//
#include "lefsecommand.h"
+#include "linearalgebra.h"
+
+//**********************************************************************************************************************
+vector<string> LefseCommand::setParameters(){
+ try {
+ CommandParameter pdesign("design", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(pdesign);
+ CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none","summary",false,true,true); parameters.push_back(pshared);
+ CommandParameter pclass("class", "String", "", "", "", "", "","",false,false); parameters.push_back(pclass);
+ CommandParameter psubclass("subclass", "String", "", "", "", "", "","",false,false); parameters.push_back(psubclass);
+ CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
+ CommandParameter pclasses("classes", "String", "", "", "", "", "","",false,false); parameters.push_back(pclasses);
+ CommandParameter palpha("anova_alpha", "Number", "", "0.05", "", "", "","",false,false); parameters.push_back(palpha);
+ CommandParameter pwalpha("wilcoxon_alpha", "Number", "", "0.05", "", "", "","",false,false); parameters.push_back(pwalpha);
+ //every command must have inputdir and outputdir. This allows mothur users to redirect input and output files.
+ 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); }
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "LefseCommand", "setParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string LefseCommand::getHelpString(){
+ try {
+ string helpString = "";
+ helpString += "The lefse command allows you to ....\n";
+ helpString += "The lefse command parameters are: shared, design, class, subclass, label, classes, wilcoxon_alpha, anova_alpha.\n";
+ helpString += "The class parameter is used to indicate the which category you would like used for the Kruskal Wallis analysis. If none is provided first category is used.\n";
+ helpString += "The subclass parameter is used to indicate the .....If none is provided second category is used, or if only one category subclass is ignored. \n";
+ helpString += "The classes parameter is used to indicate the classes you would like to use. Clases should be inputted in the following format: classes=label<value1|value2|value3>-label<value1|value2>. For example to include groups from treatment with value early or late and age= young or old. class=treatment<Early|Late>-age<young|old>.\n";
+ helpString += "The label parameter is used to indicate which distances in the shared file you would like to use. labels are separated by dashes.\n";
+ helpString += "The lefse command should be in the following format: lefse(shared=final.an.shared, design=final.design, class=treatment, subclass=age).\n";
+ return helpString;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "LefseCommand", "getHelpString");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string LefseCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
+
+ if (type == "summary") { pattern = "[filename],[distance],lefse_summary"; }
+ else if (type == "kruskall-wallis") { pattern = "[filename],[distance],kruskall_wallis"; }
+ else if (type == "wilcoxon") { pattern = "[filename],[distance],wilcoxon"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "LefseCommand", "getOutputPattern");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+LefseCommand::LefseCommand(){
+ try {
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["summary"] = tempOutNames;
+ outputTypes["kruskall-wallis"] = tempOutNames;
+ outputTypes["wilcoxon"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "LefseCommand", "LefseCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+LefseCommand::LefseCommand(string option) {
+ try {
+ abort = false; calledHelp = false;
+ allLines = 1;
+
+ //allow user to run help
+ if(option == "help") { help(); abort = true; calledHelp = true; }
+ else if(option == "citation") { citation(); abort = true; calledHelp = true;}
+
+ else {
+ //valid paramters for this command
+ vector<string> myArray = setParameters();
+
+ OptionParser parser(option);
+ map<string,string> parameters = parser.getParameters();
+
+ ValidParameters validParameter;
+ map<string,string>::iterator it;
+ //check to make sure all parameters are valid for command
+ for (it = parameters.begin(); it != parameters.end(); it++) {
+ if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
+ }
+
+ vector<string> tempOutNames;
+ outputTypes["summary"] = tempOutNames;
+ outputTypes["kruskall-wallis"] = tempOutNames;
+ outputTypes["wilcoxon"] = tempOutNames;
+
+ //if the user changes the input directory command factory will send this info to us in the output parameter
+ string inputDir = validParameter.validFile(parameters, "inputdir", false);
+ if (inputDir == "not found"){ inputDir = ""; }
+ else {
+
+ string path;
+ it = parameters.find("design");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = m->hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["desing"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("shared");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = m->hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["shared"] = inputDir + it->second; }
+ }
+ }
+
+ //get shared file, it is required
+ sharedfile = validParameter.validFile(parameters, "shared", true);
+ if (sharedfile == "not open") { sharedfile = ""; abort = true; }
+ else if (sharedfile == "not found") {
+ //if there is a current shared file, use it
+ sharedfile = m->getSharedFile();
+ if (sharedfile != "") { m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
+ else { m->mothurOut("You have no current sharedfile and the shared parameter is required."); m->mothurOutEndLine(); abort = true; }
+ }else { m->setSharedFile(sharedfile); }
+
+ //get shared file, it is required
+ designfile = validParameter.validFile(parameters, "design", true);
+ if (designfile == "not open") { designfile = ""; abort = true; }
+ else if (designfile == "not found") {
+ //if there is a current shared file, use it
+ designfile = m->getDesignFile();
+ if (designfile != "") { m->mothurOut("Using " + designfile + " as input file for the design parameter."); m->mothurOutEndLine(); }
+ else { m->mothurOut("You have no current design file and the design parameter is required."); m->mothurOutEndLine(); abort = true; }
+ }else { m->setDesignFile(designfile); }
+
+ //if the user changes the output directory command factory will send this info to us in the output parameter
+ outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){
+ outputDir = m->hasPath(sharedfile); //if user entered a file with a path then preserve it
+ }
+
+ string label = validParameter.validFile(parameters, "label", false);
+ if (label == "not found") { label = ""; }
+ else {
+ if(label != "all") { m->splitAtDash(label, labels); allLines = 0; }
+ else { allLines = 1; }
+ }
+
+ mclass = validParameter.validFile(parameters, "class", false);
+ if (mclass == "not found") { mclass = ""; }
+
+ subclass = validParameter.validFile(parameters, "subclass", false);
+ if (subclass == "not found") { subclass = ""; }
+
+ classes = validParameter.validFile(parameters, "classes", false);
+ if (classes == "not found") { classes = ""; }
+
+ string temp = validParameter.validFile(parameters, "anova_alpha", false);
+ if (temp == "not found") { temp = "0.05"; }
+ m->mothurConvert(temp, anovaAlpha);
+
+ temp = validParameter.validFile(parameters, "wilcoxon_alpha", false);
+ if (temp == "not found") { temp = "0.05"; }
+ m->mothurConvert(temp, wilcoxonAlpha);
+
+ }
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "LefseCommand", "LefseCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+
+int LefseCommand::execute(){
+ try {
+
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
+
+ DesignMap designMap(designfile);
+ //if user set classes set groups=those classes
+ if (classes != "") {
+ map<string, vector<string> > thisClasses = m->parseClasses(classes);
+ vector<string> groups = designMap.getNamesUnique(thisClasses);
+ if (groups.size() != 0) { m->setGroups(groups); }
+ else { m->mothurOut("[ERROR]: no groups meet your classes requirement, quitting.\n"); return 0; }
+ }
+
+ //if user did not select class use first column
+ if (mclass == "") { mclass = designMap.getDefaultClass(); m->mothurOut("\nYou did not provide a class, using " + mclass +".\n\n"); }
+
+ InputData input(sharedfile, "sharedfile");
+ vector<SharedRAbundVector*> lookup = input.getSharedRAbundVectors();
+ string lastLabel = lookup[0]->getLabel();
+
+ //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;
+
+
+ //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))) {
+
+ if (m->control_pressed) { for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } return 0; }
+
+ if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
+
+ m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
+
+ process(lookup, designMap);
+
+ processedLabels.insert(lookup[0]->getLabel());
+ userLabels.erase(lookup[0]->getLabel());
+ }
+
+ if ((m->anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+ string saveLabel = lookup[0]->getLabel();
+
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
+ lookup = input.getSharedRAbundVectors(lastLabel);
+ m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
+
+ process(lookup, designMap);
+
+ processedLabels.insert(lookup[0]->getLabel());
+ userLabels.erase(lookup[0]->getLabel());
+
+ //restore real lastlabel to save below
+ lookup[0]->setLabel(saveLabel);
+ }
+
+ lastLabel = lookup[0]->getLabel();
+ //prevent memory leak
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; lookup[i] = NULL; }
+
+ if (m->control_pressed) { return 0; }
+
+ //get next line to process
+ lookup = input.getSharedRAbundVectors();
+ }
+
+ if (m->control_pressed) { return 0; }
+
+ //output error messages about any remaining user labels
+ set<string>::iterator it;
+ bool needToRun = false;
+ for (it = userLabels.begin(); it != userLabels.end(); it++) {
+ m->mothurOut("Your file does not include the label " + *it);
+ if (processedLabels.count(lastLabel) != 1) {
+ m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
+ needToRun = true;
+ }else {
+ m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
+ }
+ }
+
+ //run last label if you need to
+ if (needToRun == true) {
+ for (int i = 0; i < lookup.size(); i++) { if (lookup[i] != NULL) { delete lookup[i]; } }
+ lookup = input.getSharedRAbundVectors(lastLabel);
+
+ m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
+ process(lookup, designMap);
+
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
+ }
+
+
+ //output files created by command
+ m->mothurOutEndLine();
+ m->mothurOut("Output File Names: "); m->mothurOutEndLine();
+ for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
+ m->mothurOutEndLine();
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "LefseCommand", "execute");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+
+int LefseCommand::process(vector<SharedRAbundVector*>& lookup, DesignMap& designMap) {
+ try {
+ //run kruskal wallis on each otu
+ vector<int> significantOtuLabels = runKruskalWallis(lookup, designMap);
+
+ //check for subclass
+ if (subclass != "") { significantOtuLabels = runWilcoxon(lookup, designMap, significantOtuLabels); }
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "LefseCommand", "process");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+
+vector<int> LefseCommand::runKruskalWallis(vector<SharedRAbundVector*>& lookup, DesignMap& designMap) {
+ try {
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(sharedfile));
+ variables["[distance]"] = lookup[0]->getLabel();
+ string outputFileName = getOutputFileName("kruskall-wallis",variables);
+
+ ofstream out;
+ m->openOutputFile(outputFileName, out);
+ outputNames.push_back(outputFileName); outputTypes["kruskall-wallis"].push_back(outputFileName);
+ out << "OTULabel\tKW\tPvalue\n";
+
+ vector<int> significantOtuLabels;
+ int numBins = lookup[0]->getNumBins();
+ //sanity check to make sure each treatment has a group in the shared file
+ set<string> treatments;
+ for (int j = 0; j < lookup.size(); j++) {
+ string group = lookup[j]->getGroup();
+ string treatment = designMap.get(group, mclass); //get value for this group in this category
+ treatments.insert(treatment);
+ }
+ if (treatments.size() < 2) { m->mothurOut("[ERROR]: need at least 2 things to classes to compare, quitting.\n"); m->control_pressed = true; }
+
+ LinearAlgebra linear;
+ for (int i = 0; i < numBins; i++) {
+ if (m->control_pressed) { break; }
+
+ vector<spearmanRank> values;
+ for (int j = 0; j < lookup.size(); j++) {
+ string group = lookup[j]->getGroup();
+ string treatment = designMap.get(group, mclass); //get value for this group in this category
+ spearmanRank temp(treatment, lookup[j]->getAbundance(i));
+ values.push_back(temp);
+ }
+
+ double pValue = 0.0;
+ double H = linear.calcKruskalWallis(values, pValue);
+
+ //output H and signifigance
+ out << m->currentBinLabels[i] << '\t' << H << '\t' << pValue << endl;
+
+ if (pValue < anovaAlpha) { significantOtuLabels.push_back(i); }
+ }
+ out.close();
+
+ return significantOtuLabels;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "LefseCommand", "runKruskalWallis");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+
+vector<int> LefseCommand::runWilcoxon(vector<SharedRAbundVector*>& lookup, DesignMap& designMap, vector<int> bins) {
+ try {
+ vector<int> significantOtuLabels;
+ //if it exists and meets the following requirements run Wilcoxon
+ /*
+ 1. Subclass members all belong to same main class
+ 2. Number of groups in each subclass is the same
+ 3. anything else??
+
+ */
+ vector<string> subclasses;
+ map<string, string> subclass2Class;
+ map<string, int> subclassCounts;
+ map<string, vector<int> > subClass2GroupIndex; //maps subclass name to vector of indexes in lookup from that subclass. old -> 1,2,3 means groups in location 1,2,3 of lookup are from old. Saves time below.
+ bool error = false;
+ for (int j = 0; j < lookup.size(); j++) {
+ string group = lookup[j]->getGroup();
+ string treatment = designMap.get(group, mclass); //get value for this group in this category
+ string thisSub = designMap.get(group, subclass);
+ map<string, string>::iterator it = subclass2Class.find(thisSub);
+ if (it == subclass2Class.end()) {
+ subclass2Class[thisSub] = treatment;
+ subclassCounts[thisSub] = 1;
+ vector<int> temp; temp.push_back(j);
+ subClass2GroupIndex[thisSub] = temp;
+ }
+ else {
+ subclassCounts[thisSub]++;
+ subClass2GroupIndex[thisSub].push_back(j);
+ if (it->second != treatment) {
+ error = true;
+ m->mothurOut("[ERROR]: subclass " + thisSub + " has members in " + it->second + " and " + treatment + ". Subclass members must be from the same class. Ignoring wilcoxon.\n");
+ }
+ }
+ }
+
+ if (error) { return significantOtuLabels; }
+ else { //check counts to make sure subclasses are the same size
+ set<int> counts;
+ for (map<string, int>::iterator it = subclassCounts.begin(); it != subclassCounts.end(); it++) { counts.insert(it->second); }
+ if (counts.size() > 1) { m->mothurOut("[ERROR]: subclasses must be the same size. Ignoring wilcoxon.\n");
+ return significantOtuLabels; }
+ }
+
+ int numBins = lookup[0]->getNumBins();
+ vector<compGroup> comp;
+ //find comparisons and fill comp
+ map<string, int>::iterator itB;
+ for(map<string, int>::iterator it=subclassCounts.begin();it!=subclassCounts.end();it++){
+ itB = it;itB++;
+ for(itB;itB!=subclassCounts.end();itB++){
+ compGroup temp(it->first,itB->first);
+ comp.push_back(temp);
+ }
+ }
+
+ int numComp = comp.size();
+ if (numComp < 2) { m->mothurOut("[ERROR]: Need at least 2 subclasses, Ignoring Wilcoxon.\n");
+ return significantOtuLabels; }
+
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(sharedfile));
+ variables["[distance]"] = lookup[0]->getLabel();
+ string outputFileName = getOutputFileName("wilcoxon",variables);
+
+ ofstream out;
+ m->openOutputFile(outputFileName, out);
+ outputNames.push_back(outputFileName); outputTypes["wilcoxon"].push_back(outputFileName);
+ out << "OTULabel\tComparision\tWilcoxon\tPvalue\n";
+
+ LinearAlgebra linear;
+ for (int i = 0; i < numBins; i++) {
+ if (m->control_pressed) { break; }
+
+ if (m->inUsersGroups(i, bins)) { //flagged in Kruskal Wallis
+
+ bool sig = false;
+ //for each subclass comparision
+ for (int j = 0; j < numComp; j++) {
+ //fill x and y with this comparisons data
+ vector<double> x; vector<double> y;
+
+ //fill x and y
+ vector<int> xIndexes = subClass2GroupIndex[comp[j].group1]; //indexes in lookup for this subclass
+ for (int k = 0; k < xIndexes.size(); k++) { x.push_back(lookup[xIndexes[k]]->getAbundance(i)); }
+
+ vector<int> yIndexes = subClass2GroupIndex[comp[j].group2]; //indexes in lookup for this subclass
+ for (int k = 0; k < yIndexes.size(); k++) { y.push_back(lookup[yIndexes[k]]->getAbundance(i)); }
+
+ double pValue = 0.0;
+ double H = linear.calcWilcoxon(x, y, pValue);
+
+ //output H and signifigance
+ out << m->currentBinLabels[i] << '\t' << comp[j].getCombo() << '\t' << H << '\t' << pValue << endl;
+
+ //set sig - not sure how yet
+ }
+ if (sig) { significantOtuLabels.push_back(i); }
+ }
+ }
+ out.close();
+
+ return significantOtuLabels;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "LefseCommand", "runWilcoxon");
+ exit(1);
+ }
+}
+
+//**********************************************************************************************************************
+
+
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