X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=classifysharedcommand.cpp;fp=classifysharedcommand.cpp;h=f964937b4ded24bc8f9eb001f1a8557f2ffcfd77;hb=035f86272c776e1cccaa47021e26782e49cd41e7;hp=0000000000000000000000000000000000000000;hpb=96dbe925073caefaed6e6db85659c144a806aeb1;p=mothur.git diff --git a/classifysharedcommand.cpp b/classifysharedcommand.cpp new file mode 100755 index 0000000..f964937 --- /dev/null +++ b/classifysharedcommand.cpp @@ -0,0 +1,364 @@ +// +// 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 ClassifySharedCommand::setParameters(){ + try { + //CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors); + CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pshared); + CommandParameter pdesign("design", "InputTypes", "", "", "none", "none", "none",false,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); + + 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 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::getOutputFileNameTag(string type, string inputName=""){ + try { + string tag = ""; + map >::iterator it; + + //is this a type this command creates + it = outputTypes.find(type); + if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); } + else { + if (type == "summary") { tag = "summary"; } + else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; } + } + return tag; + } + catch(exception& e) { + m->errorOut(e, "ClassifySharedCommand", "getOutputFileName"); + exit(1); + } +} +//********************************************************************************************************************** + +ClassifySharedCommand::ClassifySharedCommand() { + try { + abort = true; calledHelp = true; + setParameters(); + vector 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 myArray = setParameters(); + + OptionParser parser(option); + map parameters = parser.getParameters(); + + ValidParameters validParameter; + map::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 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 + otupersplit = validParameter.validFile(parameters, "otupersplit", false); + if (otupersplit == "not found") { otupersplit = "log2"; } + if ((otupersplit == "squareroot") || (otupersplit == "log2")) { + optimumFeatureSubsetSelectionCriteria = otupersplit; + }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; } + + // splitcriteria + splitcriteria = validParameter.validFile(parameters, "splitcriteria", false); + if (splitcriteria == "not found") { splitcriteria = "gainratio"; } + if ((splitcriteria == "gainratio") || (splitcriteria == "infogain")) { + treeSplitCriterion = splitcriteria; + }else { m->mothurOut("Not a valid tree splitting criterio. Valid tree splitting criteria are 'gainratio' and 'infogain'."); m->mothurOutEndLine(); abort = true; } + + + string temp = validParameter.validFile(parameters, "numtrees", false); if (temp == "not found"){ temp = "100"; } + m->mothurConvert(temp, numDecisionTrees); + + //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 lookup = input.getSharedRAbundVectors(); + + //read design file + designMap.readDesignMap(designfile); + + string lastLabel = lookup[0]->getLabel(); + set processedLabels; + set 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::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 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 treatmentToIntMap; + map 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 > dataSet(numRows, vector(numColumns, 0)); + + for (int i = 0; i < lookup.size(); i++) { + string sharedGroupName = lookup[i]->getGroup(); + 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); + randomForest.populateDecisionTrees(); + randomForest.calcForrestErrorRate(); + + string filename = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + lookup[0]->getLabel() + "." + getOutputFileNameTag("summary"); + outputNames.push_back(filename); outputTypes["summary"].push_back(filename); + + randomForest.calcForrestVariableImportance(filename); + + m->mothurOutEndLine(); + } + catch(exception& e) { + m->errorOut(e, "ClassifySharedCommand", "processSharedAndDesignData"); + exit(1); + } +} +//********************************************************************************************************************** +