//
#include "getmetacommunitycommand.h"
-#include "qFinderDMM.h"
+#include "communitytype.h"
+#include "kmeans.h"
+#include "validcalculator.h"
+#include "subsample.h"
//**********************************************************************************************************************
vector<string> GetMetaCommunityCommand::setParameters(){
CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none","outputType",false,true); parameters.push_back(pshared);
CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
+ CommandParameter pcalc("calc", "Multiple", "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan-kstest-sharednseqs-ochiai-anderberg-kulczynski-kulczynskicody-lennon-morisitahorn-braycurtis-whittaker-odum-canberra-structeuclidean-structchord-hellinger-manhattan-structpearson-soergel-spearman-structkulczynski-speciesprofile-hamming-structchi2-gower-memchi2-memchord-memeuclidean-mempearson-jsd", "jsd", "", "", "","",false,false,true); parameters.push_back(pcalc);
+ CommandParameter psubsample("subsample", "String", "", "", "", "", "","",false,false); parameters.push_back(psubsample);
+ CommandParameter piters("iters", "Number", "", "1000", "", "", "","",false,false); parameters.push_back(piters);
CommandParameter pminpartitions("minpartitions", "Number", "", "5", "", "", "","",false,false,true); parameters.push_back(pminpartitions);
- CommandParameter pmaxpartitions("maxpartitions", "Number", "", "10", "", "", "","",false,false,true); parameters.push_back(pmaxpartitions);
+ CommandParameter pmaxpartitions("maxpartitions", "Number", "", "100", "", "", "","",false,false,true); parameters.push_back(pmaxpartitions);
CommandParameter poptimizegap("optimizegap", "Number", "", "3", "", "", "","",false,false,true); parameters.push_back(poptimizegap);
+ CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
-
+ CommandParameter pmethod("method", "Multiple", "dmm-kmeans-pam", "dmm", "", "", "","",false,false,true); parameters.push_back(pmethod);
+
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
return myArray;
string GetMetaCommunityCommand::getHelpString(){
try {
string helpString = "";
- helpString += "The get.metacommunity command parameters are shared, label, groups, minpartitions, maxpartitions and optimizegap. The shared file is required. \n";
+ helpString += "The get.communitytype command parameters are shared, method, label, groups, minpartitions, maxpartitions, optimizegap and processors. The shared file is required. \n";
helpString += "The label parameter is used to analyze specific labels in your input. labels are separated by dashes.\n";
helpString += "The groups parameter allows you to specify which of the groups in your shared file you would like analyzed. Group names are separated by dashes.\n";
+ helpString += "The method parameter allows to select the method you would like to use. Options are dmm, kmeans and pam. Default=dmm.\n";
+ helpString += "The calc parameter allows to select the calculator you would like to use to calculate the distance matrix used by the pam method. By default the jsd calculator is used.\n";
+ helpString += "The iters parameter allows you to choose the number of times you would like to run the subsample while calculating the distance matirx for the pam method.\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 while calculating the distance matrix for the pam method.\n";
helpString += "The minpartitions parameter is used to .... Default=5.\n";
helpString += "The maxpartitions parameter is used to .... Default=10.\n";
helpString += "The optimizegap parameter is used to .... Default=3.\n";
- helpString += "The get.metacommunity command should be in the following format: get.metacommunity(shared=yourSharedFile).\n";
+ helpString += "The processors parameter allows you to specify number of processors to use. The default is 1.\n";
+ helpString += "The get.communitytype command should be in the following format: get.communitytype(shared=yourSharedFile).\n";
return helpString;
}
catch(exception& e) {
if (type == "fit") { pattern = "[filename],[distance],mix.fit"; }
else if (type == "relabund") { pattern = "[filename],[distance],[tag],mix.relabund"; }
- else if (type == "design") { pattern = "[filename],mix.design"; }
+ else if (type == "design") { pattern = "[filename],[distance],mix.design"; }
else if (type == "matrix") { pattern = "[filename],[distance],[tag],mix.posterior"; }
else if (type == "parameters") { pattern = "[filename],[distance],mix.parameters"; }
else if (type == "summary") { pattern = "[filename],[distance],mix.summary"; }
temp = validParameter.validFile(parameters, "optimizegap", false); if (temp == "not found"){ temp = "3"; }
m->mothurConvert(temp, optimizegap);
+ temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); }
+ m->setProcessors(temp);
+ m->mothurConvert(temp, processors);
+
string groups = validParameter.validFile(parameters, "groups", false);
if (groups == "not found") { groups = ""; }
else { m->splitAtDash(groups, Groups); }
if(label != "all") { m->splitAtDash(label, labels); allLines = 0; }
else { allLines = 1; }
}
+
+ method = validParameter.validFile(parameters, "method", false);
+ if (method == "not found") { method = "dmm"; }
+
+ if ((method == "dmm") || (method == "kmeans") || (method == "pam")) { }
+ else { m->mothurOut("[ERROR]: " + method + " is not a valid method. Valid algorithms are dmm, kmeans and pam."); m->mothurOutEndLine(); abort = true; }
+
+ calc = validParameter.validFile(parameters, "calc", false);
+ if (calc == "not found") { calc = "jsd"; }
+ else {
+ if (calc == "default") { calc = "jsd"; }
+ }
+ m->splitAtDash(calc, Estimators);
+ if (m->inUsersGroups("citation", Estimators)) {
+ ValidCalculators validCalc; validCalc.printCitations(Estimators);
+ //remove citation from list of calcs
+ for (int i = 0; i < Estimators.size(); i++) { if (Estimators[i] == "citation") { Estimators.erase(Estimators.begin()+i); break; } }
+ }
+ if (Estimators.size() != 1) { abort = true; m->mothurOut("[ERROR]: only one calculator is allowed.\n"); }
+
+ 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; }
+ }
+
+ if (subsample == false) { iters = 0; }
}
}
set<string> processedLabels;
set<string> userLabels = labels;
+ 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; return 0; }
+ }
+
+
//as long as you are not at the end of the file or done wih the lines you want
while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
- process(lookup);
+ createProcesses(lookup);
processedLabels.insert(lookup[0]->getLabel());
userLabels.erase(lookup[0]->getLabel());
lookup = input.getSharedRAbundVectors(lastLabel);
m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
- process(lookup);
+ createProcesses(lookup);
processedLabels.insert(lookup[0]->getLabel());
userLabels.erase(lookup[0]->getLabel());
m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
- process(lookup);
+ createProcesses(lookup);
for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
}
}
}
//**********************************************************************************************************************
-int GetMetaCommunityCommand::process(vector<SharedRAbundVector*>& thislookup){
+int GetMetaCommunityCommand::createProcesses(vector<SharedRAbundVector*>& thislookup){
try {
- double minLaplace = 1e10;
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+ #else
+ processors=1; //qFinderDMM not thread safe
+ #endif
+
+ vector<int> processIDS;
+ int process = 1;
+ int num = 0;
int minPartition = 0;
+
+ //sanity check
+ if (maxpartitions < processors) { processors = maxpartitions; }
map<string, string> variables;
variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(sharedfile));
variables["[distance]"] = thislookup[0]->getLabel();
string outputFileName = getOutputFileName("fit", variables);
outputNames.push_back(outputFileName); outputTypes["fit"].push_back(outputFileName);
+
+ //divide the partitions between the processors
+ vector< vector<int> > dividedPartitions;
+ vector< vector<string> > rels, matrix;
+ vector<string> doneFlags;
+ dividedPartitions.resize(processors);
+ rels.resize(processors);
+ matrix.resize(processors);
+
+ //for each file group figure out which process will complete it
+ //want to divide the load intelligently so the big files are spread between processes
+ for (int i=1; i<=maxpartitions; i++) {
+ //cout << i << endl;
+ int processToAssign = (i+1) % processors;
+ if (processToAssign == 0) { processToAssign = processors; }
+
+ if (m->debug) { m->mothurOut("[DEBUG]: assigning " + toString(i) + " to process " + toString(processToAssign-1) + "\n"); }
+ dividedPartitions[(processToAssign-1)].push_back(i);
+
+ variables["[tag]"] = toString(i);
+ string relName = getOutputFileName("relabund", variables);
+ string mName = getOutputFileName("matrix", variables);
+ rels[(processToAssign-1)].push_back(relName);
+ matrix[(processToAssign-1)].push_back(mName);
+ }
+
+ for (int i = 0; i < processors; i++) { //read from everyone elses, just write to yours
+ string tempDoneFile = m->getRootName(m->getSimpleName(sharedfile)) + toString(i) + ".done.temp";
+ doneFlags.push_back(tempDoneFile);
+ ofstream out;
+ m->openOutputFile(tempDoneFile, out); //clear out
+ out.close();
+ }
+
+
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+
+ //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){
+ outputNames.clear();
+ num = processDriver(thislookup, dividedPartitions[process], (outputFileName + toString(getpid())), rels[process], matrix[process], doneFlags, process);
+
+ //pass numSeqs to parent
+ ofstream out;
+ string tempFile = toString(getpid()) + ".outputNames.temp";
+ m->openOutputFile(tempFile, out);
+ out << num << endl;
+ out << outputNames.size() << endl;
+ for (int i = 0; i < outputNames.size(); i++) { out << outputNames[i] << endl; }
+ out.close();
+
+ exit(0);
+ }else {
+ m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
+ for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
+ exit(0);
+ }
+ }
+
+ //do my part
+ if (method == "dmm") { m->mothurOut("K\tNLE\t\tlogDet\tBIC\t\tAIC\t\tLaplace\n"); }
+ else {
+ m->mothurOut("K\tCH\t");
+ for (int i = 0; i < thislookup.size(); i++) { m->mothurOut(thislookup[i]->getGroup() + '\t'); }
+ m->mothurOut("\n");
+ }
+ minPartition = processDriver(thislookup, dividedPartitions[0], outputFileName, rels[0], matrix[0], doneFlags, 0);
+
+ //force parent to wait until all the processes are done
+ for (int i=0;i<processIDS.size();i++) {
+ int temp = processIDS[i];
+ wait(&temp);
+ }
+
+ vector<string> tempOutputNames = outputNames;
+ for (int i=0;i<processIDS.size();i++) {
+ ifstream in;
+ string tempFile = toString(processIDS[i]) + ".outputNames.temp";
+ m->openInputFile(tempFile, in);
+ if (!in.eof()) {
+ int tempNum = 0;
+ in >> tempNum; m->gobble(in);
+ if (tempNum < minPartition) { minPartition = tempNum; }
+ in >> tempNum; m->gobble(in);
+ for (int i = 0; i < tempNum; i++) {
+ string tempName = "";
+ in >> tempName; m->gobble(in);
+ tempOutputNames.push_back(tempName);
+ }
+ }
+ in.close(); m->mothurRemove(tempFile);
+
+ m->appendFilesWithoutHeaders(outputFileName + toString(processIDS[i]), outputFileName);
+ m->mothurRemove(outputFileName + toString(processIDS[i]));
+ }
+
+ if (processors > 1) {
+ outputNames.clear();
+ for (int i = 0; i < tempOutputNames.size(); i++) { //remove files if needed
+ string name = tempOutputNames[i];
+ vector<string> parts;
+ m->splitAtChar(name, parts, '.');
+ bool keep = true;
+ if (((parts[parts.size()-1] == "relabund") || (parts[parts.size()-1] == "posterior")) && (parts[parts.size()-2] == "mix")) {
+ string tempNum = parts[parts.size()-3];
+ int num; m->mothurConvert(tempNum, num);
+ //if (num > minPartition) {
+ // m->mothurRemove(tempOutputNames[i]);
+ // keep = false; if (m->debug) { m->mothurOut("[DEBUG]: removing " + tempOutputNames[i] + ".\n"); }
+ //}
+ }
+ if (keep) { outputNames.push_back(tempOutputNames[i]); }
+ }
+
+ //reorder fit file
+ ifstream in;
+ m->openInputFile(outputFileName, in);
+ string headers = m->getline(in); m->gobble(in);
+
+ map<int, string> file;
+ while (!in.eof()) {
+ string numString, line;
+ int num;
+ in >> numString; line = m->getline(in); m->gobble(in);
+ m->mothurConvert(numString, num);
+ file[num] = line;
+ }
+ in.close();
+ ofstream out;
+ m->openOutputFile(outputFileName, out);
+ out << headers << endl;
+ for (map<int, string>::iterator it = file.begin(); it != file.end(); it++) {
+ out << it->first << '\t' << it->second << endl;
+ if (m->debug) { m->mothurOut("[DEBUG]: printing: " + toString(it->first) + '\t' + it->second + ".\n"); }
+ }
+ out.close();
+ }
+
+#else
+ m->mothurOut("K\tNLE\t\tlogDet\tBIC\t\tAIC\t\tLaplace\n");
+ minPartition = processDriver(thislookup, dividedPartitions[0], outputFileName, rels[0], matrix[0], doneFlags, 0);
+#endif
+ for (int i = 0; i < processors; i++) { //read from everyone elses, just write to yours
+ string tempDoneFile = m->getRootName(m->getSimpleName(sharedfile)) + toString(i) + ".done.temp";
+ m->mothurRemove(tempDoneFile);
+ }
+
+ if (m->control_pressed) { return 0; }
+
+ if (m->debug) { m->mothurOut("[DEBUG]: minPartition = " + toString(minPartition) + "\n"); }
+
+ //run generate Summary function for smallest minPartition
+ variables["[tag]"] = toString(minPartition);
+ vector<double> piValues = generateDesignFile(minPartition, variables);
+ if (method == "dmm") { generateSummaryFile(minPartition, variables, piValues); } //pam doesn't make a relabund file
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetMetaCommunityCommand", "createProcesses");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+int GetMetaCommunityCommand::processDriver(vector<SharedRAbundVector*>& thislookup, vector<int>& parts, string outputFileName, vector<string> relabunds, vector<string> matrix, vector<string> doneFlags, int processID){
+ try {
+
+ double minLaplace = 1e10;
+ int minPartition = 1;
+ vector<double> minSilhouettes; minSilhouettes.resize(thislookup.size(), 0);
+
+ ofstream fitData, silData;
+ if (method == "dmm") {
+ m->openOutputFile(outputFileName, fitData);
+ fitData.setf(ios::fixed, ios::floatfield);
+ fitData.setf(ios::showpoint);
+ fitData << "K\tNLE\tlogDet\tBIC\tAIC\tLaplace" << endl;
+ }else if((method == "pam") || (method == "kmeans")) { //because ch is looking of maximal value
+ minLaplace = 0;
+ m->openOutputFile(outputFileName, silData);
+ silData.setf(ios::fixed, ios::floatfield);
+ silData.setf(ios::showpoint);
+ silData << "K\tCH\t";
+ for (int i = 0; i < thislookup.size(); i++) { silData << thislookup[i]->getGroup() << '\t'; }
+ silData << endl;
+ }
- ofstream fitData;
- m->openOutputFile(outputFileName, fitData);
- fitData.setf(ios::fixed, ios::floatfield);
- fitData.setf(ios::showpoint);
cout.setf(ios::fixed, ios::floatfield);
cout.setf(ios::showpoint);
vector< vector<int> > sharedMatrix;
- for (int i = 0; i < thislookup.size(); i++) { sharedMatrix.push_back(thislookup[i]->getAbundances()); }
+ vector<string> thisGroups;
+ for (int i = 0; i < thislookup.size(); i++) { sharedMatrix.push_back(thislookup[i]->getAbundances()); thisGroups.push_back(thislookup[i]->getGroup()); }
- m->mothurOut("K\tNLE\t\tlogDet\tBIC\t\tAIC\t\tLaplace\n");
- fitData << "K\tNLE\tlogDet\tBIC\tAIC\tLaplace" << endl;
+ vector< vector<double> > dists; //do we want to output this matrix??
+ if ((method == "pam") || (method == "kmeans")) { dists = generateDistanceMatrix(thislookup); }
+
+ if (m->debug) {
+ m->mothurOut("[DEBUG]: dists = \n");
+ for (int i = 0; i < dists.size(); i++) {
+ if (m->control_pressed) { break; }
+ m->mothurOut("[DEBUG]: i = " + toString(i) + '\t');
+ for (int j = 0; j < i; j++) { m->mothurOut(toString(dists[i][j]) +"\t"); }
+ m->mothurOut("\n");
+ }
+ }
- for(int numPartitions=1;numPartitions<=maxpartitions;numPartitions++){
+ for(int i=0;i<parts.size();i++){
- if (m->control_pressed) { break; }
+ int numPartitions = parts[i];
- qFinderDMM findQ(sharedMatrix, numPartitions);
+ if (m->debug) { m->mothurOut("[DEBUG]: running partition " + toString(numPartitions) + "\n"); }
- double laplace = findQ.getLaplace();
- m->mothurOut(toString(numPartitions) + '\t');
- cout << setprecision (2) << findQ.getNLL() << '\t' << findQ.getLogDet() << '\t';
- m->mothurOutJustToLog(toString(findQ.getNLL()) + '\t' + toString(findQ.getLogDet()) + '\t');
- cout << findQ.getBIC() << '\t' << findQ.getAIC() << '\t' << laplace;
- m->mothurOutJustToLog(toString(findQ.getBIC()) + '\t' + toString(findQ.getAIC()) + '\t' + toString(laplace));
+ if (m->control_pressed) { break; }
- fitData << numPartitions << '\t';
- fitData << setprecision (2) << findQ.getNLL() << '\t' << findQ.getLogDet() << '\t';
- fitData << findQ.getBIC() << '\t' << findQ.getAIC() << '\t' << laplace << endl;
+ //check to see if anyone else is done
+ for (int j = 0; j < doneFlags.size(); j++) {
+ if (!m->isBlank(doneFlags[j])) { //another process has finished
+ //are they done at a lower partition?
+ ifstream in;
+ m->openInputFile(doneFlags[j], in);
+ int tempNum;
+ in >> tempNum; in.close();
+ if (tempNum < numPartitions) { break; } //quit, because someone else has finished
+ }
+ }
- if(laplace < minLaplace){
- minPartition = numPartitions;
- minLaplace = laplace;
- m->mothurOut("***");
+ CommunityTypeFinder* finder = NULL;
+ if (method == "dmm") { finder = new qFinderDMM(sharedMatrix, numPartitions); }
+ else if (method == "kmeans") { finder = new KMeans(sharedMatrix, numPartitions); }
+ else if (method == "pam") { finder = new Pam(sharedMatrix, dists, numPartitions); }
+ else {
+ if (i == 0) { m->mothurOut(method + " is not a valid method option. I will run the command using dmm.\n"); }
+ finder = new qFinderDMM(sharedMatrix, numPartitions);
}
- m->mothurOutEndLine();
- variables["[tag]"] = toString(numPartitions);
- string relabund = getOutputFileName("relabund", variables);
- outputNames.push_back(relabund); outputTypes["relabund"].push_back(relabund);
- string matrix = getOutputFileName("matrix", variables);
- outputNames.push_back(matrix); outputTypes["matrix"].push_back(matrix);
+ double chi; vector<double> silhouettes;
+ if (method == "dmm") {
+ double laplace = finder->getLaplace();
+ if(laplace < minLaplace){
+ minPartition = numPartitions;
+ minLaplace = laplace;
+ }
+ }else {
+ chi = finder->calcCHIndex(dists);
+ silhouettes = finder->calcSilhouettes(dists);
+ if (chi > minLaplace) { //save partition with maximum ch index score
+ minPartition = numPartitions;
+ minLaplace = chi;
+ minSilhouettes = silhouettes;
+ }
+ }
+ string relabund = relabunds[i];
+ string matrixName = matrix[i];
+ outputNames.push_back(matrixName); outputTypes["matrix"].push_back(matrixName);
- findQ.printZMatrix(matrix, m->getGroups());
- findQ.printRelAbund(relabund, m->currentBinLabels);
+ finder->printZMatrix(matrixName, thisGroups);
- if(optimizegap != -1 && (numPartitions - minPartition) >= optimizegap && numPartitions >= minpartitions){ break; }
+ if (method == "dmm") {
+ finder->printFitData(cout, minLaplace);
+ finder->printFitData(fitData);
+ finder->printRelAbund(relabund, m->currentSharedBinLabels);
+ outputNames.push_back(relabund); outputTypes["relabund"].push_back(relabund);
+ }else if ((method == "pam") || (method == "kmeans")) { //print silouettes and ch values
+ finder->printSilData(cout, chi, silhouettes);
+ finder->printSilData(silData, chi, silhouettes);
+ if (method == "kmeans") {
+ finder->printRelAbund(relabund, m->currentSharedBinLabels);
+ outputNames.push_back(relabund); outputTypes["relabund"].push_back(relabund);
+ }
+ }
+ delete finder;
+
+ if(optimizegap != -1 && (numPartitions - minPartition) >= optimizegap && numPartitions >= minpartitions){
+ string tempDoneFile = m->getRootName(m->getSimpleName(sharedfile)) + toString(processID) + ".done.temp";
+ ofstream outDone;
+ m->openOutputFile(tempDoneFile, outDone);
+ outDone << minPartition << endl;
+ outDone.close();
+ break;
+ }
}
- fitData.close();
-
- //minPartition = 4;
+ if (method == "dmm") { fitData.close(); }
if (m->control_pressed) { return 0; }
-
- generateSummaryFile(minpartitions, outputTypes["relabund"][0], outputTypes["relabund"][outputTypes["relabund"].size()-1], outputTypes["matrix"][outputTypes["matrix"].size()-1], thislookup[0]->getLabel());
-
- return 0;
+ return minPartition;
}
catch(exception& e) {
- m->errorOut(e, "GetMetaCommunityCommand", "process");
+ m->errorOut(e, "GetMetaCommunityCommand", "processDriver");
exit(1);
}
}
/**************************************************************************************************/
-vector<double> GetMetaCommunityCommand::generateDesignFile(int numPartitions, string input){
+vector<double> GetMetaCommunityCommand::generateDesignFile(int numPartitions, map<string,string> variables){
try {
vector<double> piValues(numPartitions, 0);
ifstream postFile;
+ variables["[tag]"] = toString(numPartitions);
+ string input = getOutputFileName("matrix", variables);
m->openInputFile(input, postFile);//((fileRoot + toString(numPartitions) + "mix.posterior").c_str()); //matrix file
- map<string, string> variables;
- variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(input));
+ variables.erase("[tag]");
string outputFileName = getOutputFileName("design", variables);
ofstream designFile;
m->openOutputFile(outputFileName, designFile);
inline bool summaryFunction(summaryData i, summaryData j){ return i.difference > j.difference; }
/**************************************************************************************************/
-int GetMetaCommunityCommand::generateSummaryFile(int numPartitions, string reference, string partFile, string designInput, string label){
+int GetMetaCommunityCommand::generateSummaryFile(int numPartitions, map<string,string> v, vector<double> piValues){
try {
vector<summaryData> summary;
string name, header;
double mean, lci, uci;
-
- vector<double> piValues = generateDesignFile(numPartitions, designInput);
-
ifstream referenceFile;
+ map<string, string> variables;
+ variables["[filename]"] = v["[filename]"];
+ variables["[distance]"] = v["[distance]"];
+ variables["[tag]"] = "1";
+ string reference = getOutputFileName("relabund", variables);
m->openInputFile(reference, referenceFile); //((fileRoot + label + ".1mix.relabund").c_str());
+ variables["[tag]"] = toString(numPartitions);
+ string partFile = getOutputFileName("relabund", variables);
ifstream partitionFile;
m->openInputFile(partFile, partitionFile); //((fileRoot + toString(numPartitions) + "mix.relabund").c_str());
sort(summary.begin(), summary.end(), summaryFunction);
- map<string, string> variables;
- variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(sharedfile));
- variables["[distance]"] = label;
+ variables.erase("[tag]");
string outputFileName = getOutputFileName("parameters", variables);
outputNames.push_back(outputFileName); outputTypes["parameters"].push_back(outputFileName);
if (m->control_pressed) { return 0; }
string summaryFileName = getOutputFileName("summary", variables);
- outputNames.push_back(outputFileName); outputTypes["summary"].push_back(outputFileName);
+ outputNames.push_back(summaryFileName); outputTypes["summary"].push_back(summaryFileName);
ofstream summaryFile;
m->openOutputFile(summaryFileName, summaryFile); //((fileRoot + "mix.summary").c_str());
}
//**********************************************************************************************************************
+vector<vector<double> > GetMetaCommunityCommand::generateDistanceMatrix(vector<SharedRAbundVector*>& thisLookup){
+ try {
+ vector<vector<double> > results;
+
+ Calculator* matrixCalculator;
+ ValidCalculators validCalculator;
+ int i = 0;
+
+ if (validCalculator.isValidCalculator("matrix", Estimators[i]) == true) {
+ if (Estimators[i] == "sharedsobs") {
+ matrixCalculator = new SharedSobsCS();
+ }else if (Estimators[i] == "sharedchao") {
+ matrixCalculator = new SharedChao1();
+ }else if (Estimators[i] == "sharedace") {
+ matrixCalculator = new SharedAce();
+ }else if (Estimators[i] == "jabund") {
+ matrixCalculator = new JAbund();
+ }else if (Estimators[i] == "sorabund") {
+ matrixCalculator = new SorAbund();
+ }else if (Estimators[i] == "jclass") {
+ matrixCalculator = new Jclass();
+ }else if (Estimators[i] == "sorclass") {
+ matrixCalculator = new SorClass();
+ }else if (Estimators[i] == "jest") {
+ matrixCalculator = new Jest();
+ }else if (Estimators[i] == "sorest") {
+ matrixCalculator = new SorEst();
+ }else if (Estimators[i] == "thetayc") {
+ matrixCalculator = new ThetaYC();
+ }else if (Estimators[i] == "thetan") {
+ matrixCalculator = new ThetaN();
+ }else if (Estimators[i] == "kstest") {
+ matrixCalculator = new KSTest();
+ }else if (Estimators[i] == "sharednseqs") {
+ matrixCalculator = new SharedNSeqs();
+ }else if (Estimators[i] == "ochiai") {
+ matrixCalculator = new Ochiai();
+ }else if (Estimators[i] == "anderberg") {
+ matrixCalculator = new Anderberg();
+ }else if (Estimators[i] == "kulczynski") {
+ matrixCalculator = new Kulczynski();
+ }else if (Estimators[i] == "kulczynskicody") {
+ matrixCalculator = new KulczynskiCody();
+ }else if (Estimators[i] == "lennon") {
+ matrixCalculator = new Lennon();
+ }else if (Estimators[i] == "morisitahorn") {
+ matrixCalculator = new MorHorn();
+ }else if (Estimators[i] == "braycurtis") {
+ matrixCalculator = new BrayCurtis();
+ }else if (Estimators[i] == "whittaker") {
+ matrixCalculator = new Whittaker();
+ }else if (Estimators[i] == "odum") {
+ matrixCalculator = new Odum();
+ }else if (Estimators[i] == "canberra") {
+ matrixCalculator = new Canberra();
+ }else if (Estimators[i] == "structeuclidean") {
+ matrixCalculator = new StructEuclidean();
+ }else if (Estimators[i] == "structchord") {
+ matrixCalculator = new StructChord();
+ }else if (Estimators[i] == "hellinger") {
+ matrixCalculator = new Hellinger();
+ }else if (Estimators[i] == "manhattan") {
+ matrixCalculator = new Manhattan();
+ }else if (Estimators[i] == "structpearson") {
+ matrixCalculator = new StructPearson();
+ }else if (Estimators[i] == "soergel") {
+ matrixCalculator = new Soergel();
+ }else if (Estimators[i] == "spearman") {
+ matrixCalculator = new Spearman();
+ }else if (Estimators[i] == "structkulczynski") {
+ matrixCalculator = new StructKulczynski();
+ }else if (Estimators[i] == "speciesprofile") {
+ matrixCalculator = new SpeciesProfile();
+ }else if (Estimators[i] == "hamming") {
+ matrixCalculator = new Hamming();
+ }else if (Estimators[i] == "structchi2") {
+ matrixCalculator = new StructChi2();
+ }else if (Estimators[i] == "gower") {
+ matrixCalculator = new Gower();
+ }else if (Estimators[i] == "memchi2") {
+ matrixCalculator = new MemChi2();
+ }else if (Estimators[i] == "memchord") {
+ matrixCalculator = new MemChord();
+ }else if (Estimators[i] == "memeuclidean") {
+ matrixCalculator = new MemEuclidean();
+ }else if (Estimators[i] == "mempearson") {
+ matrixCalculator = new MemPearson();
+ }else if (Estimators[i] == "jsd") {
+ matrixCalculator = new JSD();
+ }else {
+ m->mothurOut("[ERROR]: " + Estimators[i] + " is not a valid calculator, please correct.\n"); m->control_pressed = true; return results;
+ }
+ }
+
+ //calc distances
+ vector< vector< vector<seqDist> > > calcDistsTotals; //each iter, then each groupCombos dists. this will be used to make .dist files
+ vector< vector<seqDist> > calcDists; calcDists.resize(1);
+
+ for (int thisIter = 0; thisIter < iters+1; thisIter++) {
+
+ vector<SharedRAbundVector*> thisItersLookup = thisLookup;
+
+ if (subsample && (thisIter != 0)) {
+ 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 results; }
+ 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;
+ }
+
+
+ driver(thisItersLookup, calcDists, matrixCalculator);
+
+ if (subsample && (thisIter != 0)) {
+ if((thisIter) % 100 == 0){ m->mothurOutJustToScreen(toString(thisIter)+"\n"); }
+ calcDistsTotals.push_back(calcDists);
+ for (int i = 0; i < calcDists.size(); i++) {
+ for (int j = 0; j < calcDists[i].size(); j++) {
+ if (m->debug) { m->mothurOut("[DEBUG]: Results: iter = " + toString(thisIter) + ", " + thisLookup[calcDists[i][j].seq1]->getGroup() + " - " + thisLookup[calcDists[i][j].seq2]->getGroup() + " distance = " + toString(calcDists[i][j].dist) + ".\n"); }
+ }
+ }
+ //clean up memory
+ for (int i = 0; i < thisItersLookup.size(); i++) { delete thisItersLookup[i]; }
+ thisItersLookup.clear();
+ }else { //print results for whole dataset
+ for (int i = 0; i < calcDists.size(); i++) {
+ if (m->control_pressed) { break; }
+
+ //initialize matrix
+ results.resize(thisLookup.size());
+ for (int k = 0; k < thisLookup.size(); k++) { results[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;
+
+ results[row][column] = dist;
+ results[column][row] = dist;
+ }
+ }
+ }
+ for (int i = 0; i < calcDists.size(); i++) { calcDists[i].clear(); }
+ }
+
+ if (iters != 0) {
+ //we need to find the average distance and standard deviation for each groups distance
+ vector< vector<seqDist> > calcAverages = m->getAverages(calcDistsTotals, "average");
+
+ //print results
+ for (int i = 0; i < calcDists.size(); i++) {
+ results.resize(thisLookup.size());
+ for (int k = 0; k < thisLookup.size(); k++) { results[k].resize(thisLookup.size(), 0.0); }
+
+ for (int j = 0; j < calcAverages[i].size(); j++) {
+ int row = calcAverages[i][j].seq1;
+ int column = calcAverages[i][j].seq2;
+ float dist = calcAverages[i][j].dist;
+
+ results[row][column] = dist;
+ results[column][row] = dist;
+ }
+ }
+ }
+
+
+ return results;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetMetaCommunityCommand", "generateDistanceMatrix");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+int GetMetaCommunityCommand::driver(vector<SharedRAbundVector*> thisLookup, vector< vector<seqDist> >& calcDists, Calculator* matrixCalculator) {
+ try {
+ vector<SharedRAbundVector*> subset;
+
+ for (int k = 0; k < thisLookup.size(); k++) { // pass cdd each set of groups to compare
+
+ for (int l = 0; l < k; l++) {
+
+ if (k != l) { //we dont need to similiarity of a groups to itself
+ subset.clear(); //clear out old pair of sharedrabunds
+ //add new pair of sharedrabunds
+ subset.push_back(thisLookup[k]); subset.push_back(thisLookup[l]);
+
+
+
+ //if this calc needs all groups to calculate the pair load all groups
+ if (matrixCalculator->getNeedsAll()) {
+ //load subset with rest of lookup for those calcs that need everyone to calc for a pair
+ for (int w = 0; w < thisLookup.size(); w++) {
+ if ((w != k) && (w != l)) { subset.push_back(thisLookup[w]); }
+ }
+ }
+
+ vector<double> tempdata = matrixCalculator->getValues(subset); //saves the calculator outputs
+
+ if (m->control_pressed) { return 1; }
+
+ seqDist temp(l, k, tempdata[0]);
+ //cout << l << '\t' << k << '\t' << tempdata[0] << endl;
+ calcDists[0].push_back(temp);
+ }
+
+ }
+ }
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "MatrixOutputCommand", "driver");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
projects / mothur.git / blobdiff