+++ /dev/null
-//
-// classifysharedcommand.cpp
-// Mothur
-//
-// Created by Abu Zaher Md. Faridee on 8/13/12.
-// Copyright (c) 2012 Schloss Lab. All rights reserved.
-//
-
-#include "classifysharedcommand.h"
-#include "randomforest.hpp"
-#include "decisiontree.hpp"
-#include "rftreenode.hpp"
-
-//**********************************************************************************************************************
-vector<string> ClassifySharedCommand::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 ClassifySharedCommand::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 ClassifySharedCommand::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);
- }
-}
-//**********************************************************************************************************************
-
-ClassifySharedCommand::ClassifySharedCommand() {
- try {
- abort = true; calledHelp = true;
- setParameters();
- vector<string> tempOutNames;
- outputTypes["summary"] = tempOutNames;
- }
- catch(exception& e) {
- m->errorOut(e, "ClassifySharedCommand", "ClassifySharedCommand");
- exit(1);
- }
-}
-
-//**********************************************************************************************************************
-ClassifySharedCommand::ClassifySharedCommand(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 ClassifySharedCommand::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 ClassifySharedCommand::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);
- }
-}
-//**********************************************************************************************************************
-
projects / mothur.git / blobdiff