lefsecommand.cpp

   1 //
   2 //  lefsecommand.cpp
   3 //  Mothur
   4 //
   5 //  Created by SarahsWork on 6/12/13.
   6 //  Copyright (c) 2013 Schloss Lab. All rights reserved.
   7 //
   8
   9 #include "lefsecommand.h"
  10 #include "linearalgebra.h"
  11
  12 //**********************************************************************************************************************
  13 vector<string> LefseCommand::setParameters(){
  14         try {
  15         CommandParameter pdesign("design", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(pdesign);
  16         CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none","summary",false,true,true); parameters.push_back(pshared);
  17         CommandParameter pclass("class", "String", "", "", "", "", "","",false,false); parameters.push_back(pclass);
  18         CommandParameter psubclass("subclass", "String", "", "", "", "", "","",false,false); parameters.push_back(psubclass);
  19                 CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
  20                 CommandParameter pclasses("classes", "String", "", "", "", "", "","",false,false); parameters.push_back(pclasses);
  21         CommandParameter palpha("anova_alpha", "Number", "", "0.05", "", "", "","",false,false); parameters.push_back(palpha);
  22         CommandParameter pwalpha("wilcoxon_alpha", "Number", "", "0.05", "", "", "","",false,false); parameters.push_back(pwalpha);
  23         //every command must have inputdir and outputdir.  This allows mothur users to redirect input and output files.
  24                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
  25                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
  26
  27                 vector<string> myArray;
  28                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  29                 return myArray;
  30         }
  31         catch(exception& e) {
  32                 m->errorOut(e, "LefseCommand", "setParameters");
  33                 exit(1);
  34         }
  35 }
  36 //**********************************************************************************************************************
  37 string LefseCommand::getHelpString(){
  38         try {
  39                 string helpString = "";
  40                 helpString += "The lefse command allows you to ....\n";
  41                 helpString += "The lefse command parameters are: shared, design, class, subclass, label, classes, wilcoxon_alpha, anova_alpha.\n";
  42                 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";
  43         helpString += "The subclass parameter is used to indicate the .....If none is provided second category is used, or if only one category subclass is ignored. \n";
  44         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";
  45         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";
  46                 helpString += "The lefse command should be in the following format: lefse(shared=final.an.shared, design=final.design, class=treatment, subclass=age).\n";
  47         return helpString;
  48         }
  49         catch(exception& e) {
  50                 m->errorOut(e, "LefseCommand", "getHelpString");
  51                 exit(1);
  52         }
  53 }
  54 //**********************************************************************************************************************
  55 string LefseCommand::getOutputPattern(string type) {
  56     try {
  57         string pattern = "";
  58
  59         if (type == "summary") {  pattern = "[filename],[distance],lefse_summary"; }
  60         else if (type == "kruskall-wallis") {  pattern = "[filename],[distance],kruskall_wallis"; }
  61         else if (type == "wilcoxon") {  pattern = "[filename],[distance],wilcoxon"; }
  62         else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
  63
  64         return pattern;
  65     }
  66     catch(exception& e) {
  67         m->errorOut(e, "LefseCommand", "getOutputPattern");
  68         exit(1);
  69     }
  70 }
  71 //**********************************************************************************************************************
  72 LefseCommand::LefseCommand(){
  73         try {
  74                 abort = true; calledHelp = true;
  75                 setParameters();
  76         vector<string> tempOutNames;
  77                 outputTypes["summary"] = tempOutNames;
  78         outputTypes["kruskall-wallis"] = tempOutNames;
  79         outputTypes["wilcoxon"] = tempOutNames;
  80         }
  81         catch(exception& e) {
  82                 m->errorOut(e, "LefseCommand", "LefseCommand");
  83                 exit(1);
  84         }
  85 }
  86 //**********************************************************************************************************************
  87 LefseCommand::LefseCommand(string option)  {
  88         try {
  89                 abort = false; calledHelp = false;
  90         allLines = 1;
  91
  92                 //allow user to run help
  93                 if(option == "help") { help(); abort = true; calledHelp = true; }
  94                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
  95
  96                 else {
  97                         //valid paramters for this command
  98                         vector<string> myArray = setParameters();
  99
 100                         OptionParser parser(option);
 101                         map<string,string> parameters = parser.getParameters();
 102
 103                         ValidParameters validParameter;
 104                         map<string,string>::iterator it;
 105                         //check to make sure all parameters are valid for command
 106                         for (it = parameters.begin(); it != parameters.end(); it++) {
 107                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 108                         }
 109
 110                         vector<string> tempOutNames;
 111             outputTypes["summary"] = tempOutNames;
 112             outputTypes["kruskall-wallis"] = tempOutNames;
 113             outputTypes["wilcoxon"] = tempOutNames;
 114
 115                         //if the user changes the input directory command factory will send this info to us in the output parameter
 116                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 117                         if (inputDir == "not found"){   inputDir = "";          }
 118                         else {
 119
 120                 string path;
 121                                 it = parameters.find("design");
 122                                 //user has given a template file
 123                                 if(it != parameters.end()){
 124                                         path = m->hasPath(it->second);
 125                                         //if the user has not given a path then, add inputdir. else leave path alone.
 126                                         if (path == "") {       parameters["desing"] = inputDir + it->second;           }
 127                                 }
 128
 129                 it = parameters.find("shared");
 130                                 //user has given a template file
 131                                 if(it != parameters.end()){
 132                                         path = m->hasPath(it->second);
 133                                         //if the user has not given a path then, add inputdir. else leave path alone.
 134                                         if (path == "") {       parameters["shared"] = inputDir + it->second;           }
 135                                 }
 136             }
 137
 138             //get shared file, it is required
 139                         sharedfile = validParameter.validFile(parameters, "shared", true);
 140                         if (sharedfile == "not open") { sharedfile = ""; abort = true; }
 141                         else if (sharedfile == "not found") {
 142                                 //if there is a current shared file, use it
 143                                 sharedfile = m->getSharedFile();
 144                                 if (sharedfile != "") { m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
 145                                 else {  m->mothurOut("You have no current sharedfile and the shared parameter is required."); m->mothurOutEndLine(); abort = true; }
 146                         }else { m->setSharedFile(sharedfile); }
 147
 148             //get shared file, it is required
 149                         designfile = validParameter.validFile(parameters, "design", true);
 150                         if (designfile == "not open") { designfile = ""; abort = true; }
 151                         else if (designfile == "not found") {
 152                                 //if there is a current shared file, use it
 153                                 designfile = m->getDesignFile();
 154                                 if (designfile != "") { m->mothurOut("Using " + designfile + " as input file for the design parameter."); m->mothurOutEndLine(); }
 155                                 else {  m->mothurOut("You have no current design file and the design parameter is required."); m->mothurOutEndLine(); abort = true; }
 156                         }else { m->setDesignFile(designfile); }
 157
 158             //if the user changes the output directory command factory will send this info to us in the output parameter
 159                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
 160                                 outputDir = m->hasPath(sharedfile); //if user entered a file with a path then preserve it
 161                         }
 162
 163             string label = validParameter.validFile(parameters, "label", false);
 164                         if (label == "not found") { label = ""; }
 165                         else {
 166                                 if(label != "all") {  m->splitAtDash(label, labels);  allLines = 0;  }
 167                                 else { allLines = 1;  }
 168                         }
 169
 170             mclass = validParameter.validFile(parameters, "class", false);
 171                         if (mclass == "not found") { mclass = ""; }
 172
 173             subclass = validParameter.validFile(parameters, "subclass", false);
 174                         if (subclass == "not found") { subclass = ""; }
 175
 176             classes = validParameter.validFile(parameters, "classes", false);
 177                         if (classes == "not found") { classes = ""; }
 178
 179             string temp = validParameter.validFile(parameters, "anova_alpha", false);
 180                         if (temp == "not found") { temp = "0.05"; }
 181                         m->mothurConvert(temp, anovaAlpha);
 182
 183             temp = validParameter.validFile(parameters, "wilcoxon_alpha", false);
 184                         if (temp == "not found") { temp = "0.05"; }
 185                         m->mothurConvert(temp, wilcoxonAlpha);
 186
 187                 }
 188
 189         }
 190         catch(exception& e) {
 191                 m->errorOut(e, "LefseCommand", "LefseCommand");
 192                 exit(1);
 193         }
 194 }
 195 //**********************************************************************************************************************
 196
 197 int LefseCommand::execute(){
 198         try {
 199
 200                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 201
 202         DesignMap designMap(designfile);
 203         //if user set classes set groups=those classes
 204         if (classes != "") {
 205             map<string, vector<string> > thisClasses = m->parseClasses(classes);
 206             vector<string> groups = designMap.getNamesUnique(thisClasses);
 207             if (groups.size() != 0) { m->setGroups(groups); }
 208             else { m->mothurOut("[ERROR]: no groups meet your classes requirement, quitting.\n"); return 0; }
 209         }
 210
 211         //if user did not select class use first column
 212         if (mclass == "") {  mclass = designMap.getDefaultClass(); m->mothurOut("\nYou did not provide a class, using " + mclass +".\n\n"); }
 213
 214         InputData input(sharedfile, "sharedfile");
 215         vector<SharedRAbundVector*> lookup = input.getSharedRAbundVectors();
 216         string lastLabel = lookup[0]->getLabel();
 217
 218         //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 219         set<string> processedLabels;
 220         set<string> userLabels = labels;
 221
 222
 223         //as long as you are not at the end of the file or done wih the lines you want
 224         while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 225
 226             if (m->control_pressed) { for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }  return 0; }
 227
 228             if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
 229
 230                 m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 231
 232                 process(lookup, designMap);
 233
 234                 processedLabels.insert(lookup[0]->getLabel());
 235                 userLabels.erase(lookup[0]->getLabel());
 236             }
 237
 238             if ((m->anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 239                 string saveLabel = lookup[0]->getLabel();
 240
 241                 for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 242                 lookup = input.getSharedRAbundVectors(lastLabel);
 243                 m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 244
 245                 process(lookup, designMap);
 246
 247                 processedLabels.insert(lookup[0]->getLabel());
 248                 userLabels.erase(lookup[0]->getLabel());
 249
 250                 //restore real lastlabel to save below
 251                 lookup[0]->setLabel(saveLabel);
 252             }
 253
 254             lastLabel = lookup[0]->getLabel();
 255             //prevent memory leak
 256             for (int i = 0; i < lookup.size(); i++) {  delete lookup[i]; lookup[i] = NULL; }
 257
 258             if (m->control_pressed) { return 0; }
 259
 260             //get next line to process
 261             lookup = input.getSharedRAbundVectors();
 262         }
 263
 264         if (m->control_pressed) {  return 0; }
 265
 266         //output error messages about any remaining user labels
 267         set<string>::iterator it;
 268         bool needToRun = false;
 269         for (it = userLabels.begin(); it != userLabels.end(); it++) {
 270             m->mothurOut("Your file does not include the label " + *it);
 271             if (processedLabels.count(lastLabel) != 1) {
 272                 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 273                 needToRun = true;
 274             }else {
 275                 m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 276             }
 277         }
 278
 279         //run last label if you need to
 280         if (needToRun == true)  {
 281             for (int i = 0; i < lookup.size(); i++) { if (lookup[i] != NULL) { delete lookup[i]; } }
 282             lookup = input.getSharedRAbundVectors(lastLabel);
 283
 284             m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 285             process(lookup, designMap);
 286
 287             for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 288         }
 289
 290
 291         //output files created by command
 292                 m->mothurOutEndLine();
 293                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 294                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 295                 m->mothurOutEndLine();
 296         return 0;
 297
 298     }
 299         catch(exception& e) {
 300                 m->errorOut(e, "LefseCommand", "execute");
 301                 exit(1);
 302         }
 303 }
 304 //**********************************************************************************************************************
 305
 306 int LefseCommand::process(vector<SharedRAbundVector*>& lookup, DesignMap& designMap) {
 307         try {
 308         //run kruskal wallis on each otu
 309         vector<int> significantOtuLabels = runKruskalWallis(lookup, designMap);
 310
 311         //check for subclass
 312         if (subclass != "") {  significantOtuLabels = runWilcoxon(lookup, designMap, significantOtuLabels);  }
 313
 314         return 0;
 315     }
 316         catch(exception& e) {
 317                 m->errorOut(e, "LefseCommand", "process");
 318                 exit(1);
 319         }
 320 }
 321 //**********************************************************************************************************************
 322
 323 vector<int> LefseCommand::runKruskalWallis(vector<SharedRAbundVector*>& lookup, DesignMap& designMap) {
 324         try {
 325         map<string, string> variables;
 326         variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(sharedfile));
 327         variables["[distance]"] = lookup[0]->getLabel();
 328                 string outputFileName = getOutputFileName("kruskall-wallis",variables);
 329
 330                 ofstream out;
 331                 m->openOutputFile(outputFileName, out);
 332                 outputNames.push_back(outputFileName); outputTypes["kruskall-wallis"].push_back(outputFileName);
 333         out << "OTULabel\tKW\tPvalue\n";
 334
 335         vector<int> significantOtuLabels;
 336         int numBins = lookup[0]->getNumBins();
 337         //sanity check to make sure each treatment has a group in the shared file
 338         set<string> treatments;
 339         for (int j = 0; j < lookup.size(); j++) {
 340             string group = lookup[j]->getGroup();
 341             string treatment = designMap.get(group, mclass); //get value for this group in this category
 342             treatments.insert(treatment);
 343         }
 344         if (treatments.size() < 2) { m->mothurOut("[ERROR]: need at least 2 things to classes to compare, quitting.\n"); m->control_pressed = true; }
 345
 346         LinearAlgebra linear;
 347         for (int i = 0; i < numBins; i++) {
 348             if (m->control_pressed) { break; }
 349
 350             vector<spearmanRank> values;
 351             for (int j = 0; j < lookup.size(); j++) {
 352                 string group = lookup[j]->getGroup();
 353                 string treatment = designMap.get(group, mclass); //get value for this group in this category
 354                 spearmanRank temp(treatment, lookup[j]->getAbundance(i));
 355                 values.push_back(temp);
 356             }
 357
 358             double pValue = 0.0;
 359             double H = linear.calcKruskalWallis(values, pValue);
 360
 361             //output H and signifigance
 362             out << m->currentBinLabels[i] << '\t' << H << '\t' << pValue << endl;
 363
 364             if (pValue < anovaAlpha) {  significantOtuLabels.push_back(i);  }
 365         }
 366         out.close();
 367
 368         return significantOtuLabels;
 369     }
 370         catch(exception& e) {
 371                 m->errorOut(e, "LefseCommand", "runKruskalWallis");
 372                 exit(1);
 373         }
 374 }
 375 //**********************************************************************************************************************
 376
 377 vector<int> LefseCommand::runWilcoxon(vector<SharedRAbundVector*>& lookup, DesignMap& designMap, vector<int> bins) {
 378     try {
 379         vector<int> significantOtuLabels;
 380         //if it exists and meets the following requirements run Wilcoxon
 381         /*
 382          1. Subclass members all belong to same main class
 383          2. Number of groups in each subclass is the same
 384          3. anything else??
 385
 386          */
 387         vector<string> subclasses;
 388         map<string, string> subclass2Class;
 389         map<string, int> subclassCounts;
 390         map<string, vector<int> > subClass2GroupIndex; //maps subclass name to vector of indexes in lookup from that subclass. old -> 1,2,3 means groups in location 1,2,3 of lookup are from old.  Saves time below.
 391         bool error = false;
 392         for (int j = 0; j < lookup.size(); j++) {
 393             string group = lookup[j]->getGroup();
 394             string treatment = designMap.get(group, mclass); //get value for this group in this category
 395             string thisSub = designMap.get(group, subclass);
 396             map<string, string>::iterator it = subclass2Class.find(thisSub);
 397             if (it == subclass2Class.end()) {
 398                 subclass2Class[thisSub] = treatment;
 399                 subclassCounts[thisSub] = 1;
 400                 vector<int> temp; temp.push_back(j);
 401                 subClass2GroupIndex[thisSub] = temp;
 402             }
 403             else {
 404                 subclassCounts[thisSub]++;
 405                 subClass2GroupIndex[thisSub].push_back(j);
 406                 if (it->second != treatment) {
 407                     error = true;
 408                     m->mothurOut("[ERROR]: subclass " + thisSub + " has members in " + it->second + " and " + treatment + ". Subclass members must be from the same class. Ignoring wilcoxon.\n");
 409                 }
 410             }
 411         }
 412
 413         if (error) { return significantOtuLabels; }
 414         else { //check counts to make sure subclasses are the same size
 415             set<int> counts;
 416             for (map<string, int>::iterator it = subclassCounts.begin(); it != subclassCounts.end(); it++) { counts.insert(it->second); }
 417             if (counts.size() > 1) { m->mothurOut("[ERROR]: subclasses must be the same size. Ignoring wilcoxon.\n");
 418                 return significantOtuLabels;  }
 419         }
 420
 421         int numBins = lookup[0]->getNumBins();
 422         vector<compGroup> comp;
 423         //find comparisons and fill comp
 424         map<string, int>::iterator itB;
 425         for(map<string, int>::iterator it=subclassCounts.begin();it!=subclassCounts.end();it++){
 426             itB = it;itB++;
 427             for(itB;itB!=subclassCounts.end();itB++){
 428                 compGroup temp(it->first,itB->first);
 429                 comp.push_back(temp);
 430             }
 431         }
 432
 433         int numComp = comp.size();
 434         if (numComp < 2) {  m->mothurOut("[ERROR]: Need at least 2 subclasses, Ignoring Wilcoxon.\n");
 435             return significantOtuLabels;  }
 436
 437         map<string, string> variables;
 438         variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(sharedfile));
 439         variables["[distance]"] = lookup[0]->getLabel();
 440         string outputFileName = getOutputFileName("wilcoxon",variables);
 441
 442         ofstream out;
 443         m->openOutputFile(outputFileName, out);
 444         outputNames.push_back(outputFileName); outputTypes["wilcoxon"].push_back(outputFileName);
 445         out << "OTULabel\tComparision\tWilcoxon\tPvalue\n";
 446
 447         LinearAlgebra linear;
 448         for (int i = 0; i < numBins; i++) {
 449             if (m->control_pressed) { break; }
 450
 451             if (m->inUsersGroups(i, bins)) { //flagged in Kruskal Wallis
 452
 453                 bool sig = false;
 454                 //for each subclass comparision
 455                 for (int j = 0; j < numComp; j++) {
 456                     //fill x and y with this comparisons data
 457                     vector<double> x; vector<double> y;
 458
 459                     //fill x and y
 460                     vector<int> xIndexes = subClass2GroupIndex[comp[j].group1]; //indexes in lookup for this subclass
 461                     for (int k = 0; k < xIndexes.size(); k++) { x.push_back(lookup[xIndexes[k]]->getAbundance(i)); }
 462
 463                     vector<int> yIndexes = subClass2GroupIndex[comp[j].group2]; //indexes in lookup for this subclass
 464                     for (int k = 0; k < yIndexes.size(); k++) { y.push_back(lookup[yIndexes[k]]->getAbundance(i)); }
 465
 466                     double pValue = 0.0;
 467                     double H = linear.calcWilcoxon(x, y, pValue);
 468
 469                     //output H and signifigance
 470                     out << m->currentBinLabels[i] << '\t' << comp[j].getCombo() << '\t' << H << '\t' << pValue << endl;
 471
 472                     //set sig - not sure how yet
 473                 }
 474                 if (sig) {  significantOtuLabels.push_back(i);  }
 475             }
 476         }
 477         out.close();
 478
 479         return significantOtuLabels;
 480     }
 481     catch(exception& e) {
 482         m->errorOut(e, "LefseCommand", "runWilcoxon");
 483         exit(1);
 484     }
 485 }
 486
 487 //**********************************************************************************************************************
 488
 489