kruskalwalliscommand.cpp

   1 /*
   2  * File:   kruskalwalliscommand.cpp
   3  * Author: kiverson
   4  *
   5  * Created on June 26, 2012, 11:06 AM
   6  */
   7
   8 #include "kruskalwalliscommand.h"
   9 #include "linearalgebra.h"
  10
  11 //**********************************************************************************************************************
  12 vector<string> KruskalWallisCommand::setParameters(){
  13         try {
  14         CommandParameter pdesign("design", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(pdesign);
  15         CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none","summary",false,true,true); parameters.push_back(pshared);
  16         CommandParameter pclass("class", "String", "", "", "", "", "","",false,false); parameters.push_back(pclass);
  17                 CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
  18         //every command must have inputdir and outputdir.  This allows mothur users to redirect input and output files.
  19                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
  20                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
  21
  22                 vector<string> myArray;
  23                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  24                 return myArray;
  25         }
  26         catch(exception& e) {
  27                 m->errorOut(e, "KruskalWallisCommand", "setParameters");
  28                 exit(1);
  29         }
  30 }
  31 //**********************************************************************************************************************
  32 string KruskalWallisCommand::getHelpString(){
  33         try {
  34                 string helpString = "";
  35                 helpString += "The kruskal.wallis command allows you to ....\n";
  36                 helpString += "The kruskal.wallis command parameters are: shared, design, class, label and classes.\n";
  37                 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";
  38         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";
  39                 helpString += "The kruskal.wallis command should be in the following format: kruskal.wallis(shared=final.an.shared, design=final.design, class=treatment).\n";
  40         return helpString;
  41         }
  42         catch(exception& e) {
  43                 m->errorOut(e, "KruskalWallisCommand", "getHelpString");
  44                 exit(1);
  45         }
  46 }
  47 //**********************************************************************************************************************
  48 string KruskalWallisCommand::getOutputPattern(string type) {
  49     try {
  50         string pattern = "";
  51
  52         if (type == "kruskall-wallis") {  pattern = "[filename],[distance],kruskall_wallis"; }
  53         else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
  54
  55         return pattern;
  56     }
  57     catch(exception& e) {
  58         m->errorOut(e, "KruskalWallisCommand", "getOutputPattern");
  59         exit(1);
  60     }
  61 }
  62 //**********************************************************************************************************************
  63 KruskalWallisCommand::KruskalWallisCommand(){
  64         try {
  65                 abort = true; calledHelp = true;
  66                 setParameters();
  67         vector<string> tempOutNames;
  68         outputTypes["kruskall-wallis"] = tempOutNames;
  69         }
  70         catch(exception& e) {
  71                 m->errorOut(e, "KruskalWallisCommand", "KruskalWallisCommand");
  72                 exit(1);
  73         }
  74 }
  75 //**********************************************************************************************************************
  76 KruskalWallisCommand::KruskalWallisCommand(string option)  {
  77         try {
  78                 abort = false; calledHelp = false;
  79         allLines = 1;
  80
  81                 //allow user to run help
  82                 if(option == "help") { help(); abort = true; calledHelp = true; }
  83                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
  84
  85                 else {
  86                         //valid paramters for this command
  87                         vector<string> myArray = setParameters();
  88
  89                         OptionParser parser(option);
  90                         map<string,string> parameters = parser.getParameters();
  91
  92                         ValidParameters validParameter;
  93                         map<string,string>::iterator it;
  94                         //check to make sure all parameters are valid for command
  95                         for (it = parameters.begin(); it != parameters.end(); it++) {
  96                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  97                         }
  98
  99                         vector<string> tempOutNames;
 100             outputTypes["kruskall-wallis"] = tempOutNames;
 101
 102                         //if the user changes the input directory command factory will send this info to us in the output parameter
 103                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 104                         if (inputDir == "not found"){   inputDir = "";          }
 105                         else {
 106
 107                 string path;
 108                                 it = parameters.find("design");
 109                                 //user has given a template file
 110                                 if(it != parameters.end()){
 111                                         path = m->hasPath(it->second);
 112                                         //if the user has not given a path then, add inputdir. else leave path alone.
 113                                         if (path == "") {       parameters["desing"] = inputDir + it->second;           }
 114                                 }
 115
 116                 it = parameters.find("shared");
 117                                 //user has given a template file
 118                                 if(it != parameters.end()){
 119                                         path = m->hasPath(it->second);
 120                                         //if the user has not given a path then, add inputdir. else leave path alone.
 121                                         if (path == "") {       parameters["shared"] = inputDir + it->second;           }
 122                                 }
 123             }
 124
 125             //get shared file, it is required
 126                         sharedfile = validParameter.validFile(parameters, "shared", true);
 127                         if (sharedfile == "not open") { sharedfile = ""; abort = true; }
 128                         else if (sharedfile == "not found") {
 129                                 //if there is a current shared file, use it
 130                                 sharedfile = m->getSharedFile();
 131                                 if (sharedfile != "") { m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
 132                                 else {  m->mothurOut("You have no current sharedfile and the shared parameter is required."); m->mothurOutEndLine(); abort = true; }
 133                         }else { m->setSharedFile(sharedfile); }
 134
 135             //get shared file, it is required
 136                         designfile = validParameter.validFile(parameters, "design", true);
 137                         if (designfile == "not open") { designfile = ""; abort = true; }
 138                         else if (designfile == "not found") {
 139                                 //if there is a current shared file, use it
 140                                 designfile = m->getDesignFile();
 141                                 if (designfile != "") { m->mothurOut("Using " + designfile + " as input file for the design parameter."); m->mothurOutEndLine(); }
 142                                 else {  m->mothurOut("You have no current design file and the design parameter is required."); m->mothurOutEndLine(); abort = true; }
 143                         }else { m->setDesignFile(designfile); }
 144
 145             //if the user changes the output directory command factory will send this info to us in the output parameter
 146                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
 147                                 outputDir = m->hasPath(sharedfile); //if user entered a file with a path then preserve it
 148                         }
 149
 150             string label = validParameter.validFile(parameters, "label", false);
 151                         if (label == "not found") { label = ""; }
 152                         else {
 153                                 if(label != "all") {  m->splitAtDash(label, labels);  allLines = 0;  }
 154                                 else { allLines = 1;  }
 155                         }
 156
 157             mclass = validParameter.validFile(parameters, "class", false);
 158                         if (mclass == "not found") { mclass = ""; }
 159
 160                 }
 161
 162         }
 163         catch(exception& e) {
 164                 m->errorOut(e, "KruskalWallisCommand", "KruskalWallisCommand");
 165                 exit(1);
 166         }
 167 }
 168 //**********************************************************************************************************************
 169
 170 int KruskalWallisCommand::execute(){
 171         try {
 172
 173                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 174
 175         DesignMap designMap(designfile);
 176
 177         //if user did not select class use first column
 178         if (mclass == "") {  mclass = designMap.getDefaultClass(); m->mothurOut("\nYou did not provide a class, using " + mclass +".\n\n"); }
 179
 180         InputData input(sharedfile, "sharedfile");
 181         vector<SharedRAbundVector*> lookup = input.getSharedRAbundVectors();
 182         string lastLabel = lookup[0]->getLabel();
 183
 184         //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 185         set<string> processedLabels;
 186         set<string> userLabels = labels;
 187
 188
 189         //as long as you are not at the end of the file or done wih the lines you want
 190         while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 191
 192             if (m->control_pressed) { for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }  return 0; }
 193
 194             if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
 195
 196                 m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 197
 198                 process(lookup, designMap);
 199
 200                 processedLabels.insert(lookup[0]->getLabel());
 201                 userLabels.erase(lookup[0]->getLabel());
 202             }
 203
 204             if ((m->anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 205                 string saveLabel = lookup[0]->getLabel();
 206
 207                 for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 208                 lookup = input.getSharedRAbundVectors(lastLabel);
 209                 m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 210
 211                 process(lookup, designMap);
 212
 213                 processedLabels.insert(lookup[0]->getLabel());
 214                 userLabels.erase(lookup[0]->getLabel());
 215
 216                 //restore real lastlabel to save below
 217                 lookup[0]->setLabel(saveLabel);
 218             }
 219
 220             lastLabel = lookup[0]->getLabel();
 221             //prevent memory leak
 222             for (int i = 0; i < lookup.size(); i++) {  delete lookup[i]; lookup[i] = NULL; }
 223
 224             if (m->control_pressed) { return 0; }
 225
 226             //get next line to process
 227             lookup = input.getSharedRAbundVectors();
 228         }
 229
 230         if (m->control_pressed) {  return 0; }
 231
 232         //output error messages about any remaining user labels
 233         set<string>::iterator it;
 234         bool needToRun = false;
 235         for (it = userLabels.begin(); it != userLabels.end(); it++) {
 236             m->mothurOut("Your file does not include the label " + *it);
 237             if (processedLabels.count(lastLabel) != 1) {
 238                 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 239                 needToRun = true;
 240             }else {
 241                 m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 242             }
 243         }
 244
 245         //run last label if you need to
 246         if (needToRun == true)  {
 247             for (int i = 0; i < lookup.size(); i++) { if (lookup[i] != NULL) { delete lookup[i]; } }
 248             lookup = input.getSharedRAbundVectors(lastLabel);
 249
 250             m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 251             process(lookup, designMap);
 252
 253             for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 254         }
 255
 256
 257         //output files created by command
 258                 m->mothurOutEndLine();
 259                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 260                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 261                 m->mothurOutEndLine();
 262         return 0;
 263
 264     }
 265         catch(exception& e) {
 266                 m->errorOut(e, "KruskalWallisCommand", "execute");
 267                 exit(1);
 268         }
 269 }
 270 //**********************************************************************************************************************
 271
 272 int KruskalWallisCommand::process(vector<SharedRAbundVector*>& lookup, DesignMap& designMap) {
 273         try {
 274         map<string, string> variables;
 275         variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(sharedfile));
 276         variables["[distance]"] = lookup[0]->getLabel();
 277                 string outputFileName = getOutputFileName("kruskall-wallis",variables);
 278
 279                 ofstream out;
 280                 m->openOutputFile(outputFileName, out);
 281                 outputNames.push_back(outputFileName); outputTypes["kruskall-wallis"].push_back(outputFileName);
 282         out << "OTULabel\tKW\tPvalue\n";
 283
 284         int numBins = lookup[0]->getNumBins();
 285         //sanity check to make sure each treatment has a group in the shared file
 286         set<string> treatments;
 287         for (int j = 0; j < lookup.size(); j++) {
 288             string group = lookup[j]->getGroup();
 289             string treatment = designMap.get(group, mclass); //get value for this group in this category
 290             treatments.insert(treatment);
 291         }
 292         if (treatments.size() < 2) { m->mothurOut("[ERROR]: need at least 2 things to classes to compare, quitting.\n"); m->control_pressed = true; }
 293
 294         LinearAlgebra linear;
 295         for (int i = 0; i < numBins; i++) {
 296             if (m->control_pressed) { break; }
 297
 298             vector<spearmanRank> values;
 299             for (int j = 0; j < lookup.size(); j++) {
 300                 string group = lookup[j]->getGroup();
 301                 string treatment = designMap.get(group, mclass); //get value for this group in this category
 302                 spearmanRank temp(treatment, lookup[j]->getAbundance(i));
 303                 values.push_back(temp);
 304             }
 305
 306             double pValue = 0.0;
 307             double H = linear.calcKruskalWallis(values, pValue);
 308
 309             //output H and signifigance
 310             out << m->currentSharedBinLabels[i] << '\t' << H << '\t' << pValue << endl;
 311         }
 312         out.close();
 313
 314         return 0;
 315     }
 316         catch(exception& e) {
 317                 m->errorOut(e, "KruskalWallisCommand", "process");
 318                 exit(1);
 319         }
 320 }
 321 //**********************************************************************************************************************
 322
 323