--- /dev/null
+//
+// classifysharedcommand.cpp
+// Mothur
+//
+// Created by Abu Zaher Md. Faridee on 8/13/12.
+// Copyright (c) 2012 Schloss Lab. All rights reserved.
+//
+
+#include "classifyrfsharedcommand.h"
+#include "randomforest.hpp"
+#include "decisiontree.hpp"
+#include "rftreenode.hpp"
+
+//**********************************************************************************************************************
+vector<string> ClassifyRFSharedCommand::setParameters(){
+ try {
+ //CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
+ CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none","summary",false,true,true); parameters.push_back(pshared);
+ CommandParameter pdesign("design", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(pdesign);
+ CommandParameter potupersplit("otupersplit", "Multiple", "log2-squareroot", "log2", "", "", "","",false,false); parameters.push_back(potupersplit);
+ CommandParameter psplitcriteria("splitcriteria", "Multiple", "gainratio-infogain", "gainratio", "", "", "","",false,false); parameters.push_back(psplitcriteria);
+ CommandParameter pnumtrees("numtrees", "Number", "", "100", "", "", "","",false,false); parameters.push_back(pnumtrees);
+
+ // parameters related to pruning
+ CommandParameter pdopruning("prune", "Boolean", "", "T", "", "", "", "", false, false); parameters.push_back(pdopruning);
+ CommandParameter ppruneaggrns("pruneaggressiveness", "Number", "", "0.9", "", "", "", "", false, false); parameters.push_back(ppruneaggrns);
+ CommandParameter pdiscardhetrees("discarderrortrees", "Boolean", "", "T", "", "", "", "", false, false); parameters.push_back(pdiscardhetrees);
+ CommandParameter phetdiscardthreshold("errorthreshold", "Number", "", "0.4", "", "", "", "", false, false); parameters.push_back(phetdiscardthreshold);
+ CommandParameter psdthreshold("stdthreshold", "Number", "", "0.0", "", "", "", "", false, false); parameters.push_back(psdthreshold);
+ // pruning params end
+
+ CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
+ CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
+ 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, "ClassifySharedCommand", "setParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string ClassifyRFSharedCommand::getHelpString(){
+ try {
+ string helpString = "";
+ helpString += "The classify.shared command allows you to ....\n";
+ helpString += "The classify.shared command parameters are: shared, design, label, groups, otupersplit.\n";
+ helpString += "The label parameter is used to analyze specific labels in your input.\n";
+ helpString += "The groups parameter allows you to specify which of the groups in your designfile you would like analyzed.\n";
+ helpString += "The classify.shared should be in the following format: \n";
+ helpString += "classify.shared(shared=yourSharedFile, design=yourDesignFile)\n";
+ return helpString;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ClassifySharedCommand", "getHelpString");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string ClassifyRFSharedCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
+
+ if (type == "summary") { pattern = "[filename],[distance],summary"; } //makes file like: amazon.0.03.fasta
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ClassifySharedCommand", "getOutputPattern");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+
+ClassifyRFSharedCommand::ClassifyRFSharedCommand() {
+ try {
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["summary"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ClassifySharedCommand", "ClassifySharedCommand");
+ exit(1);
+ }
+}
+
+//**********************************************************************************************************************
+ClassifyRFSharedCommand::ClassifyRFSharedCommand(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;
+
+ //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("shared");
+ //user has given a shared 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; }
+ }
+
+ it = parameters.find("design");
+ //user has given a design 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["design"] = inputDir + it->second; }
+ }
+
+ }
+ //check for parameters
+ //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 design file, it is required
+ designfile = validParameter.validFile(parameters, "design", true);
+ if (designfile == "not open") { sharedfile = ""; 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 designfile 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
+ }
+
+ // NEW CODE for OTU per split selection criteria
+ string temp = validParameter.validFile(parameters, "splitcriteria", false);
+ if (temp == "not found") { temp = "gainratio"; }
+ if ((temp == "gainratio") || (temp == "infogain")) {
+ treeSplitCriterion = temp;
+ } else { m->mothurOut("Not a valid tree splitting criterio. Valid tree splitting criteria are 'gainratio' and 'infogain'.");
+ m->mothurOutEndLine();
+ abort = true;
+ }
+
+ temp = validParameter.validFile(parameters, "numtrees", false); if (temp == "not found"){ temp = "100"; }
+ m->mothurConvert(temp, numDecisionTrees);
+
+ // parameters for pruning
+ temp = validParameter.validFile(parameters, "prune", false);
+ if (temp == "not found") { temp = "f"; }
+ doPruning = m->isTrue(temp);
+
+ temp = validParameter.validFile(parameters, "pruneaggressiveness", false);
+ if (temp == "not found") { temp = "0.9"; }
+ m->mothurConvert(temp, pruneAggressiveness);
+
+ temp = validParameter.validFile(parameters, "discarderrortrees", false);
+ if (temp == "not found") { temp = "f"; }
+ discardHighErrorTrees = m->isTrue(temp);
+
+ temp = validParameter.validFile(parameters, "errorthreshold", false);
+ if (temp == "not found") { temp = "0.4"; }
+ m->mothurConvert(temp, highErrorTreeDiscardThreshold);
+
+ temp = validParameter.validFile(parameters, "otupersplit", false);
+ if (temp == "not found") { temp = "log2"; }
+ if ((temp == "squareroot") || (temp == "log2")) {
+ optimumFeatureSubsetSelectionCriteria = temp;
+ } else { m->mothurOut("Not a valid OTU per split selection method. Valid OTU per split selection methods are 'log2' and 'squareroot'.");
+ m->mothurOutEndLine();
+ abort = true;
+ }
+
+ temp = validParameter.validFile(parameters, "stdthreshold", false);
+ if (temp == "not found") { temp = "0.0"; }
+ m->mothurConvert(temp, featureStandardDeviationThreshold);
+
+ // end of pruning params
+
+ //Groups must be checked later to make sure they are valid. SharedUtilities has functions of check the validity, just make to so m->setGroups() after the checks. If you are using these with a shared file no need to check the SharedRAbundVector class will call SharedUtilites for you, kinda nice, huh?
+ string groups = validParameter.validFile(parameters, "groups", false);
+ if (groups == "not found") { groups = ""; }
+ else { m->splitAtDash(groups, Groups); }
+ m->setGroups(Groups);
+
+ //Commonly used to process list, rabund, sabund, shared and relabund files. Look at "smart distancing" examples below in the execute function.
+ 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; }
+ }
+ }
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ClassifySharedCommand", "ClassifySharedCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+int ClassifyRFSharedCommand::execute() {
+ try {
+
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
+
+ InputData input(sharedfile, "sharedfile");
+ vector<SharedRAbundVector*> lookup = input.getSharedRAbundVectors();
+
+ //read design file
+ designMap.readDesignMap(designfile);
+
+ string lastLabel = lookup[0]->getLabel();
+ 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();
+
+ processSharedAndDesignData(lookup);
+
+ 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();
+ processSharedAndDesignData(lookup);
+
+ 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();
+
+ processSharedAndDesignData(lookup);
+
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
+
+ }
+
+ 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, "ClassifySharedCommand", "execute");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+
+void ClassifyRFSharedCommand::processSharedAndDesignData(vector<SharedRAbundVector*> lookup){
+ try {
+// for (int i = 0; i < designMap->getNamesOfGroups().size(); i++) {
+// string groupName = designMap->getNamesOfGroups()[i];
+// cout << groupName << endl;
+// }
+
+// for (int i = 0; i < designMap->getNumSeqs(); i++) {
+// string sharedGroupName = designMap->getNamesSeqs()[i];
+// string treatmentName = designMap->getGroup(sharedGroupName);
+// cout << sharedGroupName << " : " << treatmentName << endl;
+// }
+
+ map<string, int> treatmentToIntMap;
+ map<int, string> intToTreatmentMap;
+ for (int i = 0; i < designMap.getNumGroups(); i++) {
+ string treatmentName = designMap.getNamesOfGroups()[i];
+ treatmentToIntMap[treatmentName] = i;
+ intToTreatmentMap[i] = treatmentName;
+ }
+
+ int numSamples = lookup.size();
+ int numFeatures = lookup[0]->getNumBins();
+
+ int numRows = numSamples;
+ int numColumns = numFeatures + 1; // extra one space needed for the treatment/outcome
+
+ vector< vector<int> > dataSet(numRows, vector<int>(numColumns, 0));
+
+ vector<string> names;
+
+ for (int i = 0; i < lookup.size(); i++) {
+ string sharedGroupName = lookup[i]->getGroup();
+ names.push_back(sharedGroupName);
+ string treatmentName = designMap.getGroup(sharedGroupName);
+
+ int j = 0;
+ for (; j < lookup[i]->getNumBins(); j++) {
+ int otuCount = lookup[i]->getAbundance(j);
+ dataSet[i][j] = otuCount;
+ }
+ dataSet[i][j] = treatmentToIntMap[treatmentName];
+ }
+
+ RandomForest randomForest(dataSet, numDecisionTrees, treeSplitCriterion, doPruning, pruneAggressiveness, discardHighErrorTrees, highErrorTreeDiscardThreshold, optimumFeatureSubsetSelectionCriteria, featureStandardDeviationThreshold);
+
+ randomForest.populateDecisionTrees();
+ randomForest.calcForrestErrorRate();
+ randomForest.printConfusionMatrix(intToTreatmentMap);
+
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + "RF.";
+ variables["[distance]"] = lookup[0]->getLabel();
+ string filename = getOutputFileName("summary", variables);
+ outputNames.push_back(filename); outputTypes["summary"].push_back(filename);
+ randomForest.calcForrestVariableImportance(filename);
+
+ //
+ map<string, string> variable;
+ variable["[filename]"] = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + "misclassifications.";
+ variable["[distance]"] = lookup[0]->getLabel();
+ string mc_filename = getOutputFileName("summary", variable);
+ outputNames.push_back(mc_filename); outputTypes["summary"].push_back(mc_filename);
+ randomForest.getMissclassifications(mc_filename, intToTreatmentMap, names);
+ //
+
+ m->mothurOutEndLine();
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ClassifySharedCommand", "processSharedAndDesignData");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+
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