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//
// 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));
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, doPruning, pruneAggressiveness, discardHighErrorTrees, highErrorTreeDiscardThreshold, optimumFeatureSubsetSelectionCriteria, featureStandardDeviationThreshold);
randomForest.populateDecisionTrees();
randomForest.calcForrestErrorRate();
map<string, string> variables;
variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(sharedfile));
variables["[distance]"] = lookup[0]->getLabel();
string filename = getOutputFileName("summary", variables);
outputNames.push_back(filename); outputTypes["summary"].push_back(filename);
randomForest.calcForrestVariableImportance(filename);
m->mothurOutEndLine();
}
catch(exception& e) {
m->errorOut(e, "ClassifySharedCommand", "processSharedAndDesignData");
exit(1);
}
}
//**********************************************************************************************************************
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