiters", "Number", "", "1000", "", "", "","",false,false); parameters.push_back(psubsampleiters);
+ CommandParameter psubsample("subsample", "String", "", "", "", "", "","",false,false); parameters.push_back(psubsample);
+ CommandParameter pjumble("jumble", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(pjumble);
+ CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
+ CommandParameter psets("sets", "String", "", "", "", "", "","",false,false); parameters.push_back(psets);
+ CommandParameter pgroupmode("groupmode", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(pgroupmode);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
helpString += "The freq parameter is used indicate when to output your data, by default it is set to 100. But you can set it to a percentage of the number of sequence. For example freq=0.10, means 10%. \n";
helpString += "Example rarefaction.shared(label=unique-0.01-0.03, iters=10000, groups=B-C, jumble=T, calc=sharedobserved).\n";
helpString += "The default values for iters is 1000, freq is 100, and calc is sharedobserved which calculates the shared rarefaction curve for the observed richness.\n";
+ helpString += "The subsampleiters parameter allows you to choose the number of times you would like to run the subsample.\n";
+ helpString += "The subsample parameter allows you to enter the size pergroup of the sample or you can set subsample=T and mothur will use the size of your smallest group.\n";
helpString += "The default value for groups is all the groups in your groupfile, and jumble is true.\n";
helpString += validCalculator.printCalc("sharedrarefaction");
helpString += "The label parameter is used to analyze specific labels in your input.\n";
exit(1);
}
}
-
+//**********************************************************************************************************************
+string RareFactSharedCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
+
+ if (type == "sharedrarefaction") { pattern = "[filename],shared.rarefaction"; }
+ else if (type == "sharedr_nseqs") { pattern = "[filename],shared.r_nseqs"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "RareFactSharedCommand", "getOutputPattern");
+ exit(1);
+ }
+}
//**********************************************************************************************************************
RareFactSharedCommand::RareFactSharedCommand(){
try {
temp = validParameter.validFile(parameters, "groupmode", false); if (temp == "not found") { temp = "T"; }
groupMode = m->isTrue(temp);
+
+ temp = validParameter.validFile(parameters, "subsampleiters", 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; }
+ }
+
+ if (subsample == false) { iters = 1; }
}
}
}
}
-
+
+ /******************************************************/
+ if (subsample) {
+ if (subsampleSize == -1) { //user has not set size, set size = smallest samples size
+ subsampleSize = subset[0]->getNumSeqs();
+ for (int i = 1; i < subset.size(); i++) {
+ int thisSize = subset[i]->getNumSeqs();
+
+ if (thisSize < subsampleSize) { subsampleSize = thisSize; }
+ }
+ }else {
+ newGroups.clear();
+ vector<SharedRAbundVector*> temp;
+ for (int i = 0; i < subset.size(); i++) {
+ if (subset[i]->getNumSeqs() < subsampleSize) {
+ m->mothurOut(subset[i]->getGroup() + " contains " + toString(subset[i]->getNumSeqs()) + ". Eliminating."); m->mothurOutEndLine();
+ delete subset[i];
+ }else {
+ newGroups.push_back(subset[i]->getGroup());
+ temp.push_back(subset[i]);
+ }
+ }
+ subset = temp;
+ }
+
+ if (subset.size() < 2) { m->mothurOut("You have not provided enough valid groups. I cannot run the command."); m->mothurOutEndLine(); m->control_pressed = true; return 0; }
+ }
+ /******************************************************/
+
+ map<string, string> variables;
+ variables["[filename]"] = fileNameRoot;
ValidCalculators validCalculator;
for (int i=0; i<Estimators.size(); i++) {
if (validCalculator.isValidCalculator("sharedrarefaction", Estimators[i]) == true) {
if (Estimators[i] == "sharedobserved") {
- rDisplays.push_back(new RareDisplay(new SharedSobs(), new SharedThreeColumnFile(fileNameRoot+"shared.rarefaction", "")));
- outputNames.push_back(fileNameRoot+"shared.rarefaction"); outputTypes["sharedrarefaction"].push_back(fileNameRoot+"shared.rarefaction");
+ rDisplays.push_back(new RareDisplay(new SharedSobs(), new SharedThreeColumnFile(getOutputFileName("sharedrarefaction",variables), "")));
+ outputNames.push_back(getOutputFileName("sharedrarefaction",variables)); outputTypes["sharedrarefaction"].push_back(getOutputFileName("sharedrarefaction",variables));
}else if (Estimators[i] == "sharednseqs") {
- rDisplays.push_back(new RareDisplay(new SharedNSeqs(), new SharedThreeColumnFile(fileNameRoot+"shared.r_nseqs", "")));
- outputNames.push_back(fileNameRoot+"shared.r_nseqs"); outputTypes["sharedr_nseqs"].push_back(fileNameRoot+"shared.r_nseqs");
+ rDisplays.push_back(new RareDisplay(new SharedNSeqs(), new SharedThreeColumnFile(getOutputFileName("sharedr_nseqs",variables), "")));
+ outputNames.push_back(getOutputFileName("sharedr_nseqs",variables)); outputTypes["sharedr_nseqs"].push_back(getOutputFileName("sharedr_nseqs",variables));
}
}
file2Group[outputNames.size()-1] = thisSet;
rCurve->getSharedCurve(freq, nIters);
delete rCurve;
+ if (subsample) { subsampleLookup(subset, fileNameRoot); }
+
processedLabels.insert(subset[0]->getLabel());
userLabels.erase(subset[0]->getLabel());
}
rCurve->getSharedCurve(freq, nIters);
delete rCurve;
+ if (subsample) { subsampleLookup(subset, fileNameRoot); }
+
processedLabels.insert(subset[0]->getLabel());
userLabels.erase(subset[0]->getLabel());
rCurve = new Rarefact(subset, rDisplays);
rCurve->getSharedCurve(freq, nIters);
delete rCurve;
+
+ if (subsample) { subsampleLookup(subset, fileNameRoot); }
+
for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
}
}
}
//**********************************************************************************************************************
+int RareFactSharedCommand::subsampleLookup(vector<SharedRAbundVector*>& thisLookup, string fileNameRoot) {
+ try {
+
+ map<string, vector<string> > filenames;
+ for (int thisIter = 0; thisIter < iters; thisIter++) {
+
+ vector<SharedRAbundVector*> thisItersLookup = thisLookup;
+
+ //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
+
+ //make copy of lookup so we don't get access violations
+ vector<SharedRAbundVector*> newLookup;
+ for (int k = 0; k < thisItersLookup.size(); k++) {
+ SharedRAbundVector* temp = new SharedRAbundVector();
+ temp->setLabel(thisItersLookup[k]->getLabel());
+ temp->setGroup(thisItersLookup[k]->getGroup());
+ newLookup.push_back(temp);
+ }
+
+ //for each bin
+ for (int k = 0; k < thisItersLookup[0]->getNumBins(); k++) {
+ if (m->control_pressed) { for (int j = 0; j < newLookup.size(); j++) { delete newLookup[j]; } return 0; }
+ for (int j = 0; j < thisItersLookup.size(); j++) { newLookup[j]->push_back(thisItersLookup[j]->getAbundance(k), thisItersLookup[j]->getGroup()); }
+ }
+
+ tempLabels = sample.getSample(newLookup, subsampleSize);
+ thisItersLookup = newLookup;
+
+
+ Rarefact* rCurve;
+ vector<Display*> rDisplays;
+
+ string thisfileNameRoot = fileNameRoot + toString(thisIter);
+
+ map<string, string> variables;
+ variables["[filename]"] = thisfileNameRoot;
+
+ ValidCalculators validCalculator;
+ for (int i=0; i<Estimators.size(); i++) {
+ if (validCalculator.isValidCalculator("sharedrarefaction", Estimators[i]) == true) {
+ if (Estimators[i] == "sharedobserved") {
+ rDisplays.push_back(new RareDisplay(new SharedSobs(), new SharedThreeColumnFile(getOutputFileName("sharedrarefaction",variables), "")));
+ filenames["sharedrarefaction"].push_back(getOutputFileName("sharedrarefaction",variables));
+ }else if (Estimators[i] == "sharednseqs") {
+ rDisplays.push_back(new RareDisplay(new SharedNSeqs(), new SharedThreeColumnFile(getOutputFileName("sharedr_nseqs",variables), "")));
+ filenames["sharedr_nseqs"].push_back(getOutputFileName("sharedr_nseqs",variables));
+ }
+ }
+ }
+
+ rCurve = new Rarefact(thisItersLookup, rDisplays);
+ rCurve->getSharedCurve(freq, nIters);
+ delete rCurve;
+
+ //clean up memory
+ for (int i = 0; i < thisItersLookup.size(); i++) { delete thisItersLookup[i]; }
+ thisItersLookup.clear();
+ for(int i=0;i<rDisplays.size();i++){ delete rDisplays[i]; }
+ }
+
+ //create std and ave outputs
+ vector< vector< vector< double > > > results; //iter -> numSampled -> data
+ for (map<string, vector<string> >::iterator it = filenames.begin(); it != filenames.end(); it++) {
+ vector<string> thisTypesFiles = it->second;
+ vector<string> columnHeaders;
+ for (int i = 0; i < thisTypesFiles.size(); i++) {
+ ifstream in;
+ m->openInputFile(thisTypesFiles[i], in);
+
+ string headers = m->getline(in); m->gobble(in);
+ columnHeaders = m->splitWhiteSpace(headers);
+ int numCols = columnHeaders.size();
+
+ vector<vector<double> > thisFilesLines;
+ while (!in.eof()) {
+ if (m->control_pressed) { break; }
+ vector<double> data; data.resize(numCols, 0);
+ //read numSampled line
+ for (int j = 0; j < numCols; j++) { in >> data[j]; m->gobble(in); }
+ thisFilesLines.push_back(data);
+ }
+ in.close();
+ results.push_back(thisFilesLines);
+ m->mothurRemove(thisTypesFiles[i]);
+ }
+
+ if (!m->control_pressed) {
+ //process results
+ map<string, string> variables; variables["[filename]"] = fileNameRoot + "ave-std." + thisLookup[0]->getLabel() + ".";
+
+ string outputFile = getOutputFileName(it->first,variables);
+ ofstream out;
+ m->openOutputFile(outputFile, out);
+ outputNames.push_back(outputFile); outputTypes[it->first].push_back(outputFile);
+
+ out << columnHeaders[0] << '\t' << "method\t";
+ for (int i = 1; i < columnHeaders.size(); i++) { out << columnHeaders[i] << '\t'; }
+ out << endl;
+
+ vector< vector<double> > aveResults; aveResults.resize(results[0].size());
+ for (int i = 0; i < aveResults.size(); i++) { aveResults[i].resize(results[0][i].size(), 0.0); }
+
+ for (int thisIter = 0; thisIter < iters; thisIter++) { //sum all groups dists for each calculator
+ for (int i = 0; i < aveResults.size(); i++) { //initialize sums to zero.
+ aveResults[i][0] = results[thisIter][i][0];
+ for (int j = 1; j < aveResults[i].size(); j++) {
+ aveResults[i][j] += results[thisIter][i][j];
+ }
+ }
+ }
+
+ for (int i = 0; i < aveResults.size(); i++) { //finds average.
+ for (int j = 1; j < aveResults[i].size(); j++) {
+ aveResults[i][j] /= (float) iters;
+ }
+ }
+
+ //standard deviation
+ vector< vector<double> > stdResults; stdResults.resize(results[0].size());
+ for (int i = 0; i < stdResults.size(); i++) { stdResults[i].resize(results[0][i].size(), 0.0); }
+
+ 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 < stdResults.size(); i++) {
+ stdResults[i][0] = aveResults[i][0];
+ for (int j = 1; j < stdResults[i].size(); j++) {
+ stdResults[i][j] += ((results[thisIter][i][j] - aveResults[i][j]) * (results[thisIter][i][j] - aveResults[i][j]));
+ }
+ }
+ }
+
+ for (int i = 0; i < stdResults.size(); i++) { //finds average.
+ out << aveResults[i][0] << '\t' << "ave\t";
+ for (int j = 1; j < aveResults[i].size(); j++) { out << aveResults[i][j] << '\t'; }
+ out << endl;
+ out << stdResults[i][0] << '\t' << "std\t";
+ for (int j = 1; j < stdResults[i].size(); j++) {
+ stdResults[i][j] /= (float) iters;
+ stdResults[i][j] = sqrt(stdResults[i][j]);
+ out << stdResults[i][j] << '\t';
+ }
+ out << endl;
+ }
+ out.close();
+ }
+ }
+
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "RareFactSharedCommand", "subsample");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
vector<string> RareFactSharedCommand::createGroupFile(vector<string>& outputNames) {
try {
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