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                 CommandParameter pclasses("classes", "String", "", "", "", "", "","",false,false); parameters.push_back(pclasses);
  19         //every command must have inputdir and outputdir.  This allows mothur users to redirect input and output files.
  20                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
  21                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
  22
  23                 vector<string> myArray;
  24                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  25                 return myArray;
  26         }
  27         catch(exception& e) {
  28                 m->errorOut(e, "KruskalWallisCommand", "setParameters");
  29                 exit(1);
  30         }
  31 }
  32 //**********************************************************************************************************************
  33 string KruskalWallisCommand::getHelpString(){
  34         try {
  35                 string helpString = "";
  36                 helpString += "The kruskal.wallis command allows you to ....\n";
  37                 helpString += "The kruskal.wallis command parameters are: shared, design, class,  label and classes.\n";
  38                 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";
  39         helpString += "The classes parameter is used to indicate the classes you would like to use. Clases should be inputted in the following format: classes=label<value1|value2|value3>-label<value1|value2>. For example to include groups from treatment with value early or late and age= young or old.  class=treatment<Early|Late>-age<young|old>.\n";
  40         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";
  41                 helpString += "The kruskal.wallis command should be in the following format: kruskal.wallis(shared=final.an.shared, design=final.design, class=treatment).\n";
  42         return helpString;
  43         }
  44         catch(exception& e) {
  45                 m->errorOut(e, "KruskalWallisCommand", "getHelpString");
  46                 exit(1);
  47         }
  48 }
  49 //**********************************************************************************************************************
  50 string KruskalWallisCommand::getOutputPattern(string type) {
  51     try {
  52         string pattern = "";
  53
  54         if (type == "kruskall-wallis") {  pattern = "[filename],[distance],kruskall_wallis"; }
  55         else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
  56
  57         return pattern;
  58     }
  59     catch(exception& e) {
  60         m->errorOut(e, "KruskalWallisCommand", "getOutputPattern");
  61         exit(1);
  62     }
  63 }
  64 //**********************************************************************************************************************
  65 KruskalWallisCommand::KruskalWallisCommand(){
  66         try {
  67                 abort = true; calledHelp = true;
  68                 setParameters();
  69         vector<string> tempOutNames;
  70         outputTypes["kruskall-wallis"] = tempOutNames;
  71         }
  72         catch(exception& e) {
  73                 m->errorOut(e, "KruskalWallisCommand", "KruskalWallisCommand");
  74                 exit(1);
  75         }
  76 }
  77 //**********************************************************************************************************************
  78 KruskalWallisCommand::KruskalWallisCommand(string option)  {
  79         try {
  80                 abort = false; calledHelp = false;
  81         allLines = 1;
  82
  83                 //allow user to run help
  84                 if(option == "help") { help(); abort = true; calledHelp = true; }
  85                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
  86
  87                 else {
  88                         //valid paramters for this command
  89                         vector<string> myArray = setParameters();
  90
  91                         OptionParser parser(option);
  92                         map<string,string> parameters = parser.getParameters();
  93
  94                         ValidParameters validParameter;
  95                         map<string,string>::iterator it;
  96                         //check to make sure all parameters are valid for command
  97                         for (it = parameters.begin(); it != parameters.end(); it++) {
  98                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  99                         }
 100
 101                         vector<string> tempOutNames;
 102             outputTypes["kruskall-wallis"] = tempOutNames;
 103
 104                         //if the user changes the input directory command factory will send this info to us in the output parameter
 105                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 106                         if (inputDir == "not found"){   inputDir = "";          }
 107                         else {
 108
 109                 string path;
 110                                 it = parameters.find("design");
 111                                 //user has given a template file
 112                                 if(it != parameters.end()){
 113                                         path = m->hasPath(it->second);
 114                                         //if the user has not given a path then, add inputdir. else leave path alone.
 115                                         if (path == "") {       parameters["desing"] = inputDir + it->second;           }
 116                                 }
 117
 118                 it = parameters.find("shared");
 119                                 //user has given a template file
 120                                 if(it != parameters.end()){
 121                                         path = m->hasPath(it->second);
 122                                         //if the user has not given a path then, add inputdir. else leave path alone.
 123                                         if (path == "") {       parameters["shared"] = inputDir + it->second;           }
 124                                 }
 125             }
 126
 127             //get shared file, it is required
 128                         sharedfile = validParameter.validFile(parameters, "shared", true);
 129                         if (sharedfile == "not open") { sharedfile = ""; abort = true; }
 130                         else if (sharedfile == "not found") {
 131                                 //if there is a current shared file, use it
 132                                 sharedfile = m->getSharedFile();
 133                                 if (sharedfile != "") { m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
 134                                 else {  m->mothurOut("You have no current sharedfile and the shared parameter is required."); m->mothurOutEndLine(); abort = true; }
 135                         }else { m->setSharedFile(sharedfile); }
 136
 137             //get shared file, it is required
 138                         designfile = validParameter.validFile(parameters, "design", true);
 139                         if (designfile == "not open") { designfile = ""; abort = true; }
 140                         else if (designfile == "not found") {
 141                                 //if there is a current shared file, use it
 142                                 designfile = m->getDesignFile();
 143                                 if (designfile != "") { m->mothurOut("Using " + designfile + " as input file for the design parameter."); m->mothurOutEndLine(); }
 144                                 else {  m->mothurOut("You have no current design file and the design parameter is required."); m->mothurOutEndLine(); abort = true; }
 145                         }else { m->setDesignFile(designfile); }
 146
 147             //if the user changes the output directory command factory will send this info to us in the output parameter
 148                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
 149                                 outputDir = m->hasPath(sharedfile); //if user entered a file with a path then preserve it
 150                         }
 151
 152             string label = validParameter.validFile(parameters, "label", false);
 153                         if (label == "not found") { label = ""; }
 154                         else {
 155                                 if(label != "all") {  m->splitAtDash(label, labels);  allLines = 0;  }
 156                                 else { allLines = 1;  }
 157                         }
 158
 159             mclass = validParameter.validFile(parameters, "class", false);
 160                         if (mclass == "not found") { mclass = ""; }
 161
 162             classes = validParameter.validFile(parameters, "classes", false);
 163                         if (classes == "not found") { classes = ""; }
 164
 165                 }
 166
 167         }
 168         catch(exception& e) {
 169                 m->errorOut(e, "KruskalWallisCommand", "KruskalWallisCommand");
 170                 exit(1);
 171         }
 172 }
 173 //**********************************************************************************************************************
 174
 175 int KruskalWallisCommand::execute(){
 176         try {
 177
 178                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 179
 180         DesignMap designMap(designfile);
 181         //if user set classes set groups=those classes
 182         if (classes != "") {
 183             map<string, vector<string> > thisClasses = m->parseClasses(classes);
 184             vector<string> groups = designMap.getNamesUnique(thisClasses);
 185             if (groups.size() != 0) { m->setGroups(groups); }
 186             else { m->mothurOut("[ERROR]: no groups meet your classes requirement, quitting.\n"); return 0; }
 187         }
 188
 189         //if user did not select class use first column
 190         if (mclass == "") {  mclass = designMap.getDefaultClass(); m->mothurOut("\nYou did not provide a class, using " + mclass +".\n\n"); }
 191
 192         InputData input(sharedfile, "sharedfile");
 193         vector<SharedRAbundVector*> lookup = input.getSharedRAbundVectors();
 194         string lastLabel = lookup[0]->getLabel();
 195
 196         //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 197         set<string> processedLabels;
 198         set<string> userLabels = labels;
 199
 200
 201         //as long as you are not at the end of the file or done wih the lines you want
 202         while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 203
 204             if (m->control_pressed) { for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }  return 0; }
 205
 206             if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
 207
 208                 m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 209
 210                 process(lookup, designMap);
 211
 212                 processedLabels.insert(lookup[0]->getLabel());
 213                 userLabels.erase(lookup[0]->getLabel());
 214             }
 215
 216             if ((m->anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 217                 string saveLabel = lookup[0]->getLabel();
 218
 219                 for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 220                 lookup = input.getSharedRAbundVectors(lastLabel);
 221                 m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 222
 223                 process(lookup, designMap);
 224
 225                 processedLabels.insert(lookup[0]->getLabel());
 226                 userLabels.erase(lookup[0]->getLabel());
 227
 228                 //restore real lastlabel to save below
 229                 lookup[0]->setLabel(saveLabel);
 230             }
 231
 232             lastLabel = lookup[0]->getLabel();
 233             //prevent memory leak
 234             for (int i = 0; i < lookup.size(); i++) {  delete lookup[i]; lookup[i] = NULL; }
 235
 236             if (m->control_pressed) { return 0; }
 237
 238             //get next line to process
 239             lookup = input.getSharedRAbundVectors();
 240         }
 241
 242         if (m->control_pressed) {  return 0; }
 243
 244         //output error messages about any remaining user labels
 245         set<string>::iterator it;
 246         bool needToRun = false;
 247         for (it = userLabels.begin(); it != userLabels.end(); it++) {
 248             m->mothurOut("Your file does not include the label " + *it);
 249             if (processedLabels.count(lastLabel) != 1) {
 250                 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 251                 needToRun = true;
 252             }else {
 253                 m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 254             }
 255         }
 256
 257         //run last label if you need to
 258         if (needToRun == true)  {
 259             for (int i = 0; i < lookup.size(); i++) { if (lookup[i] != NULL) { delete lookup[i]; } }
 260             lookup = input.getSharedRAbundVectors(lastLabel);
 261
 262             m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 263             process(lookup, designMap);
 264
 265             for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 266         }
 267
 268
 269         //output files created by command
 270                 m->mothurOutEndLine();
 271                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 272                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 273                 m->mothurOutEndLine();
 274         return 0;
 275
 276     }
 277         catch(exception& e) {
 278                 m->errorOut(e, "KruskalWallisCommand", "execute");
 279                 exit(1);
 280         }
 281 }
 282 //**********************************************************************************************************************
 283
 284 int KruskalWallisCommand::process(vector<SharedRAbundVector*>& lookup, DesignMap& designMap) {
 285         try {
 286         map<string, string> variables;
 287         variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(sharedfile));
 288         variables["[distance]"] = lookup[0]->getLabel();
 289                 string outputFileName = getOutputFileName("kruskall-wallis",variables);
 290
 291                 ofstream out;
 292                 m->openOutputFile(outputFileName, out);
 293                 outputNames.push_back(outputFileName); outputTypes["kruskall-wallis"].push_back(outputFileName);
 294         out << "OTULabel\tKW\tPvalue\n";
 295
 296         int numBins = lookup[0]->getNumBins();
 297         //sanity check to make sure each treatment has a group in the shared file
 298         set<string> treatments;
 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             treatments.insert(treatment);
 303         }
 304         if (treatments.size() < 2) { m->mothurOut("[ERROR]: need at least 2 things to classes to compare, quitting.\n"); m->control_pressed = true; }
 305
 306         LinearAlgebra linear;
 307         for (int i = 0; i < numBins; i++) {
 308             if (m->control_pressed) { break; }
 309
 310             vector<spearmanRank> values;
 311             for (int j = 0; j < lookup.size(); j++) {
 312                 string group = lookup[j]->getGroup();
 313                 string treatment = designMap.get(group, mclass); //get value for this group in this category
 314                 spearmanRank temp(treatment, lookup[j]->getAbundance(i));
 315                 values.push_back(temp);
 316             }
 317
 318             double pValue = 0.0;
 319             double H = linear.calcKruskalWallis(values, pValue);
 320
 321             //output H and signifigance
 322             out << m->currentBinLabels[i] << '\t' << H << '\t' << pValue << endl;
 323         }
 324         out.close();
 325
 326         return 0;
 327     }
 328         catch(exception& e) {
 329                 m->errorOut(e, "KruskalWallisCommand", "process");
 330                 exit(1);
 331         }
 332 }
 333 //**********************************************************************************************************************
 334
 335